C4_O2_Behavior
Alan Ivory
2026-01-08
Set-up
Install necessary packages and import appropriate data
pacman::p_load(tidyverse, readxl, raster, vegan, tigris, sf, sjPlot, sp, spOccupancy, ggrepel, lme4, lmerTest, MuMIn, brms, MCMCvis, cmdstanr, lubridate, forcats)
# Install dependencies
#install.packages(c("posterior", "RcppParallel", "jsonlite"))
# Then install cmdstanr from the Stan developers’ repository
#install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
# Tree PCQ Data
tree_data <- read_excel("C:/Users/DrewIvory/OneDrive - University of Florida/Desktop/School/PHD/01_Projects/05_SharedData/Field_Data_FL_AL_MS.xlsx",
sheet = "Tree_PCQ")
# Soil Data
fuel_data <- read_excel("C:/Users/DrewIvory/OneDrive - University of Florida/Desktop/School/PHD/01_Projects/05_SharedData/Field_Data_FL_AL_MS.xlsx",
sheet = "Fuel_Sampling")
# Veg Data
Veg_Cover <- read_excel("C:/Users/DrewIvory/OneDrive - University of Florida/Desktop/School/PHD/01_Projects/05_SharedData/Field_Data_FL_AL_MS.xlsx",
sheet = "Veg_Cover")
# Shrub Cover Data
shrub_data <- read_excel("C:/Users/DrewIvory/OneDrive - University of Florida/Desktop/School/PHD/01_Projects/05_SharedData/Field_Data_FL_AL_MS.xlsx",
sheet = "Shrub_Cover")
# Site Data
CameraData <- read_excel("C:/Users/DrewIvory/OneDrive - University of Florida/Desktop/School/PHD/01_Projects/04_Wildlife/02_Data/CameraData.xlsx")
CameraLoc <- read_excel("C:/Users/DrewIvory/OneDrive - University of Florida/Desktop/School/PHD/01_Projects/04_Wildlife/02_Data/CameraLoc.xlsx",
sheet = "CameraLocations")
# Add effort data
effort_matrix <- read_excel("C:/Users/DrewIvory/OneDrive - University of Florida/Desktop/School/PHD/01_Projects/04_Wildlife/02_Data/CameraLoc.xlsx",
sheet = "Effort_Matrix_Full") %>%
pivot_longer(cols = matches("^202[4-5]-"), names_to = "week", values_to = "days") %>%
filter(days == "7") %>%
dplyr::select(Plot, week)Number of quadrats sampled per plot
I moved this from a later section because the filtering process removed quadrats that did not capture any species. Rows labeled as “None” were removed, suggesting that the number of quadrats sampled per plot is not consistent across all plots.
# Count the total number of quadrats per plot
quadrat_count <- Veg_Cover %>%
group_by(Plot) %>%
summarize(total_quadrats = n_distinct(Quadrat), .groups = "drop")Filter All data to only include specified species (Per PLANTS database)
#Filter tree data to only include trees with "tree" in the growth column
tree_data <- dplyr::filter(tree_data, Growth == "Tree")
#Filter Veg Cover to exclude Shrubs and Trees
Veg_Cover <- dplyr::filter(Veg_Cover, Growth != "Shrub" & Growth != "Tree")
#Filter Shrub Cover to only include Shrubs and Trees
shrub_data <- dplyr::filter(shrub_data, Growth == "Shrub" | Growth == "Tree")Filter all data to only include species found at 3% of all sites
# Calculate the total number of sites
total_sites <- nrow(CameraLoc)
# Function to filter data by frequency
filter_by_frequency <- function(df) {
# Group data by species and calculate the frequency
freq <- df %>%
group_by(Species) %>%
summarise(Frequency = n_distinct(Plot) / nrow(CameraLoc) * 100) %>%
filter(Frequency >= 3)
# Filter the original data to include only species with frequency >= 3%
filtered_df <- df %>%
filter(Species %in% freq$Species)
return(filtered_df)
}
# Filter tree data by frequency
tree_data <- filter_by_frequency(tree_data)
# Filter Veg Cover data by frequency
Veg_Cover <- filter_by_frequency(Veg_Cover)
# Filter Shrub Cover data by frequency
shrub_data <- filter_by_frequency(shrub_data)Shrub Cover Conversion
# Total length of Shrub cover at a site
shrub_cover <- shrub_data %>%
mutate(Cover = Line_End - Line_Start) %>%
group_by(Species_Name, Plot) %>%
summarise(Shrub_Total_Cover = sum(Cover, na.rm = TRUE), .groups = "drop") %>%
mutate(Shrub_Percent_Cover = Shrub_Total_Cover / 3000 * 100)
# Summed length of shrub over at a site
shrub_cover_summed <- shrub_cover %>%
group_by(Plot) %>%
summarize(total_shrub_cover = sum(Shrub_Total_Cover, na.rm = TRUE), .groups = "drop")Herbacous Cover Conversion
# Combine Plot and Quadrat columns
Veg_Cover <- Veg_Cover %>%
mutate(Plot_Quadrat = paste(Plot, Quadrat, sep = '_'))
# Join with CogonSites to get site information
Veg_Cover <- Veg_Cover %>%
left_join(CameraLoc, by = "Plot")
# Sum species cover across quadrats for each species at each plot
veg_cover_summed <- Veg_Cover %>%
group_by(Plot, Species_Name) %>%
summarize(total_cover = sum(Cover_Per, na.rm = TRUE), .groups = "drop")
# Calculate average herbaceous species cover
avg_species_cover <- veg_cover_summed %>%
left_join(quadrat_count, by = "Plot") %>%
mutate(avg_cover = total_cover / total_quadrats)Merging Herb cover with Shrub
This species matrix includes herbaceous and shrub species
# Merge shrub cover with herbaceous average cover
combined_cover <- avg_species_cover %>%
full_join(
shrub_cover %>%
dplyr::select(Plot, Species_Name, Shrub_Percent_Cover),
by = c("Plot", "Species_Name")
) %>%
mutate(
overlap_flag = ifelse(!is.na(avg_cover) & !is.na(Shrub_Percent_Cover), TRUE, FALSE), # Flag overlaps
final_cover = case_when(
!is.na(avg_cover) & is.na(Shrub_Percent_Cover) ~ avg_cover, # Use herbaceous cover if no shrub data
is.na(avg_cover) & !is.na(Shrub_Percent_Cover) ~ Shrub_Percent_Cover, # Use shrub cover if no herbaceous data
TRUE ~ NA_real_ # Leave as NA where overlaps exist
)
)
# Species Matrix
species_matrix <- combined_cover %>%
dplyr::select(Plot, Species_Name, final_cover) %>%
pivot_wider(
names_from = Species_Name,
values_from = final_cover,
values_fill = 0
)Summarize Cogongrass Cover
avg_cogongrass_cover <- species_matrix %>%
group_by(Plot) %>%
summarize(Avg_Cogongrass_Cover = sum(Imperata_cylindrica, na.rm = TRUE) / n(), .groups = "drop")Herbacous Shannon Diversity Index
# Summarize species cover by site
site_species_cover <- Veg_Cover %>%
group_by(Plot, Species_Name) %>%
summarize(total_cover = sum(Cover_Per, na.rm = TRUE)) %>%
ungroup()## `summarise()` has grouped output by 'Plot'. You can override using the
