Cardinal Extension - Exp2
2023-05-31
interpret_bayes_factor <- function(BF10) {
if (!is.numeric(BF10) || length(BF10) != 1 || BF10 <= 0) {
stop("Bayes factor must be a single positive numeric value.")
}
if (BF10 < 1) {
BF01 <- 1 / BF10
interpretation <- if (BF01 < 3) {
"Anecdotal evidence for the null hypothesis"
} else if (BF01 < 10) {
"Moderate evidence for the null hypothesis"
} else if (BF01 < 30) {
"Strong evidence for the null hypothesis"
} else if (BF01 < 100) {
"Very strong evidence for the null hypothesis"
} else {
"Extreme evidence for the null hypothesis"
}
} else {
interpretation <- if (BF10 < 3) {
"Anecdotal evidence for the alternative hypothesis"
} else if (BF10 < 10) {
"Moderate evidence for the alternative hypothesis"
} else if (BF10 < 30) {
"Strong evidence for the alternative hypothesis"
} else if (BF10 < 100) {
"Very strong evidence for the alternative hypothesis"
} else {
"Extreme evidence for the alternative hypothesis"
}
}
cat("Bayes Factor (BF10):", BF10, "\n")
if (BF10 < 1) {
cat("Equivalent BF01:", round(1 / BF10, 3), "\n")
}
cat("Interpretation:", interpretation, "\n")
}df.ce <- read.csv("../../data/PROCESSED_DATA/cardinal_extension.csv")
df.ee_pair <- read.csv("../../data/PROCESSED_DATA/exact_equality_pair.csv")
df.ee_visible <- read.csv("../../data/PROCESSED_DATA/exact_equality_visible.csv")
df.cv <- read.csv("../../data/PROCESSED_DATA/counting_violations.csv")
df.cp <- read.csv("../../data/PROCESSED_DATA/counting_procedures.csv")
df.ppt <- read.csv("../../data/PROCESSED_DATA/ppt.csv")Exclusions
- complete fewer than 8 out of 9 trials in Cardinal Extension
- complete fewer than 5 out of 6 trials in Exact Equality with Full Sets
- complete fewer than 5 out of 6 trials in Exact Equality with Sequential Pairs
- complete fewer than 5 out of 6 trials in Counting Procedure
- complete fewer than 10 out of 12 trials in Counting Violations
Actual exclusions is done afterwards…
ce.ppt_excluded_completion <- df.ce %>%
filter(is.na(ce.final_count) & ce.set_chosen == "none") %>%
group_by(pid) %>%
summarise(n_no_count = n()) %>%
filter(n_no_count > 1) %>%
pull(pid)
ee.visible.ppt_excluded_completion <- df.ee_visible %>%
filter(is.na(ee.response)) %>%
group_by(pid) %>%
summarise(n_no_resp = n()) %>%
filter(n_no_resp > 1) %>%
pull(pid)
ee.pair.ppt_excluded_completion <- df.ee_pair %>%
filter(is.na(ee.response)) %>%
group_by(pid) %>%
summarise(n_no_resp = n()) %>%
filter(n_no_resp > 1) %>%
pull(pid)
cp.ppt_excluded_completion <- df.cp %>%
filter(is.na(cp.set_given)) %>%
group_by(pid) %>%
summarise(n_no_resp = n()) %>%
filter(n_no_resp > 1) %>%
pull(pid)
cv.ppt_excluded_completion <- df.cv %>%
filter(is.na(cv.response)) %>%
group_by(pid) %>%
summarise(n_no_resp = n()) %>%
filter(n_no_resp > 1) %>%
pull(pid)Demographics Stats
df.ppt %>%
ungroup() %>%
count(age_years) %>%
mutate(percentage = n / sum(n) * 100) %>%
knitr::kable()| age_years | n | percentage |
|---|---|---|
| 3 | 15 | 24.19355 |
| 4 | 21 | 33.87097 |
| 5 | 14 | 22.58065 |
| 6 | 12 | 19.35484 |
df.ppt_gender <- df.ppt %>%
ungroup() %>%
count(gender) %>%
knitr::kable()
df.ppt %>%
ungroup() %>%
summarise(min_age = min(age_years_cont),
max_age = max(age_years_cont),
mean_age = mean(age_years_cont),
sd_age = sd(age_years_cont))## min_age max_age mean_age sd_age
## 1 3.063014 6.969863 4.875033 1.061759df.ce <- df.ce %>%
mutate(ce.trial_type = factor(ce.trial_type, levels = c("small", "large-DR", "large-NDR"),
labels = c("small", "large-DR", "large-NR")))
df.ee <- bind_rows(df.ee_pair, df.ee_visible)Results
Cardinal Extension
Plot by trial
ggplot(data = df.ce %>%
filter(!pid %in% ce.ppt_excluded_completion),
mapping = aes(x = ce.trial_type, y = ce.correct_set_chosen, color = ce.trial_type)) +
geom_jitter(height = 0,
alpha = 0.5) +
stat_summary(fun.data = "mean_cl_boot",
geom = "pointrange") +
theme(legend.position = "none") +
#facet_grid(experimenter~location) +
labs(y = "Cardinal extension success (by trial)",
x = "Trial Type",
title = "Correct set chosen") 
ggplot(data = df.ce %>%
filter(!pid %in% ce.ppt_excluded_completion),
mapping = aes(x = ce.trial_type, y = ce.correct_set_chosen, color = ce.trial_type)) +
geom_jitter(height = 0,
alpha = 0.5) +
stat_summary(fun.data = "mean_cl_boot",
geom = "pointrange",
color = "black",
alpha = 0.5,
mapping = aes(x = ce.trial_type,
y = ce.correct_set_chosen_no_first_count),
shape = "square") +
stat_summary(fun.data = "mean_cl_boot",
geom = "pointrange") +
theme(legend.position = "none") +
facet_grid(~location) +
labs(y = "Cardinal extension success (by trial)",
x = "Trial Type",
title = "Correct set chosen") 
df.ce %>%
filter(!pid %in% ce.ppt_excluded_completion) %>%
filter(ce.correct_set_chosen != ce.correct_set_chosen_no_first_count)## pid location experimenter knower_level
## 1 RMO-SC-02 Royal Montessori School Oceanside Khuyen 6
## 2 RMO-SC-02 Royal Montessori School Oceanside Khuyen 6
## 3 SB-CSP-16 Seaside Bayside Longcheng 6
## 4 SB-CSP-16 Seaside Bayside Longcheng 6
## 5 SB-CSP-16 Seaside Bayside Longcheng 6
## 6 SB-CSP-16 Seaside Bayside Longcheng 6
## 7 SB-CSP-16 Seaside Bayside Longcheng 6
## 8 CCL-RP-05 Christian Creative Chelsea 6
## 9 CCL-M-03 Christian Creative Alexa 5
## 10 TGS-JS-12 Gillispie Alexa 6
## 11 GKP-FL-07 Grace Kids Preschool Chelsea 6
## kl.strategy task stim_set task_block trial_n_block
## 1 1-1 cardinal_extension 1 NA 2
## 2 1-1 cardinal_extension 1 NA 4
## 3 C cardinal_extension 2 NA 1
## 4 C cardinal_extension 2 NA 2
## 5 C cardinal_extension 2 NA 4
## 6 C cardinal_extension 2 NA 6
## 7 C cardinal_extension 2 NA 8
## 8 C, S cardinal_extension 2 NA 1
## 9 C, 1-1 cardinal_extension 3 NA 3
## 10 C, 1-1 cardinal_extension 2 NA 1
## 11 1-1 cardinal_extension 4 NA 8
## ce.set_chosen ce.first_count ce.correction_after_prompt ce.first_set_chosen
## 1 both 3 1 top
## 2 both 2 1 bottom
## 3 both 10 18 top
## 4 both 10 14 bottom
## 5 both 2 3 top
## 6 both 3 5 top
## 7 both 3 4 top
## 8 both 10 19 top
## 9 both 3 3 top
## 10 top 10 9
## 11 top 2 2
## ce.precount ee.response cp.set_asked cp.set_given cp.initial_set_given
## 1 N NA NA NA NA
## 2 N NA NA NA NA
## 3 N NA NA NA NA
## 4 N NA NA NA NA
## 5 N NA NA NA NA
## 6 N NA NA NA NA
## 7 N NA NA NA NA
## 8 N NA NA NA NA
## 9 N NA NA NA NA
## 10 N NA NA NA NA
## 11 N NA NA NA NA
## cp.strategy cv.response hc.response hc.mistake exclude correct_count_exclude
## 1 NA NA NA NA N
## 2 NA NA NA NA N
## 3 NA NA NA NA N
## 4 NA NA NA NA N
## 5 NA NA NA NA N
## 6 NA NA NA NA N
## 7 NA NA NA NA N
## 8 NA NA NA NA N
## 9 NA NA NA NA N
## 10 NA NA NA NA N
## 11 NA NA NA NA N
## notes X X.1 X.2 age_months age_years age_years_cont
## 1 NA NA NA 47 3 3.926027
## 2 NA NA NA 47 3 3.926027
## 3 NA NA NA 47 3 3.983562
## 4 NA NA NA 47 3 3.983562
## 5 Did not point to the screen NA NA NA 47 3 3.983562
## 6 NA NA NA 47 3 3.983562
## 7 NA NA NA 47 3 3.983562
## 8 NA NA NA 55 4 4.619178
## 9 NA NA NA 