updated_names_analysis
Sarah E Taylor
2024-02-29
Last updated: 2024-02-29
Checks: 7 0
Knit directory: LocksofLineage/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 5c2d3c1 | Sarah E Taylor | 2024-02-29 | added upset plot |
| html | 4e1c9c0 | Sarah E Taylor | 2024-02-29 | Build site. |
| Rmd | b54f044 | Sarah E Taylor | 2024-02-29 | Recoded the traits and re-did the logistic regressions and odds ratio matrices |
Recoding the data
data <- read_csv("data/Raw_Data/data_to_use.csv")Rows: 238 Columns: 17
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (16): family, Genus, species, subspecies, Sexual_dimorphism, Sexual_Dimo...
dbl (1): Size_Dimorphism
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.# 5 species were recorded as maybe having a natal coat because the sources were conflicting, for now they will be counted as not having a natal coat
# Cheirogaleus major, Macaca sylvanus, Procolobus pennantii, Presbytis femoralis, Pongo pygmaeusdata <- data %>%
mutate(across(c(Sexual_dimorphism, Natal_coat, Sexual_dichromatism), ~if_else(. == "Yes", 1, 0)))# Reclassifying how we distinguish natal coat types
data <- data %>%
mutate(Simple_Natal_Coat_Type = case_when(
Natal_Coat_Type %in% c("Con to dad", "con to both", "con to mom") ~ "conspicuous",
Natal_Coat_Type == "incon" ~ "inconspicuous",
TRUE ~ "none" # This will catch all other cases not specified above
))
# Add a column with all conspicuous natal coats as 1 and inconspicuous as 0
data <- data %>%
mutate(
Natal_Coat_Conspicuous = ifelse(Simple_Natal_Coat_Type == "conspicuous", 1, 0),
Natal_Coat_Inconspicuous = ifelse(Simple_Natal_Coat_Type == "inconspicuous", 1, 0),
Natal_Coat_Present = ifelse(Simple_Natal_Coat_Type %in% c("conspicuous", "inconspicuous"), 1, 0)
)
#Natal coats can be inconspicuous (close in color to parents) or conspicuous (obviously a different color). #When they are conspicuous they can be contrasting to either the mothers coats or the fathers or both. # This is recoding the different types of conspicuous natal coats and sexual dichromatism from separate traits into a continuous change ie infant -> adult female (change/no change), infant -> adult male (change/no change), if both change is another category. If a natal coat is conspicuous to dad it is similar or inconspicuous to mom so the males change when they mature.
data <- data %>%
mutate(Maturation_Color_Change = case_when(
Natal_Coat_Type == "Con to dad" ~ "Males only",
Natal_Coat_Type == "con to both" ~ "Both",
Natal_Coat_Type == "con to mom" ~ "Females only",
TRUE ~ "None"))
# Add binary columns for the different maturation changes
data <- data %>%
mutate(Maturation_Males_Only = ifelse(Maturation_Color_Change == "Males only", 1, 0),
Maturation_Females_Only = ifelse(Maturation_Color_Change == "Females only", 1, 0),
Maturation_Both = ifelse(Maturation_Color_Change == "Both", 1, 0),
Maturation_None = ifelse(Maturation_Color_Change == "None", 1, 0))data <- data %>%
mutate(Sexual_Dichromatism_Complete = ifelse(Sexual_dichromatism_type == "Complete", 1, 0),
Sexual_Dichromatism_Partial = ifelse(Sexual_dichromatism_type == "Partial", 1, 0),
Sexual_Dichromatism_Present = ifelse(Sexual_dichromatism_type %in% c("Complete", "Partial"), 1, 0))write_csv(data, "data/recoded_data.csv")Format data for phylolm
Phylogenetic tree: mammaltree
Number of tips: 5987
Number of nodes: 5986
Branch lengths:
mean: 2.680715
variance: 24.17565
distribution summary:
Min. 1st Qu. Median 3rd Qu. Max.
0.0000000 0.5284341 1.3073255 2.9454665 106.6007500
No root edge.
First ten tip labels: X_Shuotherium
X_Pseudotribos
X_Asfaltomylos
X_Obdurodon
Zaglossus_bartoni
Zaglossus_bruijnii
Zaglossus_attenboroughi
Tachyglossus_aculeatus
Ornithorhynchus_anatinus
X_Teinolophos
No node labels.Rows: 238 Columns: 29
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (15): family, Genus, species, subspecies, Sexual_Dimorph_type, Location,...