## `.groups` argument.# Calculate Shannon diversity per site
Veg_shannon_diversity <- site_species_cover %>%
group_by(Plot) %>%
mutate(proportion = total_cover / sum(total_cover)) %>%
summarize(Veg_shannon_index = -sum(proportion * log(proportion), na.rm = TRUE))
print(Veg_shannon_diversity)## # A tibble: 206 × 2
## Plot Veg_shannon_index
## <chr> <dbl>
## 1 BI200 2.28
## 2 BI201 2.20
## 3 BI202 1.50
## 4 BI97 1.82
## 5 BI99 3.06
## 6 BN210 2.97
## 7 BN211 2.43
## 8 BN212 2.22
## 9 BN96 3.05
## 10 BN98 2.79
## # ℹ 196 more rowsVegetation Height
if (!is.numeric(fuel_data$Height)) {
fuel_data$Height <- as.numeric(as.character(fuel_data$Height))
}## Warning: NAs introduced by coercion# Calculate average vegetation height per plot
veg_height <- fuel_data %>%
group_by(Plot) %>%
summarize(avg_veg_height = mean(Height, na.rm = TRUE), .groups = "drop")Tree Metrics
# Tree density from point-centered quarter data
if (!is.numeric(tree_data$Distance)) {
tree_data$Distance <- as.numeric(as.character(tree_data$Distance))
}
tree_density_data <- tree_data %>%
group_by(Plot) %>%
summarize(Average_Distance = mean(Distance) / 100, # Convert to meters
Tree_Density = 10000 / (Average_Distance^2)) # Convert to trees per hectare
# Average canopy cover from vegetation quadrats
tree_canopy_data <- Veg_Cover %>%
distinct(Plot, Quadrat, .keep_all = TRUE) %>% # Ensure each quadrat counts once per plot
group_by(Plot) %>%
summarize(Avg_Canopy_Cover = mean(Canopy_Cover, na.rm = TRUE), .groups = "drop") # Calculate the average canopy cover per plot
cor(tree_density_data$Tree_Density, tree_canopy_data$Avg_Canopy_Cover)## [1] 0.2742307Objective 2: Determine whether wildlife behaviors differ in and around cogongrass patches, specifically as it relates to whether specific taxa avoid cogongrass invaded areas.
Behavior Occurence
CameraData <- CameraData%>%
dplyr::select(-Status)
O2_data <- CameraData %>%
left_join(CameraLoc_O2, by = "Plot")
O2_data <- O2_data %>%
mutate(
DateTime = update(Date,
hour = hour(Time),
minute = minute(Time),
second = second(Time))
)
gap_mins <- 30
O2_data <- O2_data %>%
filter(!is.na(DateTime)) %>%
arrange(Plot, Name, DateTime) %>%
group_by(Plot, Name) %>%
group_modify(~{
df <- .x
keep <- logical(nrow(df))
last_kept <- as.POSIXct(NA, tz = tz(df$DateTime[1]))
for (i in seq_len(nrow(df))) {
if (is.na(last_kept) || difftime(df$DateTime[i], last_kept, units = "mins") > gap_mins) {
keep[i] <- TRUE
last_kept <- df$DateTime[i]
}
}
df[keep, , drop = FALSE]
}) %>%
ungroup()
dat <- O2_data %>%
filter(!is.na(Behavior), !is.na(Status), !is.na(BehLoc)) %>%
mutate(
# time-of-day as proportion of a 24-hour day, then z-score and quadratic
time_prop = (hour(DateTime)*3600 + minute(DateTime)*60 + second(DateTime)) / 86400,
time_z = as.numeric(scale(time_prop)),
time_z2 = time_z^2,
# temperature standardized (optional)
temp_z = as.numeric(scale(Air.TemperatureC)),
# month factor to absorb temporal clustering
Month = factor(month(DateTime)),
# set factor baselines
Behavior = factor(Behavior, ordered = FALSE),
Behavior = relevel(Behavior, ref = "Local_Search"),
Status = factor(Status, levels = c("Non_Invaded","Invaded")),
BehLoc = factor(BehLoc, levels = c("Non_Patch","Patch")), # ensure Non_Patch vs Patch
Plot = factor(Plot),
Name = factor(Name),
Site = factor(Site),
Camera.Type = factor(Camera.Type)
)Behavior Model
# Priors (weakly informative, regularizing)
priors <- c(
prior(normal(0, 1), class = "b", dpar = "muForaging"),
prior(normal(0, 1), class = "b", dpar = "muTransit"),
prior(student_t(3, 0, 2.5), class = "Intercept", dpar = "muForaging"),
prior(student_t(3, 0, 2.5), class = "Intercept", dpar = "muTransit"),
prior(exponential(1), class = "sd", dpar = "muForaging"),
prior(exponential(1), class = "sd", dpar = "muTransit")
)
# 1) BETWEEN SITES: Do behaviors differ at invaded vs non-invaded sites?
# Multilevel multinomial (categorical) model with population-level effects and random intercepts
model_status <- brm(
bf(Behavior ~ Status * Name +
(1 | Site) + (1 | Camera.Type) + (1 | Month)),
family = categorical(link = "logit", refcat = "Local_Search"),
data = dat,
prior = priors,
chains = 4, cores = 4, iter = 4000, warmup = 2000,
control = list(adapt_delta = 0.95, max_treedepth = 12)
)## Compiling Stan program...## Start sampling## Warning: There were 9 divergent transitions after warmup. See
## https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
## to find out why this is a problem and how to eliminate them.## Warning: Examine the pairs() plot to diagnose sampling problems# Quick fit diagnostics / model comparison
summary(model_status)## Warning: There were 9 divergent transitions after warmup. Increasing
## adapt_delta above 0.95 may help. See
## http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup## Family: categorical
## Links: muForaging = logit; muTransit = logit
## Formula: Behavior ~ Status * Name + (1 | Site) + (1 | Camera.Type) + (1 | Month)
## Data: dat (Number of observations: 2815)
## Draws: 4 chains, each with iter = 4000; warmup = 2000; thin = 1;
## total post-warmup draws = 8000
##
## Multilevel Hyperparameters:
## ~Camera.Type (Number of levels: 4)
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS
## sd(muForaging_Intercept) 0.39 0.34 0.01 1.27 1.00 2171
## sd(muTransit_Intercept) 0.21 0.21 0.01 0.76 1.00 3603
## Tail_ESS
## sd(muForaging_Intercept) 3490
## sd(muTransit_Intercept) 4649
##
## ~Month (Number of levels: 9)
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS
## sd(muForaging_Intercept) 0.67 0.23 0.36 1.23 1.00 3458
## sd(muTransit_Intercept) 0.17 0.11 0.01 0.42 1.00 2712
## Tail_ESS
## sd(muForaging_Intercept) 5344
## sd(muTransit_Intercept) 3149
##
## ~Site (Number of levels: 5)
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS
## sd(muForaging_Intercept) 0.17 0.17 0.00 0.63 1.00 4535
## sd(muTransit_Intercept) 0.48 0.25 0.20 1.12 1.00 4648
## Tail_ESS
## sd(muForaging_Intercept) 5585
## sd(muTransit_Intercept) 5344
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI
## muForaging_Intercept -0.50 0.51 -1.53
## muTransit_Intercept 1.50 0.41 0.67
## muForaging_StatusInvaded -0.21 0.44 -1.08
## muForaging_NameDasypus_novemcinctus 1.83 0.53 0.80
## muForaging_NameDidelphis_virginiana 0.90 0.74 -0.56
## muForaging_NameLynx_rufus -0.44 0.88 -2.21
## muForaging_NameMeleagris_gallopavo 0.23 0.67 -1.10
## muForaging_NameOdocoileus_virginianus 1.11 0.37 0.39
## muForaging_NameProcyon_lotor -0.72 0.55 -1.82
## muForaging_NameSciurus_carolinensis 0.07 0.68 -1.30
## muForaging_NameSylvilagus_floridanus 1.52 0.60 0.37
## muForaging_StatusInvaded:NameDasypus_novemcinctus 0.53 0.62 -0.67
## muForaging_StatusInvaded:NameDidelphis_virginiana 0.08 0.81 -1.51
## muForaging_StatusInvaded:NameLynx_rufus -0.19 0.93 -2.06
## muForaging_StatusInvaded:NameMeleagris_gallopavo 0.12 0.86 -1.59
## muForaging_StatusInvaded:NameOdocoileus_virginianus -0.14 0.45 -1.02
## muForaging_StatusInvaded:NameProcyon_lotor -0.17 0.67 -1.48
## muForaging_StatusInvaded:NameSciurus_carolinensis 0.16 0.76 -1.37
## muForaging_StatusInvaded:NameSylvilagus_floridanus 0.44 0.74 -1.01
## muTransit_StatusInvaded 0.20 0.38 -0.55
## muTransit_NameDasypus_novemcinctus 0.70 0.50 -0.25
## muTransit_NameDidelphis_virginiana 0.22 0.67 -1.09
## muTransit_NameLynx_rufus 1.47 0.74 0.06
## muTransit_NameMeleagris_gallopavo 0.06 0.57 -1.07
## muTransit_NameOdocoileus_virginianus -0.17 0.29 -0.75
## muTransit_NameProcyon_lotor -0.49 0.41 -1.28
## muTransit_NameSciurus_carolinensis -0.86 0.60 -2.02
## muTransit_NameSylvilagus_floridanus -0.11 0.58 -1.24
## muTransit_StatusInvaded:NameDasypus_novemcinctus 0.02 0.59 -1.12
## muTransit_StatusInvaded:NameDidelphis_virginiana 0.35 0.73 -1.06
## muTransit_StatusInvaded:NameLynx_rufus 0.62 0.88 -1.10
## muTransit_StatusInvaded:NameMeleagris_gallopavo -0.24 0.79 -1.77
## muTransit_StatusInvaded:NameOdocoileus_virginianus -0.26 0.39 -1.02
## muTransit_StatusInvaded:NameProcyon_lotor -0.07 0.50 -1.06
## muTransit_StatusInvaded:NameSciurus_carolinensis -0.49 0.68 -1.82
## muTransit_StatusInvaded:NameSylvilagus_floridanus 0.14 0.71 -1.24
## u-95% CI Rhat Bulk_ESS
## muForaging_Intercept 0.50 1.00 5109
## muTransit_Intercept 2.31 1.00 5885
## muForaging_StatusInvaded 0.65 1.00 6276
## muForaging_NameDasypus_novemcinctus 2.90 1.00 7840
## muForaging_NameDidelphis_virginiana 2.33 1.00 13785
## muForaging_NameLynx_rufus 1.21 1.00 13665
## muForaging_NameMeleagris_gallopavo 1.51 1.00 10151
## muForaging_NameOdocoileus_virginianus 1.84 1.00 7661
## muForaging_NameProcyon_lotor 0.34 1.00 8797
## muForaging_NameSciurus_carolinensis 1.38 1.00 10805
## muForaging_NameSylvilagus_floridanus 2.71 1.00 9701
## muForaging_StatusInvaded:NameDasypus_novemcinctus 1.77 1.00 7898
## muForaging_StatusInvaded:NameDidelphis_virginiana 1.67 1.00 14392
## muForaging_StatusInvaded:NameLynx_rufus 1.60 1.00 15460
## muForaging_StatusInvaded:NameMeleagris_gallopavo 1.76 1.00 13545
## muForaging_StatusInvaded:NameOdocoileus_virginianus 0.75 1.00 6375
## muForaging_StatusInvaded:NameProcyon_lotor 1.15 1.00 9843
## muForaging_StatusInvaded:NameSciurus_carolinensis 1.64 1.00 11199
## muForaging_StatusInvaded:NameSylvilagus_floridanus 1.87 1.00 10543
## muTransit_StatusInvaded 0.95 1.00 5543
## muTransit_NameDasypus_novemcinctus 1.70 1.00 9515
## muTransit_NameDidelphis_virginiana 1.56 1.00 11722
## muTransit_NameLynx_rufus 2.97 1.00 14084
## muTransit_NameMeleagris_gallopavo 1.17 1.00 11546
## muTransit_NameOdocoileus_virginianus 0.39 1.00 7061
## muTransit_NameProcyon_lotor 0.31 1.00 8237
## muTransit_NameSciurus_carolinensis 0.30 1.00 11366
## muTransit_NameSylvilagus_floridanus 1.01 1.00 10966
## muTransit_StatusInvaded:NameDasypus_novemcinctus 1.16 1.00 8186
## muTransit_StatusInvaded:NameDidelphis_virginiana 1.79 1.00 10916
## muTransit_StatusInvaded:NameLynx_rufus 2.38 1.00 15476
## muTransit_StatusInvaded:NameMeleagris_gallopavo 1.33 1.00 13876
## muTransit_StatusInvaded:NameOdocoileus_virginianus 0.50 1.00 5601
## muTransit_StatusInvaded:NameProcyon_lotor 0.93 1.00 6806
## muTransit_StatusInvaded:NameSciurus_carolinensis 0.85 1.00 9887
## muTransit_StatusInvaded:NameSylvilagus_floridanus 1.53 1.00 10521
## Tail_ESS
## muForaging_Intercept 5699
## muTransit_Intercept 5660
## muForaging_StatusInvaded 5942
## muForaging_NameDasypus_novemcinctus 6355
## muForaging_NameDidelphis_virginiana 6511
## muForaging_NameLynx_rufus 6075
## muForaging_NameMeleagris_gallopavo 6257
## muForaging_NameOdocoileus_virginianus 5968
## muForaging_NameProcyon_lotor 5888
## muForaging_NameSciurus_carolinensis 6292
## muForaging_NameSylvilagus_floridanus 6521
## muForaging_StatusInvaded:NameDasypus_novemcinctus 6030
## muForaging_StatusInvaded:NameDidelphis_virginiana 6692
## muForaging_StatusInvaded:NameLynx_rufus 6242
## muForaging_StatusInvaded:NameMeleagris_gallopavo 6379
## muForaging_StatusInvaded:NameOdocoileus_virginianus 5781
## muForaging_StatusInvaded:NameProcyon_lotor 6149
## muForaging_StatusInvaded:NameSciurus_carolinensis 5990
## muForaging_StatusInvaded:NameSylvilagus_floridanus 6478
## muTransit_StatusInvaded 5935
## muTransit_NameDasypus_novemcinctus 6964
## muTransit_NameDidelphis_virginiana 6378
## muTransit_NameLynx_rufus 5882
## muTransit_NameMeleagris_gallopavo 5728
## muTransit_NameOdocoileus_virginianus 6712
## muTransit_NameProcyon_lotor 6808
## muTransit_NameSciurus_carolinensis 6935
## muTransit_NameSylvilagus_floridanus 6058
## muTransit_StatusInvaded:NameDasypus_novemcinctus 6354
## muTransit_StatusInvaded:NameDidelphis_virginiana 6111
## muTransit_StatusInvaded:NameLynx_rufus 5915
## muTransit_StatusInvaded:NameMeleagris_gallopavo 6164
## muTransit_StatusInvaded:NameOdocoileus_virginianus 5820
## muTransit_StatusInvaded:NameProcyon_lotor 5888
## muTransit_StatusInvaded:NameSciurus_carolinensis 6885
## muTransit_StatusInvaded:NameSylvilagus_floridanus 6370
##
## Draws were sampled using sampling(NUTS). 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(model_status)
waic(model_status)## Warning:
## 5 (0.2%) p_waic estimates greater than 0.4. We recommend trying loo instead.##
## Computed from 8000 by 2815 log-likelihood matrix.
##
## Estimate SE
## elpd_waic -2539.0 31.4
## p_waic 43.4 1.9
## waic 5078.1 62.8
##
## 5 (0.2%) p_waic estimates greater than 0.4. We recommend trying loo instead.loo(model_status)##
## Computed from 8000 by 2815 log-likelihood matrix.
##
## Estimate SE
## elpd_loo -2539.2 31.4
## p_loo 43.6 1.9
## looic 5078.4 62.8
## ------
## MCSE of elpd_loo is 0.1.
## MCSE and ESS estimates assume MCMC draws (r_eff in [0.5, 1.6]).
##
## All Pareto k estimates are good (k < 0.7).
## See help('pareto-k-diagnostic') for details.# Posterior predictions contrasting Invaded vs Non_Invaded, marginalizing random effects
# Need to work on this later
# Visualize the interaction
#ce_status_name <- conditional_effects(model_status,
# effects = "Status:Name",
# categorical = TRUE)
#plot(ce_status_name)Behavior Model Within cogongrass patches
# 2) WITHIN INVADED: Do behaviors differ inside vs outside cogongrass patches?
dat_inv <- dat %>% filter(Status == "Invaded")
# Priors for the within-invaded model (same structure, applies to both non-reference categories)
priors_inv <- c(
prior(normal(0, 1), class = "b", dpar = "muForaging"),
prior(normal(0, 1), class = "b", dpar = "muTransit"),
prior(student_t(3, 0, 2.5), class = "Intercept", dpar = "muForaging"),
prior(student_t(3, 0, 2.5), class = "Intercept", dpar = "muTransit"),
prior(exponential(1), class = "sd", dpar = "muForaging"),
prior(exponential(1), class = "sd", dpar = "muTransit")
)
model_loc <- brm(
bf(Behavior ~ BehLoc * Name +
(1 | Site) + (1 | Camera.Type) + (1 | Month)),
family = categorical(link = "logit", refcat = "Local_Search"),
data = dat_inv,
prior = priors_inv,
chains = 4, cores = 4, iter = 4000, warmup = 2000,
control = list(adapt_delta = 0.95, max_treedepth = 12)
)## Compiling Stan program...## Start sampling## Warning: There were 1 divergent transitions after warmup. See
## https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
## to find out why this is a problem and how to eliminate them.## Warning: Examine the pairs() plot to diagnose sampling problemssummary(model_loc)## Warning: There were 1 divergent transitions after warmup. Increasing
## adapt_delta above 0.95 may help. See
## http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup## Family: categorical
## Links: muForaging = logit; muTransit = logit
## Formula: Behavior ~ BehLoc * Name + (1 | Site) + (1 | Camera.Type) + (1 | Month)
## Data: dat_inv (Number of observations: 1300)
## Draws: 4 chains, each with iter = 4000; warmup = 2000; thin = 1;
## total post-warmup draws = 8000
##
## Multilevel Hyperparameters:
## ~Camera.Type (Number of levels: 4)
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS
## sd(muForaging_Intercept) 0.64 0.46 0.04 1.81 1.00 2560
## sd(muTransit_Intercept) 0.55 0.36 0.12 1.47 1.00 3260
## Tail_ESS
## sd(muForaging_Intercept) 2890
## sd(muTransit_Intercept) 3823
##
## ~Month (Number of levels: 9)
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS
## sd(muForaging_Intercept) 0.43 0.20 0.12 0.90 1.00 2716
## sd(muTransit_Intercept) 0.24 0.16 0.01 0.62 1.00 2188
## Tail_ESS
## sd(muForaging_Intercept) 2802
## sd(muTransit_Intercept) 3113
##
## ~Site (Number of levels: 5)
## Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS
## sd(muForaging_Intercept) 0.70 0.41 0.14 1.70 1.00 3091
## sd(muTransit_Intercept) 0.60 0.32 0.21 1.41 1.00 4222
## Tail_ESS
## sd(muForaging_Intercept) 2635
## sd(muTransit_Intercept) 5184
##
## Regression Coefficients:
## Estimate Est.Error l-95% CI
## muForaging_Intercept -0.02 0.71 -1.39
## muTransit_Intercept 0.93 0.61 -0.29
## muForaging_BehLocPatch -1.30 0.62 -2.54
## muForaging_NameDasypus_novemcinctus 1.60 0.54 0.53
## muForaging_NameDidelphis_virginiana 0.34 0.76 -1.17
## muForaging_NameLynx_rufus -0.60 0.87 -2.33
## muForaging_NameMeleagris_gallopavo 0.13 0.85 -1.56
## muForaging_NameOdocoileus_virginianus 0.28 0.45 -0.59
## muForaging_NameProcyon_lotor -1.22 0.57 -2.38
## muForaging_NameSciurus_carolinensis -0.15 0.66 -1.45
## muForaging_NameSylvilagus_floridanus 1.06 0.67 -0.23
## muForaging_BehLocPatch:NameDasypus_novemcinctus -0.33 0.82 -1.96
## muForaging_BehLocPatch:NameDidelphis_virginiana -0.16 0.95 -2.01
## muForaging_BehLocPatch:NameLynx_rufus -0.01 1.00 -1.96
## muForaging_BehLocPatch:NameMeleagris_gallopavo -0.06 1.01 -2.09
## muForaging_BehLocPatch:NameOdocoileus_virginianus -0.27 0.65 -1.53
## muForaging_BehLocPatch:NameProcyon_lotor -0.15 0.95 -2.04
## muForaging_BehLocPatch:NameSciurus_carolinensis -0.04 1.01 -2.03
## muForaging_BehLocPatch:NameSylvilagus_floridanus -0.11 0.97 -2.03
## muTransit_BehLocPatch 1.84 0.51 0.84
## muTransit_NameDasypus_novemcinctus 0.48 0.51 -0.53
## muTransit_NameDidelphis_virginiana 0.15 0.67 -1.14
## muTransit_NameLynx_rufus 1.46 0.74 0.07
## muTransit_NameMeleagris_gallopavo -0.33 0.80 -1.89
## muTransit_NameOdocoileus_virginianus -0.64 0.40 -1.42
## muTransit_NameProcyon_lotor -0.43 0.44 -1.29
## muTransit_NameSciurus_carolinensis -0.80 0.59 -1.97
## muTransit_NameSylvilagus_floridanus -0.14 0.64 -1.38
## muTransit_BehLocPatch:NameDasypus_novemcinctus -0.36 0.73 -1.75
## muTransit_BehLocPatch:NameDidelphis_virginiana 