46 3 3.873973
## 10 NA NA NA 71 5 5.991781
## 11 NA NA NA 45 3 3.816438
## age_zscored ce.magnitude ce.ratio ce.trial_type ce.n_item1 ce.n_item2
## 1 -0.9407232 small <NA> small 3 1
## 2 -0.9407232 small <NA> small 2 1
## 3 -0.8858839 large NDR large-NR 10 9
## 4 -0.8858839 large DR large-DR 5 10
## 5 -0.8858839 small <NA> small 1 2
## 6 -0.8858839 small <NA> small 3 2
## 7 -0.8858839 small <NA> small 1 3
## 8 -0.2800404 large NDR large-NR 10 9
## 9 -0.9903397 small <NA> small 3 2
## 10 1.0282681 large NDR large-NR 10 9
## 11 -1.0451790 small <NA> small 1 2
## ce.loc_item1 ce.item1 ce.item2 ce.final_count ce.trial_ratio
## 1 top backpack book 1 1-3
## 2 bottom basket bowl 1 1-2
## 3 bottom book toothbrush 18 9-10
## 4 bottom key balloon 14 5-10
## 5 bottom hat bowl 3 1-2
## 6 top ball train 5 2-3
## 7 bottom spoon backpack 4 1-3
## 8 bottom book toothbrush 19 9-10
## 9 bottom key lunchbox 3 2-3
## 10 bottom book toothbrush 9 9-10
## 11 top bowl book 2 1-2
## ce.target_count ce.target_set ce.strict_correct_set_chosen ce.correct_count
## 1 3 top 0 0
## 2 2 bottom 0 0
## 3 10 bottom 0 0
## 4 10 top 0 0
## 5 2 top 0 0
## 6 3 top 0 0
## 7 3 top 0 0
## 8 10 bottom 0 0
## 9 3 bottom 0 1
## 10 10 bottom 0 0
## 11 2 bottom 0 1
## ce.correct_set_chosen_no_first_count ce.correct_set_chosen
## 1 0 1
## 2 0 1
## 3 0 1
## 4 0 1
## 5 0 1
## 6 0 1
## 7 0 1
## 8 0 1
## 9 0 1
## 10 0 1
## 11 0 1
## ce.correct_count_when_correct_set_chosen ce.count_error
## 1 0 -2
## 2 0 -1
## 3 0 8
## 4 0 4
## 5 0 1
## 6 0 2
## 7 0 1
## 8 0 9
## 9 1 0
## 10 0 -1
## 11 1 0
## ce.correct_count_approx ce.correct_count_approx_when_correct_set_chosen
## 1 0 0
## 2 1 1
## 3 0 0
## 4 0 0
## 5 1 1
## 6 0 0
## 7 1 1
## 8 0 0
## 9 1 1
## 10 1 1
## 11 1 1test.df.ce <- df.ce %>%
filter(!pid %in% ce.ppt_excluded_completion) %>%
mutate(choice_strategy =
case_when(
ce.correct_set_chosen == 1 ~ "chose one set, correct",
ce.set_chosen == "both" ~ "both sets chosen",
ce.set_chosen == "none" ~ "no sets chosen",
ce.correct_set_chosen == 0 & ce.set_chosen %in% c("top", "bottom") ~ "chose one set, incorrect"
))Plot by participant
ggplot(data = df.ce %>%
filter(!pid %in% ce.ppt_excluded_completion) %>%
mutate(ce.trial_type = factor(ce.trial_type, levels = c("small", "large-DR", "large-NR"), labels = c('small sets\n (e.g., 1:2)', 'large sets,\n discriminable \n ratio (e.g., 5:10)', 'large sets,\n off-by-one \n(e.g., 9:10)'))) %>%
group_by(pid, experimenter, age_years, location, ce.trial_type) %>%
summarise(mean_correct_set = mean(ce.correct_set_chosen, na.rm = FALSE)),
mapping = aes(x = ce.trial_type, y = mean_correct_set)) +
geom_violin(aes(fill = ce.trial_type)) +
geom_jitter(height = 0,
alpha = 0.5,
aes(group = pid)) +
stat_summary(fun.data = "mean_cl_boot",
geom = "pointrange") +
geom_hline(yintercept = 0.5, linetype = 2) +
theme(legend.position = "none",
text = element_text(size = 13)) +
facet_grid(~age_years) +
labs(y = "Prop. of correct set choice",
x = "Set Size and Ratio"
) ## `summarise()` has grouped output by 'pid', 'experimenter', 'age_years',
## 'location'. You can override using the `.groups` argument.
ppt_fail_small <- df.ce %>%
group_by(pid, ce.trial_type) %>%
summarise(mean_correct_set = mean(ce.correct_set_chosen, na.rm = FALSE)) %>%
filter(ce.trial_type == "small" & mean_correct_set == 0) %>%
pull(pid)## `summarise()` has grouped output by 'pid'. You can override using the `.groups`
## argument.# could the prompt be confusing?
# kids might guess correctly and then didn't understand why they should count.
# but this only account for 8 trials (7 of which the kid is then coded as 'wrong')
df.ce %>% filter(ce.first_count == ce.target_count & ce.final_count != ce.target_count)## pid location experimenter knower_level
## 1 RMO-SC-02 Royal Montessori School Oceanside Khuyen 6
## 2 RMO-SC-02 Royal Montessori School Oceanside Khuyen 6
## 3 SB-CSP-16 Seaside Bayside Longcheng 6
## 4 SB-CSP-16 Seaside Bayside Longcheng 6
## 5 SB-CSP-16 Seaside Bayside Longcheng 6
## 6 SB-CSP-16 Seaside Bayside Longcheng 6
## 7 SB-CSP-16 Seaside Bayside Longcheng 6
## 8 SB-IP-08 Seaside Beachside Longcheng 5
## 9 CCL-RP-05 Christian Creative Chelsea 6
## 10 TGS-JS-12 Gillispie Alexa 6
## kl.strategy task stim_set task_block trial_n_block
## 1 1-1 cardinal_extension 1 NA 2
## 2 1-1 cardinal_extension 1 NA 4
## 3 C cardinal_extension 2 NA 1
## 4 C cardinal_extension 2 NA 2
## 5 C cardinal_extension 2 NA 4
## 6 C cardinal_extension 2 NA 6
## 7 C cardinal_extension 2 NA 8
## 8 1-1, S,G cardinal_extension 3 NA 6
## 9 C, S cardinal_extension 2 NA 1
## 10 C, 1-1 cardinal_extension 2 NA 1
## ce.set_chosen ce.first_count ce.correction_after_prompt ce.first_set_chosen
## 1 both 3 1 top
## 2 both 2 1 bottom
## 3 both 10 18 top
## 4 both 10 14 bottom
## 5 both 2 3 top
## 6 both 3 5 top
## 7 both 3 4 top
## 8 top 3 4
## 9 both 10 19 top
## 10 top 10 9
## ce.precount ee.response cp.set_asked cp.set_given cp.initial_set_given
## 1 N NA NA NA NA
## 2 N NA NA NA NA
## 3 N NA NA NA NA
## 4 N NA NA NA NA
## 5 N NA NA NA NA
## 6 N NA NA NA NA
## 7 N NA NA NA NA
## 8 N NA NA NA NA
## 9 N NA NA NA NA
## 10 N NA NA NA NA
## cp.strategy cv.response hc.response hc.mistake exclude correct_count_exclude
## 1 NA NA NA NA N
## 2 NA NA NA NA N
## 3 NA NA NA NA N
## 4 NA NA NA NA N
## 5 NA NA NA NA N
## 6 NA NA NA NA N
## 7 NA NA NA NA N
## 8 NA NA NA NA N
## 9 NA NA NA NA N
## 10 NA NA NA NA N
## notes X X.1 X.2 age_months age_years age_years_cont
## 1 NA NA NA 47 3 3.926027
## 2 NA NA NA 47 3 3.926027
## 3 NA NA NA 47 3 3.983562
## 4 NA NA NA 47 3 3.983562
## 5 Did not point to the screen NA NA NA 47 3 3.983562
## 6 NA NA NA 47 3 3.983562
## 7 NA NA NA 47 3 3.983562
## 8 NA NA NA 42 3 3.526027
## 9 NA NA NA 55 4 4.619178
## 10 NA NA NA 71 5 5.991781
## age_zscored ce.magnitude ce.ratio ce.trial_type ce.n_item1 ce.n_item2
## 1 -0.9407232 small <NA> small 3 1
## 2 -0.9407232 small <NA> small 2 1
## 3 -0.8858839 large NDR large-NR 10 9
## 4 -0.8858839 large DR large-DR 5 10
## 5 -0.8858839 small <NA> small 1 2
## 6 -0.8858839 small <NA> small 3 2
## 7 -0.8858839 small <NA> small 1 3
## 8 -1.3219868 small <NA> small 3 1
## 9 -0.2800404 large NDR large-NR 10 9
## 10 1.0282681 large NDR large-NR 10 9
## ce.loc_item1 ce.item1 ce.item2 ce.final_count ce.trial_ratio
## 1 top backpack book 1 1-3
## 2 bottom basket bowl 1 1-2
## 3 bottom book toothbrush 18 9-10
## 4 bottom key balloon 14 5-10
## 5 bottom hat bowl 3 1-2
## 6 top ball train 5 2-3
## 7 bottom spoon backpack 4 1-3
## 8 top ruler book 4 1-3
## 9 bottom book toothbrush 19 9-10
## 10 bottom book toothbrush 9 9-10
## ce.target_count ce.target_set ce.strict_correct_set_chosen ce.correct_count
## 1 3 top 0 0
## 2 2 bottom 0 0
## 3 10 bottom 0 0
## 4 10 top 0 0
## 5 2 top 0 0
## 6 3 top 0 0
## 7 3 top 0 0
## 8 3 top 1 0
## 9 10 bottom 0 0
## 10 10 bottom 0 0
## ce.correct_set_chosen_no_first_count ce.correct_set_chosen
## 1 0 1
## 2 0 1
## 3 0 1
## 4 0 1
## 5 0 1
## 6 0 1
## 7 0 1
## 8 1 1
## 9 0 1
## 10 0 1
## ce.correct_count_when_correct_set_chosen ce.count_error
## 1 0 -2
## 2 0 -1
## 3 0 8
## 4 0 4
## 5 0 1
## 6 0 2
## 7 0 1
## 8 0 1
## 9 0 9
## 10 0 -1
## ce.correct_count_approx ce.correct_count_approx_when_correct_set_chosen
## 1 0 0
## 2 1 1
## 3 0 0
## 4 0 0
## 5 1 1
## 6 0 0
## 7 1 1
## 8 1 1
## 9 0 0
## 10 1 1df.ce %>% filter(pid %in% ppt_fail_small) %>%
filter(ce.trial_type == "small") %>%
