# remove inappropriate conditions
all_data <- filter(all_data, dataset != "Statistical word segementation") %>% # incomplete MA
            filter(dataset != "Pointing and vocabulary (longitudinal)") %>%  # longitidinal MA
            filter(is.na(condition_type) | condition_type == "critical") # remove control conditions from labadv

# need to recompute datasets summary data, based on filtered all_data
studies <- all_data %>%
  group_by(dataset) %>%
  summarise(num_experiments = n(),
            num_papers = length(unique(study_ID)))

subjects <- all_data %>%
  rowwise() %>%
  mutate(n_total = sum(c(n_1, n_2), na.rm = TRUE)) %>%
  distinct(dataset, study_ID, same_infant, .keep_all = TRUE) %>%
  group_by(dataset) %>%
  summarise(num_subjects = sum(n_total))

datasets <- datasets %>%
  rename(dataset = name) %>%
  select(-num_experiments, -num_papers, -num_subjects) %>%
  filter(dataset != "Statistical word segementation") %>% 
  filter(dataset != "Pointing and vocabulary (longitudinal)") %>%
  left_join(studies) %>%
  left_join(subjects) %>%
  rename(name = dataset)

# rename pointing and vocabulary 
datasets$name = plyr::mapvalues(datasets$name, from = c("Pointing and vocabulary (concurrent)"), 
                                to = c("Pointing and vocabulary"))

all_data$dataset = plyr::mapvalues(all_data$dataset , from = c("Pointing and vocabulary (concurrent)"),
                                   to = c("Pointing and vocabulary"))

Fig 3 data

# make levels df
ld.df = data.frame(dataset = datasets$name,
                   domain = c("Prosody", "Words", "Communication", "Sounds",
                              "Sounds", "Sounds", "Sounds", "Sounds", "Words",
                              "Words", "Communication", "Words"))

ld.df$domain = factor(ld.df$domain, levels = c("Prosody","Sounds", "Words", "Communication"))

single_method_datasets = c("Gaze following",
                           "Label advantage in concept learning", 
                           "Mutual exclusivity", 
                           "Pointing and vocabulary",
                           "Online word recognition")

# get model fits
all_data.resid = data.frame()
for (i in 1:length(datasets$name)) {
    d = filter(all_data, dataset == datasets$name[i])
    if (datasets$name[i] %in% single_method_datasets) {
      full.model = rma(d_calc, vi = d_var_calc, data = d)
    } else {
      full.model = rma(d_calc ~ method, vi = d_var_calc, data = d)
    }
  
  d = as.data.frame(rstandard(full.model)$resid) %>%
       cbind(d) %>%
       rename(residual.d = `rstandard(full.model)$resid`) %>%
       mutate(residual.d = residual.d + full.model$b[1]) %>% # add in intercept term
       inner_join(all_data) 
  
  all_data.resid = rbind(all_data.resid,d)
}

# merge in levels
residualized.es = all_data.resid %>%
          left_join(ld.df) %>%
          filter(dataset != "Statistical sound category learning") %>%
          filter(dataset != "Phonotactic learning") %>%
          mutate(age.years = mean_age/365) %>%
          filter(age.years < 3)

Fig 4 data

## real data
all_data.f = residualized.es %>%
  select(age.years, dataset, residual.d, n) %>%
  mutate(model = "Observed")

## simulated data
# bottom-up
x = seq(0, 3, .01)
slope = 1.1
y1 = ifelse((log(x - 1) * slope) < 0, NA, log(x - 1) * slope)
y2 = ifelse((log(x) * slope) < 0, NA, log(x) * slope)
y3 = ifelse((log(x + 1) * slope) < 0, NA, log(x + 1) * slope)

# interactive 
y4 = log((x + 1)) * .2
y5 = log((x + 1)) * .5
y6 = log((x + 1)) * 1.1

# ad hoc 
y7 = .2 * x
y8 = dnorm(x, mean = 1.7, sd = .5) 
y9 = log(x + .0001, base = .02) + .3
y9[1] = 1.47464029

# merge together simulated data
simulated.development = data.frame(age.years = c(x,x,x,x,x,x,x,x,x),
                                   residual.d = c(y3, y2, y1, y6, y5, y4, y9, y8, y7),
                                   dataset = c(rep(1:3, each = length(x)), rep(1:3, each = length(x)),
                                               rep(1:3, each = length(x))),
                                   model = rep(c("Sequential", "Simultaneous", "Ad hoc"), each = length(x) * 3),
                                   n = 1)