0.52 0.87 -1.13
## muTransit_BehLocPatch:NameLynx_rufus 0.05 0.98 -1.85
## muTransit_BehLocPatch:NameMeleagris_gallopavo 0.20 0.96 -1.66
## muTransit_BehLocPatch:NameOdocoileus_virginianus 0.08 0.52 -0.94
## muTransit_BehLocPatch:NameProcyon_lotor 0.41 0.75 -1.04
## muTransit_BehLocPatch:NameSciurus_carolinensis 0.13 0.98 -1.81
## muTransit_BehLocPatch:NameSylvilagus_floridanus 0.25 0.93 -1.57
## u-95% CI Rhat Bulk_ESS
## muForaging_Intercept 1.42 1.00 4135
## muTransit_Intercept 2.09 1.00 3508
## muForaging_BehLocPatch -0.10 1.00 6202
## muForaging_NameDasypus_novemcinctus 2.67 1.00 5944
## muForaging_NameDidelphis_virginiana 1.81 1.00 10072
## muForaging_NameLynx_rufus 1.10 1.00 11512
## muForaging_NameMeleagris_gallopavo 1.77 1.00 11002
## muForaging_NameOdocoileus_virginianus 1.15 1.00 5686
## muForaging_NameProcyon_lotor -0.11 1.00 6919
## muForaging_NameSciurus_carolinensis 1.12 1.00 8209
## muForaging_NameSylvilagus_floridanus 2.40 1.00 7977
## muForaging_BehLocPatch:NameDasypus_novemcinctus 1.29 1.00 8822
## muForaging_BehLocPatch:NameDidelphis_virginiana 1.67 1.00 12247
## muForaging_BehLocPatch:NameLynx_rufus 1.93 1.00 12029
## muForaging_BehLocPatch:NameMeleagris_gallopavo 1.93 1.00 11936
## muForaging_BehLocPatch:NameOdocoileus_virginianus 1.01 1.00 6331
## muForaging_BehLocPatch:NameProcyon_lotor 1.69 1.00 11733
## muForaging_BehLocPatch:NameSciurus_carolinensis 1.92 1.00 11422
## muForaging_BehLocPatch:NameSylvilagus_floridanus 1.76 1.00 12961
## muTransit_BehLocPatch 2.85 1.00 5040
## muTransit_NameDasypus_novemcinctus 1.48 1.00 5514
## muTransit_NameDidelphis_virginiana 1.51 1.00 8903
## muTransit_NameLynx_rufus 2.97 1.00 9054
## muTransit_NameMeleagris_gallopavo 1.25 1.00 10498
## muTransit_NameOdocoileus_virginianus 0.14 1.00 4546
## muTransit_NameProcyon_lotor 0.43 1.00 5135
## muTransit_NameSciurus_carolinensis 0.35 1.00 7840
## muTransit_NameSylvilagus_floridanus 1.12 1.00 8015
## muTransit_BehLocPatch:NameDasypus_novemcinctus 1.11 1.00 8504
## muTransit_BehLocPatch:NameDidelphis_virginiana 2.25 1.00 10838
## muTransit_BehLocPatch:NameLynx_rufus 1.99 1.00 11696
## muTransit_BehLocPatch:NameMeleagris_gallopavo 2.09 1.00 12654
## muTransit_BehLocPatch:NameOdocoileus_virginianus 1.11 1.00 5208
## muTransit_BehLocPatch:NameProcyon_lotor 1.92 1.00 9527
## muTransit_BehLocPatch:NameSciurus_carolinensis 2.11 1.00 12118
## muTransit_BehLocPatch:NameSylvilagus_floridanus 2.08 1.00 10788
## Tail_ESS
## muForaging_Intercept 4305
## muTransit_Intercept 4100
## muForaging_BehLocPatch 5202
## muForaging_NameDasypus_novemcinctus 6354
## muForaging_NameDidelphis_virginiana 6478
## muForaging_NameLynx_rufus 6142
## muForaging_NameMeleagris_gallopavo 5976
## muForaging_NameOdocoileus_virginianus 6071
## muForaging_NameProcyon_lotor 6760
## muForaging_NameSciurus_carolinensis 6154
## muForaging_NameSylvilagus_floridanus 6360
## muForaging_BehLocPatch:NameDasypus_novemcinctus 6069
## muForaging_BehLocPatch:NameDidelphis_virginiana 5952
## muForaging_BehLocPatch:NameLynx_rufus 5722
## muForaging_BehLocPatch:NameMeleagris_gallopavo 5477
## muForaging_BehLocPatch:NameOdocoileus_virginianus 5894
## muForaging_BehLocPatch:NameProcyon_lotor 5761
## muForaging_BehLocPatch:NameSciurus_carolinensis 5961
## muForaging_BehLocPatch:NameSylvilagus_floridanus 6207
## muTransit_BehLocPatch 4978
## muTransit_NameDasypus_novemcinctus 5973
## muTransit_NameDidelphis_virginiana 5861
## muTransit_NameLynx_rufus 5806
## muTransit_NameMeleagris_gallopavo 6078
## muTransit_NameOdocoileus_virginianus 5641
## muTransit_NameProcyon_lotor 5684
## muTransit_NameSciurus_carolinensis 6238
## muTransit_NameSylvilagus_floridanus 5927
## muTransit_BehLocPatch:NameDasypus_novemcinctus 6247
## muTransit_BehLocPatch:NameDidelphis_virginiana 5893
## muTransit_BehLocPatch:NameLynx_rufus 5981
## muTransit_BehLocPatch:NameMeleagris_gallopavo 6543
## muTransit_BehLocPatch:NameOdocoileus_virginianus 4970
## muTransit_BehLocPatch:NameProcyon_lotor 5746
## muTransit_BehLocPatch:NameSciurus_carolinensis 5153
## muTransit_BehLocPatch:NameSylvilagus_floridanus 5870
##
## Draws were sampled using sampling(NUTS). 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(model_loc)
waic(model_loc)## Warning:
## 6 (0.5%) p_waic estimates greater than 0.4. We recommend trying loo instead.##
## Computed from 8000 by 1300 log-likelihood matrix.
##
## Estimate SE
## elpd_waic -1008.8 24.7
## p_waic 37.1 1.9
## waic 2017.6 49.5
##
## 6 (0.5%) p_waic estimates greater than 0.4. We recommend trying loo instead.loo(model_loc)##
## Computed from 8000 by 1300 log-likelihood matrix.
##
## Estimate SE
## elpd_loo -1008.9 24.7
## p_loo 37.2 2.0
## looic 2017.9 49.5
## ------
## MCSE of elpd_loo is 0.1.
## MCSE and ESS estimates assume MCMC draws (r_eff in [0.6, 1.7]).
##
## All Pareto k estimates are good (k < 0.7).
## See help('pareto-k-diagnostic') for details.# Posterior predictions contrasting Patch vs Outside, marginalizing random effects
# Need new code hereWithin Patch Behavior Plots
# Basic conditional effects for all predictors (must include categorical = TRUE)
conditional_effects(model_loc, categorical = TRUE)## Warning: Interactions cannot be plotted directly if 'categorical' is TRUE.