select(pid,
ce.set_chosen,
ce.final_count,
ce.first_count,
ce.trial_ratio)## pid ce.set_chosen ce.final_count ce.first_count ce.trial_ratio
## 1 BB-S-15 both 3 3 1-2
## 2 BB-S-15 both 2 2 2-3
## 3 BB-S-15 both 1 1 1-3
## 4 MOC2-BR-30 both 29 29 2-3
## 5 MOC2-BR-30 both 19 19 1-3
## 6 MOC2-BR-30 both 24 24 1-2
## 7 MOC2-GC-21 both 3 3 1-2
## 8 MOC2-GC-21 both 5 5 2-3
## 9 MOC2-GC-21 both 4 4 1-3
## 10 MOC2-LZ-24 both 4 12 1-3
## 11 MOC2-LZ-24 both 5 12 2-3
## 12 MOC2-LZ-24 both 3 12 1-2
## 13 MOC2-S-12 both 4 4 1-3
## 14 MOC2-S-12 both 3 3 1-2
## 15 MOC2-S-12 both 10 10 2-3
## 16 KA-EM-06 both 5 5 2-3
## 17 KA-EM-06 both 4 4 1-3
## 18 KA-EM-06 both 3 3 1-2
## 19 KA-AA-04 both 3 3 1-2
## 20 KA-AA-04 both 5 5 2-3
## 21 KA-AA-04 both 4 4 1-3
## 22 PV-EH-10 both 5 5 1-2
## 23 PV-EH-10 both 4 4 2-3
## 24 PV-EH-10 both 3 3 1-3
## 25 MEC-KS-02 bottom 1 1 1-2
## 26 MEC-KS-02 bottom 2 2 2-3
## 27 MEC-KS-02 bottom 1 1 1-3
## 28 MEC-FD-15 both 3 3 1-2
## 29 MEC-FD-15 both 5 5 2-3
## 30 MEC-FD-15 both 4 4 1-3
## 31 CCL-RP-05 both 3 3 1-2
## 32 CCL-RP-05 both 5 5 2-3
## 33 CCL-RP-05 both 4 4 1-3
## 34 TGS-LT-13 both 4 4 1-3
## 35 TGS-LT-13 bottom 1 2 2-3
## 36 TGS-LT-13 both 3 3 1-2ggplot(data = df.ce %>%
filter(!pid %in% ce.ppt_excluded_completion) %>%
mutate(ce.trial_type = factor(ce.trial_type, levels = c("small", "large-DR", "large-NR"), labels = c('small sets\n (e.g., 1:2)', 'large sets,\n discriminable \n ratio (e.g., 5:10)', 'large sets,\n off-by-one \n(e.g., 9:10)'))) %>%
group_by(pid, ce.trial_type, age_years_cont) %>%
summarise(mean_correct_set = mean(ce.correct_set_chosen, na.rm = FALSE)),
mapping = aes(x = age_years_cont, y = mean_correct_set, fill = ce.trial_type, color = ce.trial_type)) +
geom_smooth(method = "lm") +
geom_jitter(height = 0,
alpha = 0.5,
aes(group = pid),
color = "black") +
geom_hline(yintercept = 0.5, linetype = 2) +
facet_grid(~ce.trial_type) +
coord_cartesian(ylim = c(0, 1)) +
labs(y = "Prop. of correct set choice",
x = "Age") +
theme(legend.position = "none",
text = element_text(size = 11)) ## `summarise()` has grouped output by 'pid', 'ce.trial_type'. You can override
## using the `.groups` argument.
## `geom_smooth()` using formula = 'y ~ x'
ggplot(data = df.ee %>%
group_by(pid, age_years, ee.trial_type, ee.set) %>%
summarise(mean_correct_set = mean(ee.correct_set_chosen, na.rm = FALSE)),
mapping = aes(x = ee.set, y = mean_correct_set)) +
geom_violin(aes(fill = ee.set)) +
geom_jitter(height = 0,
alpha = 0.5,
aes(group = pid)) +
stat_summary(fun.data = "mean_cl_boot",
geom = "pointrange") +
geom_hline(yintercept = 0.5, linetype = 2) +
theme(legend.position = "none",
text = element_text(size = 13)) +
# scale_fill_manual(values=cbPalette) +
# scale_color_manual(values=cbPalette) +
facet_grid(~ee.trial_type) +
#facet_grid(ee.trial_type~age_years) +
labs(y = "Prop. of correct set choice",
x = "Set"
) ## `summarise()` has grouped output by 'pid', 'age_years', 'ee.trial_type'. You
## can override using the `.groups` argument.
ggplot(data = df.ee %>%
mutate(ee.set_size = factor(ee.set_size, levels = c('small', 'large'))) %>%
group_by(pid, age_years, ee.trial_type, ee.set_size) %>%
summarise(mean_correct_set = mean(ee.correct_set_chosen, na.rm = FALSE)),
mapping = aes(x = ee.set_size, y = mean_correct_set)) +
geom_violin(aes(fill = ee.set_size)) +
geom_jitter(height = 0,
alpha = 0.5,
aes(group = pid)) +
stat_summary(fun.data = "mean_cl_boot",
geom = "pointrange") +
geom_hline(yintercept = 0.5, linetype = 2) +
theme(legend.position = "none",
text = element_text(size = 13)) +
# scale_fill_manual(values=cbPalette) +
# scale_color_manual(values=cbPalette) +
facet_grid(~ee.trial_type) +
#facet_grid(ee.trial_type~age_years) +
labs(y = "Prop. of correct set choice",
x = "Set"
) ## `summarise()` has grouped output by 'pid', 'age_years', 'ee.trial_type'. You
## can override using the `.groups` argument.
ggplot(data = df.ee %>%
mutate(ee.set_size = factor(ee.set_size, levels = c('small', 'large'))) %>%
group_by(pid, age_years_cont, ee.trial_type, ee.set_size) %>%
summarise(mean_correct_set = mean(ee.correct_set_chosen, na.rm = FALSE)),
mapping = aes(x = age_years_cont, y = mean_correct_set, fill = ee.trial_type, color = ee.trial_type)) +
geom_smooth(method = "lm") +
geom_jitter(height = 0,
alpha = 0.5,
aes(group = pid),
color = "black") +
geom_hline(yintercept = 0.5, linetype = 2) +
facet_grid(ee.set_size~ee.trial_type) +
coord_cartesian(ylim = c(0, 1)) +
labs(y = "Prop. of correct set choice",
x = "Age") +
theme(legend.position = "none",
text = element_text(size = 11)) ## `summarise()` has grouped output by 'pid', 'age_years_cont', 'ee.trial_type'.
## You can override using the `.groups` argument.
## `geom_smooth()` using formula = 'y ~ x'
ggplot(data = df.cv %>%
group_by(pid, age_years, cv.violation_type),
mapping = aes(x = cv.violation_type, y = cv.sum_score)) +
geom_violin(aes(fill = cv.violation_type)) +
geom_jitter(height = 0,
alpha = 0.5,
aes(group = pid)) +
stat_summary(fun.data = "mean_cl_boot",
geom = "pointrange") +
theme(legend.position = "none",
text = element_text(size = 13)) +
# scale_fill_manual(values=cbPalette) +
# scale_color_manual(values=cbPalette) +
#facet_grid(~age_years) +
labs(y = "Number of correct judgments",
x = "Violation type"
) 
Bayesian
priors <- c(
prior("normal(0, 2.5)", class = "b") # weakly informative prior for slope
)fit.ce.base = brm(ce.correct_set_chosen ~ age_zscored + (1|pid) + (1|ce.trial_ratio),
family = "bernoulli",
save_pars = save_pars(all = T),
data = df.ce %>%
filter(!pid %in% ce.ppt_excluded_completion),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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## Chain 2 finished in 15.5 seconds.
##
## All 4 chains finished successfully.
## Mean chain execution time: 12.4 seconds.
## Total execution time: 15.6 seconds.## Warning: 1 of 60000 (0.0%) transitions ended with a divergence.
## See https://mc-stan.org/misc/warnings for details.fit.ce.trial_type = brm(ce.correct_set_chosen ~ ce.trial_type + age_zscored + (1|pid) + (1|ce.trial_ratio),
family = "bernoulli",
save_pars = save_pars(all = T),
data = df.ce %>%
filter(!pid %in% ce.ppt_excluded_completion),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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## Total execution time: 17.6 seconds.## Warning: 3 of 60000 (0.0%) transitions ended with a divergence.