## merge together simulated and real
simulated.development.all = mutate(simulated.development, dataset = as.factor(dataset)) %>%
  rbind(all_data.f) %>%
  mutate(model = ordered(model, levels = c("Sequential", "Simultaneous", "Ad hoc", "Observed")),
         level = ifelse(model != "Observed", dataset, 
                        ifelse(dataset == "Infant directed speech preference", 1,
                               ifelse(dataset == "Pointing and vocabulary" | dataset == "Gaze following", 4, 
                                      ifelse(dataset == "Word segmentation" | dataset == "Vowel discrimination (native)" | dataset == "Vowel discrimination (non-native)", 2, 3)))))

real.levels = levels(simulated.development.all$dataset)
fake.levels = c("1", "2", "3") 

simulated.development.all = simulated.development.all %>%
  mutate(dataset.label = as.factor(dataset)) %>%
  mutate(dataset.label = plyr::mapvalues(dataset.label, from = c("1", "2", "3", "Gaze following",  "Infant directed speech preference", "Label advantage in concept learning", "Mutual exclusivity", "Vowel discrimination (native)", "Vowel discrimination (non-native)", "Sound symbolism" , "Online word recognition" , "Word segmentation"), to = c("","","", "GF", "IDS", "LA", "ME", "VD-N", "VD-NN", "SS", "WR", "WS")))

params

fs = 16

pink1 = "#F8766D"
barf = "#D89000"
yellowgreen = "#A3A500" 
green1 = "#39B600" 
green2 = "#00BF7D" 
blue1 = "#00BFC4"
blue2 = "#00B0F6"
purple = "#9590FF"
pink2 = "#E76BF3"
pink3 = "#FF62BC"

Fig. 3

default - ggplot 10 color palatte

level.plot = ggplot(residualized.es, aes(x = age.years, y = residual.d, col = dataset)) +
  facet_grid(~ domain) +
  geom_point(aes(size = n), alpha = .1, data = filter(residualized.es, residual.d > -.5 & residual.d < 2.5 )) +
  geom_hline(yintercept = 0, linetype = "dashed") +
  geom_line(stat="smooth", method="lm", se = FALSE, size = 1, formula = y ~ log(x)) + 
  coord_cartesian(ylim = c(-.5, 2.5), xlim = c(0, 3.1)) +  # doesn't remove data from geom_smooth
  xlab("Age (years)") + 
  ylab("Method-residualized\n effect size") + 
  theme_bw() + 
  theme(legend.position = "none",
        legend.key = element_blank(),
        legend.background = element_rect(fill = "transparent"),
        axis.line= element_line(size = 3),
        axis.text = element_text(colour = "black", size = fs),
        strip.text.x = element_text(size = 14),
        axis.title = element_text(colour = "black", size = fs),
        strip.background = element_rect(fill="grey"))

direct.label(level.plot, list("top.bumptwice", dl.trans(y = y + 0.1), cex = .7))

re-arranged ggplot 10 color palatte

level.plot = ggplot(residualized.es, aes(x = age.years, y = residual.d, col = dataset)) +
  facet_grid(~ domain) +
  geom_point(aes(size = n), alpha = .1, data = filter(residualized.es, residual.d > -.5 & residual.d < 2.5 )) +
  geom_hline(yintercept = 0, linetype = "dashed") +
  geom_line(stat="smooth", method="lm", se = FALSE, size = 1, formula = y ~ log(x)) + 
  coord_cartesian(ylim = c(-.5, 2.5), xlim = c(0, 3.1)) +  # doesn't remove data from geom_smooth
  xlab("Age (years)") + 
  ylab("Method-residualized\n effect size") + 
  scale_colour_manual(values = c(pink2, blue1, purple, green2, pink1, yellowgreen, barf, green1, pink3, blue2)) +
  theme_bw() + 
  theme(legend.position = "none",
        legend.key = element_blank(),
        legend.background = element_rect(fill = "transparent"),
        axis.line= element_line(size = 3),
        axis.text = element_text(colour = "black", size = fs),
        strip.text.x = element_text(size = 14),
        axis.title = element_text(colour = "black", size = fs),
        strip.background = element_rect(fill="grey"))

direct.label(level.plot, list("top.bumptwice", dl.trans(y = y + 0.1), cex = .7))