## Please use argument 'conditions' instead.
# For specific predictors of interest:
# 1) BehLoc effect (inside vs outside patches) - your main question
ce_behloc <- conditional_effects(model_loc, effects = "BehLoc", categorical = TRUE)
plot(ce_behloc)
# Customize a specific plot:
plot(ce_behloc, plot = FALSE)[[1]] +
labs(title = "Behavior by Patch Location (Invaded Sites Only)",
x = "Location",
y = "Predicted Probability") +
theme_minimal()
# Multiple effects at once:
ce_multiple <- conditional_effects(model_loc,
effects = c("BehLoc"),
categorical = TRUE)
plot(ce_multiple)
# Conditional effects showing interaction
#ce_int <- conditional_effects(model_loc,
# effects = "BehLoc:Name",
# categorical = TRUE)
#plot(ce_int)Probability of Direction
pd <- function(x) {
max(mean(x > 0), mean(x < 0))
}
draws_loc <- as_draws_df(model_loc)
draws_status <- as_draws_df(model_status)
beta_loc <- draws_loc[, grep("^b_", colnames(draws_loc))]## Warning: Dropping 'draws_df' class as required metadata was removed.beta_status <- draws_status[, grep("^b_", colnames(draws_status))]## Warning: Dropping 'draws_df' class as required metadata was removed.pd_vals_loc <- apply(beta_loc, 2, pd)
beta_means_loc <- colMeans(beta_loc)
results_loc <- data.frame(
parameter = colnames(beta_loc),
mean = beta_means_loc,
pd = pd_vals_loc,
pd_95 = pd_vals_loc >= 0.95
)
head(results_loc)## parameter
## b_muForaging_Intercept b_muForaging_Intercept
## b_muTransit_Intercept b_muTransit_Intercept
## b_muForaging_BehLocPatch b_muForaging_BehLocPatch
## b_muForaging_NameDasypus_novemcinctus b_muForaging_NameDasypus_novemcinctus
## b_muForaging_NameDidelphis_virginiana b_muForaging_NameDidelphis_virginiana
## b_muForaging_NameLynx_rufus b_muForaging_NameLynx_rufus
## mean pd pd_95
## b_muForaging_Intercept -0.01994912 0.521125 FALSE
## b_muTransit_Intercept 0.93278774 0.940375 FALSE
## b_muForaging_BehLocPatch -1.29515701 0.984000 TRUE
## b_muForaging_NameDasypus_novemcinctus 1.60076398 0.998125 TRUE
## b_muForaging_NameDidelphis_virginiana 0.33821127 0.680750 FALSE
## b_muForaging_NameLynx_rufus -0.59868809 0.751875 FALSEpd_vals_status <- apply(beta_status, 2, pd)
beta_means_status <- colMeans(beta_status)
results_status <- data.frame(
parameter = colnames(beta_status),
mean = beta_means_status,
pd = pd_vals_status,
pd_95 = pd_vals_status >= 0.95
)
head(results_status)## parameter
## b_muForaging_Intercept b_muForaging_Intercept
## b_muTransit_Intercept b_muTransit_Intercept
## b_muForaging_StatusInvaded b_muForaging_StatusInvaded
## b_muForaging_NameDasypus_novemcinctus b_muForaging_NameDasypus_novemcinctus
## b_muForaging_NameDidelphis_virginiana b_muForaging_NameDidelphis_virginiana
## b_muForaging_NameLynx_rufus b_muForaging_NameLynx_rufus
## mean pd pd_95
## b_muForaging_Intercept -0.4971260 0.840125 FALSE
## b_muTransit_Intercept 1.5036443 0.999000 TRUE
## b_muForaging_StatusInvaded -0.2095224 0.681750 FALSE
## b_muForaging_NameDasypus_novemcinctus 1.8323876 0.999750 TRUE
## b_muForaging_NameDidelphis_virginiana 0.8988330 0.887125 FALSE
## b_muForaging_NameLynx_rufus -0.4422522 0.686750 FALSEresults_loc$parameter <- gsub("^b_", "", results_loc$parameter)
results_status$parameter <- gsub("^b_", "", results_status$parameter)
print(results_loc)## parameter
## b_muForaging_Intercept muForaging_Intercept
## b_muTransit_Intercept muTransit_Intercept
## b_muForaging_BehLocPatch muForaging_BehLocPatch
## b_muForaging_NameDasypus_novemcinctus muForaging_NameDasypus_novemcinctus
## b_muForaging_NameDidelphis_virginiana muForaging_NameDidelphis_virginiana
## b_muForaging_NameLynx_rufus muForaging_NameLynx_rufus
## b_muForaging_NameMeleagris_gallopavo muForaging_NameMeleagris_gallopavo
## b_muForaging_NameOdocoileus_virginianus muForaging_NameOdocoileus_virginianus
## b_muForaging_NameProcyon_lotor muForaging_NameProcyon_lotor
## b_muForaging_NameSciurus_carolinensis muForaging_NameSciurus_carolinensis
## b_muForaging_NameSylvilagus_floridanus muForaging_NameSylvilagus_floridanus
## b_muForaging_BehLocPatch:NameDasypus_novemcinctus muForaging_BehLocPatch:NameDasypus_novemcinctus
## b_muForaging_BehLocPatch:NameDidelphis_virginiana muForaging_BehLocPatch:NameDidelphis_virginiana
## b_muForaging_BehLocPatch:NameLynx_rufus muForaging_BehLocPatch:NameLynx_rufus
## b_muForaging_BehLocPatch:NameMeleagris_gallopavo muForaging_BehLocPatch:NameMeleagris_gallopavo
## b_muForaging_BehLocPatch:NameOdocoileus_virginianus muForaging_BehLocPatch:NameOdocoileus_virginianus
## b_muForaging_BehLocPatch:NameProcyon_lotor muForaging_BehLocPatch:NameProcyon_lotor
## b_muForaging_BehLocPatch:NameSciurus_carolinensis muForaging_BehLocPatch:NameSciurus_carolinensis
## b_muForaging_BehLocPatch:NameSylvilagus_floridanus muForaging_BehLocPatch:NameSylvilagus_floridanus
## b_muTransit_BehLocPatch muTransit_BehLocPatch
## b_muTransit_NameDasypus_novemcinctus muTransit_NameDasypus_novemcinctus
## b_muTransit_NameDidelphis_virginiana muTransit_NameDidelphis_virginiana
## b_muTransit_NameLynx_rufus muTransit_NameLynx_rufus
## b_muTransit_NameMeleagris_gallopavo muTransit_NameMeleagris_gallopavo
## b_muTransit_NameOdocoileus_virginianus muTransit_NameOdocoileus_virginianus
## b_muTransit_NameProcyon_lotor muTransit_NameProcyon_lotor