## See https://mc-stan.org/misc/warnings for details.summary(fit.ce.trial_type)## Family: bernoulli
## Links: mu = logit
## Formula: ce.correct_set_chosen ~ ce.trial_type + age_zscored + (1 | pid) + (1 | ce.trial_ratio)
## Data: df.ce %>% filter(!pid %in% ce.ppt_excluded_complet (Number of observations: 540)
## Draws: 4 chains, each with iter = 20000; warmup = 5000; thin = 1;
## total post-warmup draws = 60000
##
## Multilevel Hyperparameters:
## ~ce.trial_ratio (Number of levels: 9)
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sd(Intercept) 0.77 0.35 0.27 1.64 1.00 20047 26827
##
## ~pid (Number of levels: 60)
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sd(Intercept) 2.25 0.34 1.66 2.98 1.00 19566 30761
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS
## Intercept 1.19 0.59 0.01 2.34 1.00 26939
## ce.trial_typelargeMDR -0.41 0.70 -1.79 1.02 1.00 37982
## ce.trial_typelargeMNR -1.52 0.71 -2.91 -0.04 1.00 37061
## age_zscored 1.33 0.35 0.67 2.05 1.00 23582
## Tail_ESS
## Intercept 33104
## ce.trial_typelargeMDR 36961
## ce.trial_typelargeMNR 34219
## age_zscored 33476
##
## Draws were sampled using sample(hmc). For each parameter, Bulk_ESS
## and Tail_ESS are effective sample size measures, and Rhat is the potential
## scale reduction factor on split chains (at convergence, Rhat = 1).plot(fit.ce.trial_type,
ask = F)
pp_check(fit.ce.trial_type, ndraws = 100)
bayes_factor(fit.ce.trial_type, fit.ce.base)$bf %>% interpret_bayes_factor()# 0.10729 moderate evidence for fit.null 8/23/25## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
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## Iteration: 5## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4
## Bayes Factor (BF10): 1.019915
## Interpretation: Anecdotal evidence for the alternative hypothesisfit.ce.base = add_criterion(fit.ce.base,
criterion = "loo",
reloo = T)## No problematic observations found. Returning the original 'loo' object.fit.ce.trial_type = add_criterion(fit.ce.trial_type,
criterion = "loo",
reloo = T)## No problematic observations found. Returning the original 'loo' object.loo_compare(fit.ce.base,
fit.ce.trial_type)## elpd_diff se_diff
## fit.ce.base 0.0 0.0
## fit.ce.trial_type 0.0 0.9Note that the frequentist version of this (MLE) actually shows that the more complex model is better…
fit.ce.base.lm <- glmer(ce.correct_set_chosen ~ age_zscored + (1|pid) + (1|ce.trial_ratio),
family = "binomial",
data = df.ce %>%
filter(!pid %in% ce.ppt_excluded_completion))
summary(fit.ce.base.lm)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula: ce.correct_set_chosen ~ age_zscored + (1 | pid) + (1 | ce.trial_ratio)
## Data: df.ce %>% filter(!pid %in% ce.ppt_excluded_completion)
##
## AIC BIC logLik deviance df.resid
## 545.7 562.9 -268.9 537.7 536
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.6180 -0.4715 0.1536 0.4335 4.2992
##
## Random effects:
## Groups Name Variance Std.Dev.
## pid (Intercept) 4.1591 2.0394
## ce.trial_ratio (Intercept) 0.6869 0.8288
## Number of obs: 540, groups: pid, 60; ce.trial_ratio, 9
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.5467 0.4112 1.329 0.184
## age_zscored 1.3205 0.3279 4.028 5.63e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## age_zscored 0.088fit.ce.trial_type.lm <- glmer(ce.correct_set_chosen ~ ce.trial_type + age_zscored + (1|pid) + (1|ce.trial_ratio),
family = "binomial",
data = df.ce %>%
filter(!pid %in% ce.ppt_excluded_completion))
summary(fit.ce.trial_type.lm)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula: ce.correct_set_chosen ~ ce.trial_type + age_zscored + (1 | pid) +
## (1 | ce.trial_ratio)
## Data: df.ce %>% filter(!pid %in% ce.ppt_excluded_completion)
##
## AIC BIC logLik deviance df.resid
## 542.1 567.9 -265.1 530.1 534
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.5660 -0.4567 0.1472 0.4529 4.3252
##
## Random effects:
## Groups Name Variance Std.Dev.
## pid (Intercept) 4.1346 2.0334
## ce.trial_ratio (Intercept) 0.2108 0.4591
## Number of obs: 540, groups: pid, 60; ce.trial_ratio, 9
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.2505 0.4468 2.799 0.00513 **
## ce.trial_typelarge-DR -0.4938 0.4806 -1.027 0.30419
## ce.trial_typelarge-NR -1.6184 0.4925 -3.286 0.00102 **
## age_zscored 1.3197 0.3270 4.036 5.44e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) c._-DR c._-NR
## c.trl_ty-DR -0.552
## c.trl_ty-NR -0.573 0.506
## age_zscored 0.119 -0.022 -0.082Anova(fit.ce.trial_type.lm)## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: ce.correct_set_chosen
## Chisq Df Pr(>Chisq)
## ce.trial_type 11.339 2 0.003449 **
## age_zscored 16.287 1 5.443e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1anova(fit.ce.trial_type.lm, fit.ce.base.lm, type=3)## Data: df.ce %>% filter(!pid %in% ce.ppt_excluded_completion)
## Models:
## fit.ce.base.lm: ce.correct_set_chosen ~ age_zscored + (1 | pid) + (1 | ce.trial_ratio)
## fit.ce.trial_type.lm: ce.correct_set_chosen ~ ce.trial_type + age_zscored + (1 | pid) + (1 | ce.trial_ratio)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## fit.ce.base.lm 4 545.70 562.87 -268.85 537.70
## fit.ce.trial_type.lm 6 542.11 567.86 -265.05 530.11 7.5971 2 0.0224 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1fit.ee.base = brm(ee.correct_set_chosen ~ age_zscored + (1|pid) + (1|ee.set),
family = "bernoulli",
save_pars = save_pars(all = T),
data = df.ee,
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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## Chain 3 finished in 24.8 seconds.
##
## All 4 chains finished successfully.
## Mean chain execution time: 23.6 seconds.
## Total execution time: 25.0 seconds.## Warning: 205 of 60000 (0.0%) transitions ended with a divergence.
## See https://mc-stan.org/misc/warnings for details.fit.ee.set_size = brm(ee.correct_set_chosen ~ ee.set_size + age_zscored + (1|pid) + (1|ee.set),
family = "bernoulli",
save_pars = save_pars(all = T),
data = df.ee,
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
##
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## Chain 1 finished in 41.3 seconds.
##
## All 4 chains finished successfully.
## Mean chain execution time: 30.6 seconds.
## Total execution time: 41.4 seconds.## Warning: 1848 of 60000 (3.0%) transitions ended with a divergence.
## See https://mc-stan.org/misc/warnings for details.bayes_factor(fit.ee.set_size, fit.ee.base)$bf %>% interpret_bayes_factor() #0.13260 moderate evidence for null 8/23/25## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
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## Iteration: 5## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
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## Bayes Factor (BF10): 0.5867927
## Equivalent BF01: 1.704
## Interpretation: Anecdotal evidence for the null hypothesisfit.ee.trial_type = brm(ee.correct_set_chosen ~ ee.trial_type + ee.set_size + age_zscored + (1|pid) + (1|ee.set),
family = "bernoulli",
save_pars = save_pars(all = T),
data = df.ee,
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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##
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## Total execution time: 41.8 seconds.## Warning: 2838 of 60000 (5.0%) transitions ended with a divergence.
## See https://mc-stan.org/misc/warnings for details.bayes_factor(fit.ee.trial_type, fit.ee.base)$bf %>% interpret_bayes_factor() # 1.30061 anecdotal evidence for fit.ee.trial_type 8/23/25## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
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## Iteration: 6## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
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## Iteration: 6
## Bayes Factor (BF10): 44.71945
## Interpretation: Very strong evidence for the alternative hypothesisbayes_factor(fit.ee.trial_type, fit.ee.set_size)$bf %>% interpret_bayes_factor() #9.12468 moderate evidence for fit.ee.trial_type 5/21/25## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4
## Iteration: 5
## Iteration: 6
## Iteration: 7## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
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## Iteration: 6
## Bayes Factor (BF10): 77.72283
## Interpretation: Very strong evidence for the alternative hypothesisfit.ee.trial_type_int = brm(ee.correct_set_chosen ~ ee.trial_type * ee.set_size + age_zscored + (1|pid) + (1|ee.set),
family = "bernoulli",
save_pars = save_pars(all = T),
data = df.ee,
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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## Total execution time: 43.2 seconds.## Warning: 335 of 60000 (1.0%) transitions ended with a divergence.