Fig. 4

no alpha

## plot
ggplot(simulated.development.all,
       aes(x = age.years, y = residual.d, col = dataset)) + 
  geom_line(data = filter(simulated.development.all, model != "Observed"), 
            size = 1) +
  geom_line(stat="smooth", 
            data = filter(simulated.development.all, model == "Observed"), 
            size = 1,
            method = "lm",
            formula = y~log(x),
            se = FALSE) + 
  geom_hline(yintercept = 0, linetype = "dashed") +
  coord_cartesian(ylim = c(-.5, 2.5), xlim = c(0, 3.1)) +  # doesn't remove data from geom_smooth
  facet_grid(.~model) +
  scale_colour_manual(values=c( "grey70", "grey35", "grey20", pink2, blue1, purple, green2, pink1, 
                                yellowgreen, barf,  green1, pink3, blue2),
                      breaks = real.levels[real.levels!=fake.levels])+
  xlab("Age (years)") +
  ylab("Method-residualized\neffect size") + 
  theme_bw() + 
  theme(legend.position = "none",
        legend.key = element_blank(),
        legend.background = element_rect(fill = "transparent"),
        legend.title = element_blank(),
        axis.line= element_line(size = 3),
        axis.text = element_text(colour = "black", size = fs),
        strip.text.x = element_text(size = 14),
        axis.title = element_text(colour = "black", size = fs),
        strip.background = element_rect(fill="grey"))

alpha

## plot
ggplot(simulated.development.all,
       aes(x = age.years, y = residual.d, col = dataset)) + 
  geom_line(data = filter(simulated.development.all, model != "Observed"), 
            aes(alpha = level),
            size = 1) +
  geom_line(stat="smooth", 
            data = filter(simulated.development.all, model == "Observed"), 
            aes(alpha = level ),
            size = 1,
            method = "lm",
            formula = y~log(x),
            se = FALSE) + 
  scale_alpha(range = c(0.25, 1)) +
  coord_cartesian(ylim = c(-.5, 2.5), xlim = c(0, 3.1)) +  # doesn't remove data from geom_smooth
  geom_hline(yintercept = 0, linetype = "dashed") +
  facet_grid(.~model) +
  scale_colour_manual(values=c( "black", "black", "black", pink2, blue1, purple, green2, pink1, 
                                yellowgreen, barf,  green1, pink3, blue2),
                      breaks = real.levels[real.levels!=fake.levels])+
  xlab("Age (years)") +
  ylab("Method-residualized\neffect size") + 
  theme_bw() + 
  theme(legend.position = "none",
        legend.key = element_blank(),
        legend.background = element_rect(fill = "transparent"),
        legend.title = element_blank(),
        axis.line= element_line(size = 3),
        axis.text = element_text(colour = "black", size = fs),
        strip.text.x = element_text(size = 14),
        axis.title = element_text(colour = "black", size = fs),
        strip.background = element_rect(fill="grey"))

bw alpha

ggplot(simulated.development.all,
       aes(x = age.years, y = residual.d, color = dataset)) + 
  geom_line(data = filter(simulated.development.all, model != "Observed"), 
            aes(alpha = level),
            size = 1) +
  geom_line(stat="smooth", 
            data = filter(simulated.development.all, model == "Observed"), 
            aes(alpha = level),
            size = 1,
            method = "lm",
            formula = y~log(x),
            se = FALSE) + 
  scale_colour_manual(values=c( "black", "black", "black", "black", "black", "black", "black", "black" ,"black", "black", "black", "black", "black", "black", "black", "black")) + 
  scale_alpha(range = c(0.2, 1)) +
  coord_cartesian(ylim = c(-.5, 2.5), xlim = c(0, 3.1)) +  # doesn't remove data from geom_smooth
  geom_hline(yintercept = 0, linetype = "dashed") +
  facet_grid(.~model) +
  xlab("Age (years)") +
  ylab("Method-residualized\neffect size") + 
  theme_bw() + 
  theme(legend.position = "none",
        legend.key = element_blank(),
        legend.background = element_rect(fill = "transparent"),
        legend.title = element_blank(),
        axis.line= element_line(size = 3),
        axis.text = element_text(colour = "black", size = fs),
        strip.text.x = element_text(size = 14),
        axis.title = element_text(colour = "black", size = fs),
        strip.background = element_rect(fill="grey"))