## b_muTransit_NameSciurus_carolinensis muTransit_NameSciurus_carolinensis
## b_muTransit_NameSylvilagus_floridanus muTransit_NameSylvilagus_floridanus
## b_muTransit_BehLocPatch:NameDasypus_novemcinctus muTransit_BehLocPatch:NameDasypus_novemcinctus
## b_muTransit_BehLocPatch:NameDidelphis_virginiana muTransit_BehLocPatch:NameDidelphis_virginiana
## b_muTransit_BehLocPatch:NameLynx_rufus muTransit_BehLocPatch:NameLynx_rufus
## b_muTransit_BehLocPatch:NameMeleagris_gallopavo muTransit_BehLocPatch:NameMeleagris_gallopavo
## b_muTransit_BehLocPatch:NameOdocoileus_virginianus muTransit_BehLocPatch:NameOdocoileus_virginianus
## b_muTransit_BehLocPatch:NameProcyon_lotor muTransit_BehLocPatch:NameProcyon_lotor
## b_muTransit_BehLocPatch:NameSciurus_carolinensis muTransit_BehLocPatch:NameSciurus_carolinensis
## b_muTransit_BehLocPatch:NameSylvilagus_floridanus muTransit_BehLocPatch:NameSylvilagus_floridanus
## mean pd pd_95
## b_muForaging_Intercept -0.01994912 0.521125 FALSE
## b_muTransit_Intercept 0.93278774 0.940375 FALSE
## b_muForaging_BehLocPatch -1.29515701 0.984000 TRUE
## b_muForaging_NameDasypus_novemcinctus 1.60076398 0.998125 TRUE
## b_muForaging_NameDidelphis_virginiana 0.33821127 0.680750 FALSE
## b_muForaging_NameLynx_rufus -0.59868809 0.751875 FALSE
## b_muForaging_NameMeleagris_gallopavo 0.12963447 0.568000 FALSE
## b_muForaging_NameOdocoileus_virginianus 0.27828870 0.730375 FALSE
## b_muForaging_NameProcyon_lotor -1.22489781 0.986125 TRUE
## b_muForaging_NameSciurus_carolinensis -0.15014818 0.585000 FALSE
## b_muForaging_NameSylvilagus_floridanus 1.05591746 0.942750 FALSE
## b_muForaging_BehLocPatch:NameDasypus_novemcinctus -0.33346584 0.661125 FALSE
## b_muForaging_BehLocPatch:NameDidelphis_virginiana -0.15544018 0.560375 FALSE
## b_muForaging_BehLocPatch:NameLynx_rufus -0.01137099 0.503250 FALSE
## b_muForaging_BehLocPatch:NameMeleagris_gallopavo -0.05863503 0.520875 FALSE
## b_muForaging_BehLocPatch:NameOdocoileus_virginianus -0.26723938 0.665375 FALSE
## b_muForaging_BehLocPatch:NameProcyon_lotor -0.14545145 0.557375 FALSE
## b_muForaging_BehLocPatch:NameSciurus_carolinensis -0.04441083 0.515625 FALSE
## b_muForaging_BehLocPatch:NameSylvilagus_floridanus -0.11065258 0.541375 FALSE
## b_muTransit_BehLocPatch 1.84325821 0.999875 TRUE
## b_muTransit_NameDasypus_novemcinctus 0.47511719 0.821625 FALSE
## b_muTransit_NameDidelphis_virginiana 0.15071913 0.581250 FALSE
## b_muTransit_NameLynx_rufus 1.46354482 0.980750 TRUE
## b_muTransit_NameMeleagris_gallopavo -0.33004705 0.668500 FALSE
## b_muTransit_NameOdocoileus_virginianus -0.63991487 0.947125 FALSE
## b_muTransit_NameProcyon_lotor -0.42582094 0.831750 FALSE
## b_muTransit_NameSciurus_carolinensis -0.80401248 0.915375 FALSE
## b_muTransit_NameSylvilagus_floridanus -0.14063111 0.595000 FALSE
## b_muTransit_BehLocPatch:NameDasypus_novemcinctus -0.35798228 0.689000 FALSE
## b_muTransit_BehLocPatch:NameDidelphis_virginiana 0.51558716 0.713375 FALSE
## b_muTransit_BehLocPatch:NameLynx_rufus 0.04900257 0.516375 FALSE
## b_muTransit_BehLocPatch:NameMeleagris_gallopavo 0.19665881 0.579125 FALSE
## b_muTransit_BehLocPatch:NameOdocoileus_virginianus 0.08014374 0.559625 FALSE
## b_muTransit_BehLocPatch:NameProcyon_lotor 0.40615080 0.701625 FALSE
## b_muTransit_BehLocPatch:NameSciurus_carolinensis 0.13287221 0.546250 FALSE
## b_muTransit_BehLocPatch:NameSylvilagus_floridanus 0.24549047 0.601500 FALSEprint(results_status)## parameter
## b_muForaging_Intercept muForaging_Intercept
## b_muTransit_Intercept muTransit_Intercept
## b_muForaging_StatusInvaded muForaging_StatusInvaded
## b_muForaging_NameDasypus_novemcinctus muForaging_NameDasypus_novemcinctus
## b_muForaging_NameDidelphis_virginiana muForaging_NameDidelphis_virginiana
## b_muForaging_NameLynx_rufus muForaging_NameLynx_rufus
## b_muForaging_NameMeleagris_gallopavo muForaging_NameMeleagris_gallopavo
## b_muForaging_NameOdocoileus_virginianus muForaging_NameOdocoileus_virginianus
## b_muForaging_NameProcyon_lotor muForaging_NameProcyon_lotor
## b_muForaging_NameSciurus_carolinensis muForaging_NameSciurus_carolinensis
## b_muForaging_NameSylvilagus_floridanus muForaging_NameSylvilagus_floridanus
## b_muForaging_StatusInvaded:NameDasypus_novemcinctus muForaging_StatusInvaded:NameDasypus_novemcinctus
## b_muForaging_StatusInvaded:NameDidelphis_virginiana muForaging_StatusInvaded:NameDidelphis_virginiana
## b_muForaging_StatusInvaded:NameLynx_rufus muForaging_StatusInvaded:NameLynx_rufus
## b_muForaging_StatusInvaded:NameMeleagris_gallopavo muForaging_StatusInvaded:NameMeleagris_gallopavo
## b_muForaging_StatusInvaded:NameOdocoileus_virginianus muForaging_StatusInvaded:NameOdocoileus_virginianus
## b_muForaging_StatusInvaded:NameProcyon_lotor muForaging_StatusInvaded:NameProcyon_lotor
## b_muForaging_StatusInvaded:NameSciurus_carolinensis muForaging_StatusInvaded:NameSciurus_carolinensis
## b_muForaging_StatusInvaded:NameSylvilagus_floridanus muForaging_StatusInvaded:NameSylvilagus_floridanus
## b_muTransit_StatusInvaded muTransit_StatusInvaded
## b_muTransit_NameDasypus_novemcinctus muTransit_NameDasypus_novemcinctus
## b_muTransit_NameDidelphis_virginiana muTransit_NameDidelphis_virginiana
## b_muTransit_NameLynx_rufus muTransit_NameLynx_rufus