## See https://mc-stan.org/misc/warnings for details.bayes_factor(fit.ee.trial_type_int, fit.ee.base)$bf %>% interpret_bayes_factor() #0.38124 anecdotal evidence for null 8/23/25## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4
## Iteration: 5## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4
## Iteration: 5
## Iteration: 6
## Bayes Factor (BF10): 25.03632
## Interpretation: Strong evidence for the alternative hypothesisfit.cp.base = brm(cp.correct_response ~ age_zscored + (1|pid) + (1|cp.set_asked),
family = "bernoulli",
save_pars = save_pars(all = T),
data = df.cp,
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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##
## All 4 chains finished successfully.
## Mean chain execution time: 13.9 seconds.
## Total execution time: 14.3 seconds.## Warning: 285 of 60000 (0.0%) transitions ended with a divergence.
## See https://mc-stan.org/misc/warnings for details.summary(fit.cp.base) # older kids are better, lol## Family: bernoulli
## Links: mu = logit
## Formula: cp.correct_response ~ age_zscored + (1 | pid) + (1 | cp.set_asked)
## Data: df.cp (Number of observations: 354)
## Draws: 4 chains, each with iter = 20000; warmup = 5000; thin = 1;
## total post-warmup draws = 60000
##
## Multilevel Hyperparameters:
## ~cp.set_asked (Number of levels: 3)
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sd(Intercept) 0.58 0.63 0.02 2.33 1.00 10221 6659
##
## ~pid (Number of levels: 59)
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sd(Intercept) 1.77 0.38 1.13 2.59 1.00 20302 31450
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## Intercept 1.69 0.54 0.53 2.77 1.00 13076 6216
## age_zscored 2.51 0.45 1.71 3.48 1.00 32944 18921
##
## Draws were sampled using sample(hmc). For each parameter, Bulk_ESS
## and Tail_ESS are effective sample size measures, and Rhat is the potential
## scale reduction factor on split chains (at convergence, Rhat = 1).fit.cv.base = brm(cv.correct_judgment ~ age_zscored + (1|pid) + (1|cv.set),
family = "bernoulli",
save_pars = save_pars(all = T),
data = df.cv,
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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##
## All 4 chains finished successfully.
## Mean chain execution time: 18.5 seconds.
## Total execution time: 22.3 seconds.## Warning: 143 of 60000 (0.0%) transitions ended with a divergence.
## See https://mc-stan.org/misc/warnings for details.#pairs(fit.cv.base)
fit.cv.violation_type = brm(cv.correct_judgment ~ cv.violation_type + cv.trial_type_correct_incorrect + age_zscored + (1|pid) + (1|cv.set),
family = "bernoulli",
save_pars = save_pars(all = T),
data = df.cv,
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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##
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## Mean chain execution time: 18.8 seconds.
## Total execution time: 22.4 seconds.## Warning: 293 of 60000 (0.0%) transitions ended with a divergence.
## See https://mc-stan.org/misc/warnings for details.summary(fit.cv.violation_type)## Family: bernoulli
## Links: mu = logit
## Formula: cv.correct_judgment ~ cv.violation_type + cv.trial_type_correct_incorrect + age_zscored + (1 | pid) + (1 | cv.set)
## Data: df.cv (Number of observations: 708)
## Draws: 4 chains, each with iter = 20000; warmup = 5000; thin = 1;
## total post-warmup draws = 60000
##
## Multilevel Hyperparameters:
## ~cv.set (Number of levels: 4)
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sd(Intercept) 0.28 0.29 0.01 1.10 1.00 8645 2445
##
## ~pid (Number of levels: 59)
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sd(Intercept) 0.96 0.19 0.62 1.36 1.00 19890 33066
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI u-95% CI
## Intercept 1.59 0.31 0.99 2.22
## cv.violation_typeone_one 0.29 0.23 -0.17 0.75
## cv.violation_typestable_order 1.26 0.27 0.74 1.79
## cv.trial_type_correct_incorrectincorrect -0.86 0.21 -1.28 -0.46
## age_zscored 0.80 0.18 0.47 1.17
## Rhat Bulk_ESS Tail_ESS
## Intercept 1.00 5086 2272
## cv.violation_typeone_one 1.00 65367 45869
## cv.violation_typestable_order 1.00 61993 44483
## cv.trial_type_correct_incorrectincorrect 1.00 64498 42367
## age_zscored 1.00 28058 34210
##
## Draws were sampled using sample(hmc). For each parameter, Bulk_ESS
## and Tail_ESS are effective sample size measures, and Rhat is the potential
## scale reduction factor on split chains (at convergence, Rhat = 1).bayes_factor(fit.cv.violation_type, fit.cv.base)$bf %>% interpret_bayes_factor() # 70297.46960 very strong support for violation type + correct / incorrect 8/23/25## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
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## Iteration: 6## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
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## Iteration: 6
## Bayes Factor (BF10): 950104.3
## Interpretation: Extreme evidence for the alternative hypothesisfit.cv.violation_type_int = brm(cv.correct_judgment ~ cv.violation_type * cv.trial_type_correct_incorrect + age_zscored + (1|pid) + (1|cv.set),
family = "bernoulli",
save_pars = save_pars(all = T),
data = df.cv,
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
##
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## Mean chain execution time: 19.3 seconds.
## Total execution time: 22.9 seconds.## Warning: 210 of 60000 (0.0%) transitions ended with a divergence.
## See https://mc-stan.org/misc/warnings for details.bayes_factor(fit.cv.violation_type_int, fit.cv.violation_type)$bf %>% interpret_bayes_factor() #0.01296 very strong support for fit.cv.violation_type 8/23/25## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
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## Iteration: 6## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
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## Bayes Factor (BF10): 0.205264
## Equivalent BF01: 4.872
## Interpretation: Moderate evidence for the null hypothesisSummary Code
df.ce_summary <- df.ce %>%
filter(ce.trial_type == "large-NR") %>%
group_by(pid, age_years, age_years_cont, age_zscored) %>%
summarise(ce.mean_correct_set_chosen = mean(ce.correct_set_chosen))## `summarise()` has grouped output by 'pid', 'age_years', 'age_years_cont'. You
## can override using the `.groups` argument.df.ee_summary <- df.ee %>%
filter(ee.set_size == "large") %>%
group_by(pid, age_years, age_years_cont, age_zscored, ee.trial_type) %>%
summarise(ee.mean_correct_set_chosen = mean(ee.correct_set_chosen)) %>%
pivot_wider(names_from = ee.trial_type, values_from = ee.mean_correct_set_chosen) %>%
rename(ee.all_visible.mean_correct_set_chosen = `all-visible`,
ee.seq_pair.mean_correct_set_chosen = `seq-pair`)## `summarise()` has grouped output by 'pid', 'age_years', 'age_years_cont',
## 'age_zscored'. You can override using the `.groups` argument.df.cp_summary <- df.cp %>%
group_by(pid, age_years, age_years_cont, age_zscored) %>%
summarise(cp.mean_success = mean(cp.correct_response))## `summarise()` has grouped output by 'pid', 'age_years', 'age_years_cont'. You
## can override using the `.groups` argument.df.cv_summary <- df.cv %>%
group_by(pid, age_years, age_years_cont, age_zscored, cv.violation_type) %>%
summarise(succeeded = unique(cv.violation_succeeded),
sum_score = unique(cv.sum_score)) %>%
pivot_wider(names_from = cv.violation_type,
values_from = c(succeeded, sum_score),
names_glue = "cv.type.{cv.violation_type}.{.value}") %>%
rowwise() %>%
mutate(cv.mean_success = mean(c_across(ends_with("succeeded"))))## `summarise()` has grouped output by 'pid', 'age_years', 'age_years_cont',
## 'age_zscored'. You can override using the `.groups` argument.df.summary <- df.ce_summary %>%
full_join(df.ee_summary, by = c("pid", "age_years", "age_years_cont", "age_zscored")) %>%
full_join(df.cp_summary, by = c("pid", "age_years", "age_years_cont", "age_zscored")) %>%
full_join(df.cv_summary, by = c("pid", "age_years", "age_years_cont", "age_zscored"))cross-task predictions
Cardinal Extension and EE Visible
ggplot(data = df.summary %>%
filter(!is.na(ce.mean_correct_set_chosen) &
!is.na(ee.all_visible.mean_correct_set_chosen)),
aes(x = ce.mean_correct_set_chosen,
y = ee.all_visible.mean_correct_set_chosen)) +
geom_smooth(method = "lm") +
geom_jitter() +
facet_grid(~age_years)## `geom_smooth()` using formula = 'y ~ x'
fit.ce_summary.ee_visible.base = brm(ce.mean_correct_set_chosen ~ age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ce.mean_correct_set_chosen) &
!is.na(ee.all_visible.mean_correct_set_chosen)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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## Chain 1 finished in 0.3 seconds.
## Chain 2 finished in 0.3 seconds.
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##
## All 4 chains finished successfully.
## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.5 seconds.summary(fit.ce_summary.ee_visible.base)## Family: gaussian
## Links: mu = identity; sigma = identity
## Formula: ce.mean_correct_set_chosen ~ age_zscored
## Data: df.summary %>% filter(!is.na(ce.mean_correct_set_c (Number of observations: 61)
## Draws: 4 chains, each with iter = 20000; warmup = 5000; thin = 1;
## total post-warmup draws = 60000
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## Intercept 0.44 0.04 0.36 0.53 1.00 56928 40769
## age_zscored 0.25 0.04 0.16 0.33 1.00 53696 40437
##
## Further Distributional Parameters:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sigma 0.34 0.03 0.29 0.41 1.00 51636 40321
##
## Draws were sampled using sample(hmc). For each parameter, Bulk_ESS
## and Tail_ESS are effective sample size measures, and Rhat is the potential
## scale reduction factor on split chains (at convergence, Rhat = 1).fit.ce_summary.ee_visible = brm(ce.mean_correct_set_chosen ~ ee.all_visible.mean_correct_set_chosen + age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ce.mean_correct_set_chosen) &
!is.na(ee.all_visible.mean_correct_set_chosen)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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##
## All 4 chains finished successfully.
## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.6 seconds.summary(fit.ce_summary.ee_visible)## Family: gaussian
## Links: mu = identity; sigma = identity
## Formula: ce.mean_correct_set_chosen ~ ee.all_visible.mean_correct_set_chosen + age_zscored
## Data: df.summary %>% filter(!is.na(ce.mean_correct_set_c (Number of observations: 61)
## Draws: 4 chains, each with iter = 20000; warmup = 5000; thin = 1;
## total post-warmup draws = 60000
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI u-95% CI
## Intercept 0.37 0.12 0.13 0.61
## ee.all_visible.mean_correct_set_chosen 0.11 0.17 -0.23 0.44
## age_zscored 0.23 0.05 0.13 0.33
## Rhat Bulk_ESS Tail_ESS
## Intercept 1.00 51764 43288
## ee.all_visible.mean_correct_set_chosen 1.00 50944 43260
## age_zscored 1.00 50040 41728
##
## Further Distributional Parameters:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sigma 0.34 0.03 0.29 0.42 1.00 53184 41572
##
## Draws were sampled using sample(hmc). For each parameter, Bulk_ESS
## and Tail_ESS are effective sample size measures, and Rhat is the potential
## scale reduction factor on split chains (at convergence, Rhat = 1).bayes_factor(fit.ce_summary.ee_visible, fit.ce_summary.ee_visible.base)$bf %>% interpret_bayes_factor() #0.01655 --> very strong evidence for null 8/23/25## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
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## Iteration: 5## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4
## Iteration: 5
## Bayes Factor (BF10): 0.08198386
## Equivalent BF01: 12.198
## Interpretation: Strong evidence for the null hypothesisCardinal Extension and EE Pair
fit.ce_summary.ee_pair.base = brm(ce.mean_correct_set_chosen ~ age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ce.mean_correct_set_chosen) &
!is.na(ee.seq_pair.mean_correct_set_chosen)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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## Chain 1 finished in 0.3 seconds.
## Chain 2 finished in 0.3 seconds.
## Chain 3 finished in 0.3 seconds.
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##
## All 4 chains finished successfully.
## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.4 seconds.summary(fit.ce_summary.ee_pair.base)## Family: gaussian
## Links: mu = identity; sigma = identity
## Formula: ce.mean_correct_set_chosen ~ age_zscored
## Data: df.summary %>% filter(!is.na(ce.mean_correct_set_c (Number of observations: 59)
## Draws: 4 chains, each with iter = 20000; warmup = 5000; thin = 1;
## total post-warmup draws = 60000
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## Intercept 0.45 0.05 0.36 0.54 1.00 53865 40468
## age_zscored 0.24 0.05 0.15 0.33 1.00 54851 42105
##
## Further Distributional Parameters:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sigma 0.35 0.03 0.29 0.42 1.00 51154 40607
##
## Draws were sampled using sample(hmc). For each parameter, Bulk_ESS
## and Tail_ESS are effective sample size measures, and Rhat is the potential
## scale reduction factor on split chains (at convergence, Rhat = 1).fit.ce_summary.ee_pair = brm(ce.mean_correct_set_chosen ~ ee.seq_pair.mean_correct_set_chosen + age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ce.mean_correct_set_chosen) &
!is.na(ee.seq_pair.mean_correct_set_chosen)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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##
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## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.6 seconds.summary(fit.ce_summary.ee_pair)## Family: gaussian
## Links: mu = identity; sigma = identity
## Formula: ce.mean_correct_set_chosen ~ ee.seq_pair.mean_correct_set_chosen + age_zscored
## Data: df.summary %>% filter(!is.na(ce.mean_correct_set_c (Number of observations: 59)
## Draws: 4 chains, each with iter = 20000; warmup = 5000; thin = 1;
## total post-warmup draws = 60000
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI u-95% CI Rhat
## Intercept 0.43 0.11 0.22 0.64 1.00
## ee.seq_pair.mean_correct_set_chosen 0.04 0.16 -0.29 0.36 1.00
## age_zscored 0.24 0.05 0.13 0.34 1.00
## Bulk_ESS Tail_ESS
## Intercept 52445 43851
## ee.seq_pair.mean_correct_set_chosen 51677 45088
## age_zscored 52030 44959
##
## Further Distributional Parameters:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sigma 0.35 0.03 0.29 0.42 1.00 54571 42012
##
## Draws were sampled using sample(hmc). For each parameter, Bulk_ESS
## and Tail_ESS are effective sample size measures, and Rhat is the potential
## scale reduction factor on split chains (at convergence, Rhat = 1).bayes_factor(fit.ce_summary.ee_pair, fit.ce_summary.ee_pair.base)$bf %>% interpret_bayes_factor()## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4
## Bayes Factor (BF10): 0.06642912
## Equivalent BF01: 15.054
## Interpretation: Strong evidence for the null hypothesis#0.01571 --> very strong evidence for null 8/23/25Cardinal Extension and Give-N
fit.ce_summary.cp.base = brm(ce.mean_correct_set_chosen ~ age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ce.mean_correct_set_chosen) &
!is.na(cp.mean_success)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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##
## All 4 chains finished successfully.
## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.5 seconds.summary(fit.ce_summary.cp.base)## Family: gaussian
## Links: mu = identity; sigma = identity
## Formula: ce.mean_correct_set_chosen ~ age_zscored
## Data: df.summary %>% filter(!is.na(ce.mean_correct_set_c (Number of observations: 59)
## Draws: 4 chains, each with iter = 20000; warmup = 5000; thin = 1;
## total post-warmup draws = 60000
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## Intercept 0.45 0.05 0.36 0.54 1.00 53865 40468
## age_zscored 0.24 0.05 0.15 0.33 1.00 54851 42105
##
## Further Distributional Parameters:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sigma 0.35 0.03 0.29 0.42 1.00 51154 40607
##
## Draws were sampled using sample(hmc). For each parameter, Bulk_ESS
## and Tail_ESS are effective sample size measures, and Rhat is the potential
## scale reduction factor on split chains (at convergence, Rhat = 1).fit.ce_summary.cp = brm(ce.mean_correct_set_chosen ~ cp.mean_success + age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ce.mean_correct_set_chosen) &
!is.na(cp.mean_success)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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##
## All 4 chains finished successfully.
## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.6 seconds.summary(fit.ce_summary.cp)## Family: gaussian
## Links: mu = identity; sigma = identity
## Formula: ce.mean_correct_set_chosen ~ cp.mean_success + age_zscored
## Data: df.summary %>% filter(!is.na(ce.mean_correct_set_c (Number of observations: 59)
## Draws: 4 chains, each with iter = 20000; warmup = 5000; thin = 1;
## total post-warmup draws = 60000
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## Intercept 0.40 0.13 0.15 0.65 1.00 40286 41318
## cp.mean_success 0.07 0.17 -0.27 0.42 1.00 38591 40841
## age_zscored 0.22 0.06 0.10 0.35 1.00 38451 41141
##
## Further Distributional Parameters:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sigma 0.35 0.03 0.29 0.42 1.00 49904 40040
##
## Draws were sampled using sample(hmc). For each parameter, Bulk_ESS
## and Tail_ESS are effective sample size measures, and Rhat is the potential
## scale reduction factor on split chains (at convergence, Rhat = 1).bayes_factor(fit.ce_summary.cp, fit.ce_summary.cp.base)$bf %>% interpret_bayes_factor() #0.01711 --> very strong evidence for null 8/23/25## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4
## Bayes Factor (BF10): 0.07605436
## Equivalent BF01: 13.148
## Interpretation: Strong evidence for the null hypothesisCardinal Extension and Counting Violations
fit.ce_summary.cv.base = brm(ce.mean_correct_set_chosen ~ age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ce.mean_correct_set_chosen) &
!is.na(cv.mean_success)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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## Chain 1 finished in 0.3 seconds.
## Chain 2 finished in 0.3 seconds.
## Chain 3 finished in 0.3 seconds.
## Chain 4 finished in 0.3 seconds.
##
## All 4 chains finished successfully.
## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.4 seconds.summary(fit.ce_summary.cv.base)## Family: gaussian
## Links: mu = identity; sigma = identity
## Formula: ce.mean_correct_set_chosen ~ age_zscored
## Data: df.summary %>% filter(!is.na(ce.mean_correct_set_c (Number of observations: 59)
## Draws: 4 chains, each with iter = 20000; warmup = 5000; thin = 1;
## total post-warmup draws = 60000
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## Intercept 0.45 0.05 0.36 0.54 1.00 53865 40468
## age_zscored 0.24 0.05 0.15 0.33 1.00 54851 42105
##
## Further Distributional Parameters:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sigma 0.35 0.03 0.29 0.42 1.00 51154 40607
##
## Draws were sampled using sample(hmc). For each parameter, Bulk_ESS
## and Tail_ESS are effective sample size measures, and Rhat is the potential
## scale reduction factor on split chains (at convergence, Rhat = 1).fit.ce_summary.cv = brm(ce.mean_correct_set_chosen ~ cv.mean_success + age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ce.mean_correct_set_chosen) &
!is.na(cv.mean_success)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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##