## b_muTransit_NameMeleagris_gallopavo muTransit_NameMeleagris_gallopavo
## b_muTransit_NameOdocoileus_virginianus muTransit_NameOdocoileus_virginianus
## b_muTransit_NameProcyon_lotor muTransit_NameProcyon_lotor
## b_muTransit_NameSciurus_carolinensis muTransit_NameSciurus_carolinensis
## b_muTransit_NameSylvilagus_floridanus muTransit_NameSylvilagus_floridanus
## b_muTransit_StatusInvaded:NameDasypus_novemcinctus muTransit_StatusInvaded:NameDasypus_novemcinctus
## b_muTransit_StatusInvaded:NameDidelphis_virginiana muTransit_StatusInvaded:NameDidelphis_virginiana
## b_muTransit_StatusInvaded:NameLynx_rufus muTransit_StatusInvaded:NameLynx_rufus
## b_muTransit_StatusInvaded:NameMeleagris_gallopavo muTransit_StatusInvaded:NameMeleagris_gallopavo
## b_muTransit_StatusInvaded:NameOdocoileus_virginianus muTransit_StatusInvaded:NameOdocoileus_virginianus
## b_muTransit_StatusInvaded:NameProcyon_lotor muTransit_StatusInvaded:NameProcyon_lotor
## b_muTransit_StatusInvaded:NameSciurus_carolinensis muTransit_StatusInvaded:NameSciurus_carolinensis
## b_muTransit_StatusInvaded:NameSylvilagus_floridanus muTransit_StatusInvaded:NameSylvilagus_floridanus
## mean pd
## b_muForaging_Intercept -0.49712599 0.840125
## b_muTransit_Intercept 1.50364431 0.999000
## b_muForaging_StatusInvaded -0.20952242 0.681750
## b_muForaging_NameDasypus_novemcinctus 1.83238759 0.999750
## b_muForaging_NameDidelphis_virginiana 0.89883297 0.887125
## b_muForaging_NameLynx_rufus -0.44225224 0.686750
## b_muForaging_NameMeleagris_gallopavo 0.23322170 0.642250
## b_muForaging_NameOdocoileus_virginianus 1.11242546 0.999000
## b_muForaging_NameProcyon_lotor -0.72233174 0.907625
## b_muForaging_NameSciurus_carolinensis 0.07222432 0.551000
## b_muForaging_NameSylvilagus_floridanus 1.51951169 0.995500
## b_muForaging_StatusInvaded:NameDasypus_novemcinctus 0.53264464 0.803500
## b_muForaging_StatusInvaded:NameDidelphis_virginiana 0.07842135 0.539125
## b_muForaging_StatusInvaded:NameLynx_rufus -0.19081640 0.576500
## b_muForaging_StatusInvaded:NameMeleagris_gallopavo 0.12161121 0.557750
## b_muForaging_StatusInvaded:NameOdocoileus_virginianus -0.14050143 0.625750
## b_muForaging_StatusInvaded:NameProcyon_lotor -0.17044863 0.601500
## b_muForaging_StatusInvaded:NameSciurus_carolinensis 0.15749907 0.585750
## b_muForaging_StatusInvaded:NameSylvilagus_floridanus 0.44065558 0.720125
## b_muTransit_StatusInvaded 0.19640609 0.691250
## b_muTransit_NameDasypus_novemcinctus 0.69830625 0.927125
## b_muTransit_NameDidelphis_virginiana 0.21947944 0.626500
## b_muTransit_NameLynx_rufus 1.47100870 0.980250
## b_muTransit_NameMeleagris_gallopavo 0.05649503 0.538500
## b_muTransit_NameOdocoileus_virginianus -0.16579903 0.707000
## b_muTransit_NameProcyon_lotor -0.49305721 0.888500
## b_muTransit_NameSciurus_carolinensis -0.86328956 0.923375
## b_muTransit_NameSylvilagus_floridanus -0.11242798 0.584875
## b_muTransit_StatusInvaded:NameDasypus_novemcinctus 0.02290060 0.516500
## b_muTransit_StatusInvaded:NameDidelphis_virginiana 0.35300582 0.684375
## b_muTransit_StatusInvaded:NameLynx_rufus 0.62241854 0.762625
## b_muTransit_StatusInvaded:NameMeleagris_gallopavo -0.23957123 0.626000
## b_muTransit_StatusInvaded:NameOdocoileus_virginianus -0.25708234 0.742000
## b_muTransit_StatusInvaded:NameProcyon_lotor -0.07137579 0.556375
## b_muTransit_StatusInvaded:NameSciurus_carolinensis -0.48613475 0.763125
## b_muTransit_StatusInvaded:NameSylvilagus_floridanus 0.13595533 0.574000
## pd_95
## b_muForaging_Intercept FALSE
## b_muTransit_Intercept TRUE
## b_muForaging_StatusInvaded FALSE
## b_muForaging_NameDasypus_novemcinctus TRUE
## b_muForaging_NameDidelphis_virginiana FALSE
## b_muForaging_NameLynx_rufus FALSE
## b_muForaging_NameMeleagris_gallopavo FALSE
## b_muForaging_NameOdocoileus_virginianus TRUE
## b_muForaging_NameProcyon_lotor FALSE
## b_muForaging_NameSciurus_carolinensis FALSE
## b_muForaging_NameSylvilagus_floridanus TRUE
## b_muForaging_StatusInvaded:NameDasypus_novemcinctus FALSE
## b_muForaging_StatusInvaded:NameDidelphis_virginiana FALSE
## b_muForaging_StatusInvaded:NameLynx_rufus FALSE
## b_muForaging_StatusInvaded:NameMeleagris_gallopavo FALSE
## b_muForaging_StatusInvaded:NameOdocoileus_virginianus FALSE
## b_muForaging_StatusInvaded:NameProcyon_lotor FALSE
## b_muForaging_StatusInvaded:NameSciurus_carolinensis FALSE
## b_muForaging_StatusInvaded:NameSylvilagus_floridanus FALSE
## b_muTransit_StatusInvaded FALSE
## b_muTransit_NameDasypus_novemcinctus FALSE
## b_muTransit_NameDidelphis_virginiana FALSE
## b_muTransit_NameLynx_rufus TRUE
## b_muTransit_NameMeleagris_gallopavo FALSE
## b_muTransit_NameOdocoileus_virginianus FALSE
## b_muTransit_NameProcyon_lotor FALSE
## b_muTransit_NameSciurus_carolinensis FALSE
## b_muTransit_NameSylvilagus_floridanus FALSE
## b_muTransit_StatusInvaded:NameDasypus_novemcinctus FALSE
## b_muTransit_StatusInvaded:NameDidelphis_virginiana FALSE
## b_muTransit_StatusInvaded:NameLynx_rufus FALSE
## b_muTransit_StatusInvaded:NameMeleagris_gallopavo FALSE
## b_muTransit_StatusInvaded:NameOdocoileus_virginianus FALSE
## b_muTransit_StatusInvaded:NameProcyon_lotor FALSE
## b_muTransit_StatusInvaded:NameSciurus_carolinensis FALSE
## b_muTransit_StatusInvaded:NameSylvilagus_floridanus FALSE