## All 4 chains finished successfully.
## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.6 seconds.summary(fit.ce_summary.cv)## Family: gaussian
## Links: mu = identity; sigma = identity
## Formula: ce.mean_correct_set_chosen ~ cv.mean_success + age_zscored
## Data: df.summary %>% filter(!is.na(ce.mean_correct_set_c (Number of observations: 59)
## Draws: 4 chains, each with iter = 20000; warmup = 5000; thin = 1;
## total post-warmup draws = 60000
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## Intercept 0.47 0.09 0.30 0.64 1.00 54278 44302
## cv.mean_success -0.05 0.15 -0.34 0.25 1.00 52115 43428
## age_zscored 0.25 0.05 0.14 0.36 1.00 52898 43218
##
## Further Distributional Parameters:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sigma 0.35 0.03 0.29 0.42 1.00 55075 39215
##
## Draws were sampled using sample(hmc). For each parameter, Bulk_ESS
## and Tail_ESS are effective sample size measures, and Rhat is the potential
## scale reduction factor on split chains (at convergence, Rhat = 1).bayes_factor(fit.ce_summary.cv, fit.ce_summary.cv.base)$bf %>% interpret_bayes_factor() #0.01666 --> very strong evidence for null 8/23/25## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4
## Bayes Factor (BF10): 0.0631391
## Equivalent BF01: 15.838
## Interpretation: Strong evidence for the null hypothesisCardinal Extension and Counting Violations for each type of violation
This is one of the exploratory analysis
One-one
fit.ce_summary.cv.oneone.base = brm(ce.mean_correct_set_chosen ~ age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ce.mean_correct_set_chosen) &
!is.na(cv.mean_success)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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##
## All 4 chains finished successfully.
## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.4 seconds.summary(fit.ce_summary.cv.oneone.base)## Family: gaussian
## Links: mu = identity; sigma = identity
## Formula: ce.mean_correct_set_chosen ~ age_zscored
## Data: df.summary %>% filter(!is.na(ce.mean_correct_set_c (Number of observations: 59)
## Draws: 4 chains, each with iter = 20000; warmup = 5000; thin = 1;
## total post-warmup draws = 60000
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## Intercept 0.45 0.05 0.36 0.54 1.00 53865 40468
## age_zscored 0.24 0.05 0.15 0.33 1.00 54851 42105
##
## Further Distributional Parameters:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sigma 0.35 0.03 0.29 0.42 1.00 51154 40607
##
## Draws were sampled using sample(hmc). For each parameter, Bulk_ESS
## and Tail_ESS are effective sample size measures, and Rhat is the potential
## scale reduction factor on split chains (at convergence, Rhat = 1).fit.ce_summary.cv.oneone = brm(ce.mean_correct_set_chosen ~ cv.type.one_one.sum_score + age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ce.mean_correct_set_chosen) &
!is.na(cv.mean_success)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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##
## All 4 chains finished successfully.
## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.6 seconds.summary(fit.ce_summary.cv.oneone)## Family: gaussian
## Links: mu = identity; sigma = identity
## Formula: ce.mean_correct_set_chosen ~ cv.type.one_one.sum_score + age_zscored
## Data: df.summary %>% filter(!is.na(ce.mean_correct_set_c (Number of observations: 59)
## Draws: 4 chains, each with iter = 20000; warmup = 5000; thin = 1;
## total post-warmup draws = 60000
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS
## Intercept 0.48 0.15 0.19 0.77 1.00 49547
## cv.type.one_one.sum_score -0.01 0.05 -0.10 0.08 1.00 48502
## age_zscored 0.25 0.05 0.14 0.35 1.00 47829
## Tail_ESS
## Intercept 42172
## cv.type.one_one.sum_score 42936
## age_zscored 42946
##
## Further Distributional Parameters:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sigma 0.35 0.03 0.29 0.42 1.00 57070 39439
##
## Draws were sampled using sample(hmc). For each parameter, Bulk_ESS
## and Tail_ESS are effective sample size measures, and Rhat is the potential
## scale reduction factor on split chains (at convergence, Rhat = 1).bayes_factor(fit.ce_summary.cv.oneone, fit.ce_summary.cv.oneone.base)$bf %>% interpret_bayes_factor() #0.00585 --> very strong evidence for null 8/23/25, sad for M## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
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## Iteration: 4## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4
## Bayes Factor (BF10): 0.01891866
## Equivalent BF01: 52.858
## Interpretation: Very strong evidence for the null hypothesisfit.ce_summary.cv.oneone.binary = brm(ce.mean_correct_set_chosen ~ cv.type.one_one.succeeded + age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ce.mean_correct_set_chosen) &
!is.na(cv.mean_success)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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##
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## Mean chain execution time: 0.4 seconds.
## Total execution time: 0.6 seconds.summary(fit.ce_summary.cv.oneone.binary)## Family: gaussian
## Links: mu = identity; sigma = identity
## Formula: ce.mean_correct_set_chosen ~ cv.type.one_one.succeeded + age_zscored
## Data: df.summary %>% filter(!is.na(ce.mean_correct_set_c (Number of observations: 59)
## Draws: 4 chains, each with iter = 20000; warmup = 5000; thin = 1;
## total post-warmup draws = 60000
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS
## Intercept 0.43 0.07 0.29 0.56 1.00 49542
## cv.type.one_one.succeeded 0.04 0.11 -0.18 0.27 1.00 44683
## age_zscored 0.23 0.06 0.12 0.34 1.00 44461
## Tail_ESS
## Intercept 44114
## cv.type.one_one.succeeded 42744
## age_zscored 42100
##
## Further Distributional Parameters:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sigma 0.35 0.03 0.29 0.42 1.00 54158 42157
##
## Draws were sampled using sample(hmc). For each parameter, Bulk_ESS
## and Tail_ESS are effective sample size measures, and Rhat is the potential
## scale reduction factor on split chains (at convergence, Rhat = 1).bayes_factor(fit.ce_summary.cv.oneone.binary, fit.ce_summary.cv.oneone.base)$bf %>% interpret_bayes_factor() #0.01133 also nope 8/23/25## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
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## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4
## Bayes Factor (BF10): 0.0486146
## Equivalent BF01: 20.57
## Interpretation: Strong evidence for the null hypothesisCardinality
#maybe I don't need that baseline because it's exactly the same one as the overall CV
fit.ce_summary.cv.cardinality.base = brm(ce.mean_correct_set_chosen ~ age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ce.mean_correct_set_chosen) &
!is.na(cv.mean_success)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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##
## All 4 chains finished successfully.
## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.5 seconds.summary(fit.ce_summary.cv.cardinality.base)## Family: gaussian
## Links: mu = identity; sigma = identity
## Formula: ce.mean_correct_set_chosen ~ age_zscored
## Data: df.summary %>% filter(!is.na(ce.mean_correct_set_c (Number of observations: 59)
## Draws: 4 chains, each with iter = 20000; warmup = 5000; thin = 1;
## total post-warmup draws = 60000
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## Intercept 0.45 0.05 0.36 0.54 1.00 53865 40468
## age_zscored 0.24 0.05 0.15 0.33 1.00 54851 42105
##
## Further Distributional Parameters:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sigma 0.35 0.03 0.29 0.42 1.00 51154 40607
##
## Draws were sampled using sample(hmc). For each parameter, Bulk_ESS
## and Tail_ESS are effective sample size measures, and Rhat is the potential
## scale reduction factor on split chains (at convergence, Rhat = 1).fit.ce_summary.cv.cardinality = brm(ce.mean_correct_set_chosen ~ cv.type.cardinality.sum_score + age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ce.mean_correct_set_chosen) &
!is.na(cv.mean_success)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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##
## All 4 chains finished successfully.
## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.5 seconds.summary(fit.ce_summary.cv.cardinality)## Family: gaussian
## Links: mu = identity; sigma = identity
## Formula: ce.mean_correct_set_chosen ~ cv.type.cardinality.sum_score + age_zscored
## Data: df.summary %>% filter(!is.na(ce.mean_correct_set_c (Number of observations: 59)
## Draws: 4 chains, each with iter = 20000; warmup = 5000; thin = 1;
## total post-warmup draws = 60000
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI u-95% CI Rhat
## Intercept 0.47 0.14 0.19 0.75 1.00
## cv.type.cardinality.sum_score -0.01 0.05 -0.10 0.09 1.00
## age_zscored 0.24 0.05 0.15 0.34 1.00
## Bulk_ESS Tail_ESS
## Intercept 56347 42298
## cv.type.cardinality.sum_score 55968 44016
## age_zscored 55657 42530
##
## Further Distributional Parameters:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sigma 0.35 0.03 0.29 0.42 1.00 56845 41678
##
## Draws were sampled using sample(hmc). For each parameter, Bulk_ESS
## and Tail_ESS are effective sample size measures, and Rhat is the potential
## scale reduction factor on split chains (at convergence, Rhat = 1).bayes_factor(fit.ce_summary.cv.cardinality, fit.ce_summary.cv.cardinality.base)$bf %>% interpret_bayes_factor() #0.00447 --> very strong evidence for null 8/23/25## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4
## Bayes Factor (BF10): 0.01917521
## Equivalent BF01: 52.151
## Interpretation: Very strong evidence for the null hypothesisfit.ce_summary.cv.cardinality.binary = brm(ce.mean_correct_set_chosen ~ cv.type.cardinality.succeeded + age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ce.mean_correct_set_chosen) &
!is.na(cv.mean_success)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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##
## All 4 chains finished successfully.
## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.5 seconds.summary(fit.ce_summary.cv.cardinality.binary)## Family: gaussian
## Links: mu = identity; sigma = identity
## Formula: ce.mean_correct_set_chosen ~ cv.type.cardinality.succeeded + age_zscored
## Data: df.summary %>% filter(!is.na(ce.mean_correct_set_c (Number of observations: 59)
## Draws: 4 chains, each with iter = 20000; warmup = 5000; thin = 1;
## total post-warmup draws = 60000
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI u-95% CI Rhat
## Intercept 0.50 0.06 0.38 0.61 1.00
## cv.type.cardinality.succeeded -0.14 0.10 -0.34 0.06 1.00
## age_zscored 0.27 0.05 0.17 0.36 1.00
## Bulk_ESS Tail_ESS
## Intercept 60358 43252
## cv.type.cardinality.succeeded 57329 45124
## age_zscored 56777 44801
##
## Further Distributional Parameters:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sigma 0.34 0.03 0.29 0.42 1.00 59387 43195
##
## Draws were sampled using sample(hmc). For each parameter, Bulk_ESS
## and Tail_ESS are effective sample size measures, and Rhat is the potential
## scale reduction factor on split chains (at convergence, Rhat = 1).bayes_factor(fit.ce_summary.cv.cardinality.binary, fit.ce_summary.cv.cardinality.base)$bf %>% interpret_bayes_factor() # 0.02056 also nope 8/23/25## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
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## Iteration: 5## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4
## Bayes Factor (BF10): 0.1011225
## Equivalent BF01: 9.889
## Interpretation: Moderate evidence for the null hypothesisStable Order
# skipping this because it's exactly the same as the main CV baseline
# fit.ce_summary.cv.stableorder.base = brm(ce.mean_correct_set_chosen ~ age_zscored,
# family = "gaussian",
# save_pars = save_pars(all = T),
# data = df.summary %>%
# filter(!is.na(ce.mean_correct_set_chosen) &
# !is.na(cv.mean_success)),
# prior = priors,
# iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
# #file = "./cache/goals_mass_lang",
# seed = 1)
# summary(fit.ce_summary.cv.stableorder.base)
fit.ce_summary.cv.stableorder = brm(ce.mean_correct_set_chosen ~ cv.type.stable_order.sum_score + age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ce.mean_correct_set_chosen) &
!is.na(cv.mean_success)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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## Chain 1 finished in 0.3 seconds.
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##
## All 4 chains finished successfully.
## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.5 seconds.summary(fit.ce_summary.cv.stableorder)## Family: gaussian
## Links: mu = identity; sigma = identity
## Formula: ce.mean_correct_set_chosen ~ cv.type.stable_order.sum_score + age_zscored
## Data: df.summary %>% filter(!is.na(ce.mean_correct_set_c (Number of observations: 59)
## Draws: 4 chains, each with iter = 20000; warmup = 5000; thin = 1;
## total post-warmup draws = 60000
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI u-95% CI Rhat
## Intercept 0.54 0.21 0.13 0.95 1.00
## cv.type.stable_order.sum_score -0.03 0.06 -0.14 0.09 1.00
## age_zscored 0.25 0.05 0.15 0.34 1.00
## Bulk_ESS Tail_ESS
## Intercept 64632 43396
## cv.type.stable_order.sum_score 64616 44849
## age_zscored 64478 44675
##
## Further Distributional Parameters:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sigma 0.35 0.03 0.29 0.42 1.00 59770 43419
##
## Draws were sampled using sample(hmc). For each parameter, Bulk_ESS
## and Tail_ESS are effective sample size measures, and Rhat is the potential
## scale reduction factor on split chains (at convergence, Rhat = 1).bayes_factor(fit.ce_summary.cv.stableorder, fit.ce_summary.cv.base)$bf %>% interpret_bayes_factor() #0.00594 --> very strong evidence for null 8/23/25## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4
## Bayes Factor (BF10): 0.02535006
## Equivalent BF01: 39.448
## Interpretation: Very strong evidence for the null hypothesisfit.ce_summary.cv.stableorder.binary = brm(ce.mean_correct_set_chosen ~ cv.type.stable_order.succeeded + age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ce.mean_correct_set_chosen) &
!is.na(cv.mean_success)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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## Chain 1 finished in 0.3 seconds.
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##
## All 4 chains finished successfully.
## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.5 seconds.summary(fit.ce_summary.cv.stableorder.binary)## Family: gaussian
## Links: mu = identity; sigma = identity
## Formula: ce.mean_correct_set_chosen ~ cv.type.stable_order.succeeded + age_zscored
## Data: df.summary %>% filter(!is.na(ce.mean_correct_set_c (Number of observations: 59)
## Draws: 4 chains, each with iter = 20000; warmup = 5000; thin = 1;
## total post-warmup draws = 60000
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI u-95% CI Rhat
## Intercept 0.43 0.08 0.28 0.58 1.00
## cv.type.stable_order.succeeded 0.03 0.10 -0.16 0.22 1.00
## age_zscored 0.24 0.05 0.15 0.33 1.00
## Bulk_ESS Tail_ESS
## Intercept 62848 43363
## cv.type.stable_order.succeeded 63014 42980
## age_zscored 63229 44727
##
## Further Distributional Parameters:
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
## sigma 0.35 0.03 0.29 0.42 1.00 60386 43357
##
## Draws were sampled using sample(hmc). For each parameter, Bulk_ESS
## and Tail_ESS are effective sample size measures, and Rhat is the potential
## scale reduction factor on split chains (at convergence, Rhat = 1).bayes_factor(fit.ce_summary.cv.stableorder.binary, fit.ce_summary.cv.base)$bf %>% interpret_bayes_factor()#0.00954 --> very strong evidence for null 8/23/25## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
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## Iteration: 4## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4
## Bayes Factor (BF10): 0.04009884
## Equivalent BF01: 24.938
## Interpretation: Strong evidence for the null hypothesisEE visible
fit.ee_visible_summary.cp.base = brm(ee.all_visible.mean_correct_set_chosen ~ age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ee.all_visible.mean_correct_set_chosen) &
!is.na(cp.mean_success)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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##
## All 4 chains finished successfully.
## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.4 seconds.fit.ee_visible_summary.cp = brm(ee.all_visible.mean_correct_set_chosen ~ cp.mean_success + age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ee.all_visible.mean_correct_set_chosen) &
!is.na(cp.mean_success)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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## Total execution time: 0.6 seconds.bayes_factor(fit.ee_visible_summary.cp, fit.ee_visible_summary.cp.base)$bf %>% interpret_bayes_factor() #0.01389 strong evidence for null 8/23/25## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
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## Iteration: 4## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
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## Iteration: 5
## Bayes Factor (BF10): 0.05322675
## Equivalent BF01: 18.788
## Interpretation: Strong evidence for the null hypothesisfit.ee_visible_summary.cv.base = brm(ee.all_visible.mean_correct_set_chosen ~ age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ee.all_visible.mean_correct_set_chosen) &
!is.na(cv.mean_success)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
##
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## Chain 2 finished in 0.3 seconds.
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##
## All 4 chains finished successfully.
## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.5 seconds.fit.ee_visible_summary.cv = brm(ee.all_visible.mean_correct_set_chosen ~ cv.mean_success + age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ee.all_visible.mean_correct_set_chosen) &
!is.na(cv.mean_success)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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##
## All 4 chains finished successfully.
## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.5 seconds.bayes_factor(fit.ee_visible_summary.cv, fit.ee_visible_summary.cv.base)$bf %>% interpret_bayes_factor() #0.01834 strong evidence for null 8/23/25## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
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## Iteration: 5## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4
## Bayes Factor (BF10): 0.08417131
## Equivalent BF01: 11.881
## Interpretation: Strong evidence for the null hypothesisEE pair
fit.ee_pair_summary.cp.base = brm(ee.seq_pair.mean_correct_set_chosen ~ age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ee.seq_pair.mean_correct_set_chosen) &
!is.na(cp.mean_success)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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##
## All 4 chains finished successfully.
## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.5 seconds.fit.ee_pair_summary.cp = brm(ee.seq_pair.mean_correct_set_chosen ~ cp.mean_success + age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ee.seq_pair.mean_correct_set_chosen) &
!is.na(cp.mean_success)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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##
## All 4 chains finished successfully.
## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.6 seconds.bayes_factor(fit.ee_pair_summary.cp, fit.ee_pair_summary.cp.base)$bf %>% interpret_bayes_factor()#0.03254 strong evidence for null 8/23/25## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
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## Iteration: 4## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
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## Iteration: 4
## Bayes Factor (BF10): 0.08966985
## Equivalent BF01: 11.152
## Interpretation: Strong evidence for the null hypothesisfit.ee_pair_summary.cv.base = brm(ee.seq_pair.mean_correct_set_chosen ~ cv.mean_success + age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ee.seq_pair.mean_correct_set_chosen) &
!is.na(cv.mean_success)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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##
## All 4 chains finished successfully.
## Mean chain execution time: 0.3 seconds.
## Total execution time: 0.6 seconds.fit.ee_pair_summary.cv = brm(ee.seq_pair.mean_correct_set_chosen ~ cv.mean_success + age_zscored,
family = "gaussian",
save_pars = save_pars(all = T),
data = df.summary %>%
filter(!is.na(ee.seq_pair.mean_correct_set_chosen) &
!is.na(cv.mean_success)),
prior = priors,
iter = 20000, warmup = 5000, control = list(adapt_delta = 0.9), backend = "cmdstanr",
#file = "./cache/goals_mass_lang",
seed = 1)## Start sampling## Running MCMC with 4 chains, at most 11 in parallel...
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## Total execution time: 0.5 seconds.bayes_factor(fit.ee_pair_summary.cv, fit.ee_pair_summary.cv.base)$bf %>% interpret_bayes_factor()#1.01398 anecdotal evidence for fit.ee_pair_summary.cv 8/23/25## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4## Recompiling the model with 'rstan'## Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
## using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
## using SDK: ‘MacOSX26.2.sdk’
## clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
## In file included from <built-in>:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
## /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
## 679 | #include <cmath>
## | ^~~~~~~
## 1 error generated.
## make: *** [foo.o] Error 1## Recompilation done## Iteration: 1
## Iteration: 2
## Iteration: 3
## Iteration: 4
## Bayes Factor (BF10): 1.000108
## Interpretation: Anecdotal evidence for the alternative hypothesis