dbl (14): Sexual_dimorphism, Natal_coat, Sexual_dichromatism, Size_Dimorphis...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.# A tibble: 6 × 29
family Genus species subsp…¹ Sexua…² Sexua…³ Locat…⁴ Direc…⁵ Natal…⁶ Natal…⁷
<chr> <chr> <chr> <chr> <dbl> <chr> <chr> <chr> <dbl> <chr>
1 cercopi… alle… nigrov… <NA> 0 <NA> <NA> <NA> 1 incon
2 cheirog… allo… tricho… <NA> 0 <NA> <NA> <NA> 0 <NA>
3 cebidae alou… belzeb… <NA> 0 <NA> <NA> <NA> 0 <NA>
4 cebidae alou… caraya <NA> 1 males … Head M 1 Con to…
5 cebidae alou… guariba <NA> 1 male s… Head M 1 incon
6 cebidae alou… pallia… pallia… 1 F: les… Head, … F 1 incon
# … with 19 more variables: NC_description <chr>, Sexual_dichromatism <dbl>,
# Sexual_dichromatism_type <chr>, Where <chr>, Darker <chr>,
# SDC_description <chr>, Size_Dimorphism <dbl>, Simple_Natal_Coat_Type <chr>,
# Natal_Coat_Conspicuous <dbl>, Natal_Coat_Inconspicuous <dbl>,
# Natal_Coat_Present <dbl>, Maturation_Color_Change <chr>,
# Maturation_Males_Only <dbl>, Maturation_Females_Only <dbl>,
# Maturation_Both <dbl>, Maturation_None <dbl>, …#combine genus and species names and capitalize first letter
Binary_traits_combined = Binary_traits %>% unite("species",`Genus`, `species`) %>% mutate(species = str_to_title(species))
head(Binary_traits_combined)# A tibble: 6 × 28
family species subsp…¹ Sexua…² Sexua…³ Locat…⁴ Direc…⁵ Natal…⁶ Natal…⁷ NC_de…⁸
<chr> <chr> <chr> <dbl> <chr> <chr> <chr> <dbl> <chr> <chr>
1 cerco… Alleno… <NA> 0 <NA> <NA> <NA> 1 incon no tre…
2 cheir… Alloce… <NA> 0 <NA> <NA> <NA> 0 <NA> <NA>
3 cebid… Alouat… <NA> 0 <NA> <NA> <NA> 0 <NA> <NA>
4 cebid… Alouat… <NA> 1 males … Head M 1 Con to… infant…
5 cebid… Alouat… <NA> 1 male s… Head M 1 incon possib…
6 cebid… Alouat… pallia… 1 F: les… Head, … F 1 incon incons…
# … with 18 more variables: Sexual_dichromatism <dbl>,
# Sexual_dichromatism_type <chr>, Where <chr>, Darker <chr>,
# SDC_description <chr>, Size_Dimorphism <dbl>, Simple_Natal_Coat_Type <chr>,
# Natal_Coat_Conspicuous <dbl>, Natal_Coat_Inconspicuous <dbl>,
# Natal_Coat_Present <dbl>, Maturation_Color_Change <chr>,
# Maturation_Males_Only <dbl>, Maturation_Females_Only <dbl>,
# Maturation_Both <dbl>, Maturation_None <dbl>, …# prune tree for species in data
species_not_in_tree=setdiff(mammaltree$tip.label, Binary_traits_combined$species)
pruned.tree<-drop.tip(mammaltree,species_not_in_tree)
summary(pruned.tree)
Phylogenetic tree: pruned.tree
Number of tips: 235
Number of nodes: 234
Branch lengths:
mean: 2.864158
variance: 17.90887
distribution summary:
Min. 1st Qu. Median 3rd Qu. Max.
0.04705822 0.88148065 1.69536613 3.05008500 49.61463191
No root edge.
First ten tip labels: Nycticebus_pygmaeus
Nycticebus_coucang
Loris_tardigradus
Galagoides_thomasi
Galago_matschiei
Galago_moholi
Galago_senegalensis
Galago_gallarum
Otolemur_garnettii
Otolemur_crassicaudatus
No node labels.#prune data for species in tree
data_pruned <- Binary_traits_combined %>% filter(species %in% pruned.tree$tip.label)
head(data_pruned)# A tibble: 6 × 28
family species subsp…¹ Sexua…² Sexua…³ Locat…⁴ Direc…⁵ Natal…⁶ Natal…⁷ NC_de…⁸
<chr> <chr> <chr> <dbl> <chr> <chr> <chr> <dbl> <chr> <chr>
1 cerco… Alleno… <NA> 0 <NA> <NA> <NA> 1 incon no tre…
2 cheir… Alloce… <NA> 0 <NA> <NA> <NA> 0 <NA> <NA>
3 cebid… Alouat… <NA> 0 <NA> <NA> <NA> 0 <NA> <NA>
4 cebid… Alouat… <NA> 1 males … Head M 1 Con to… infant…
5 cebid… Alouat… <NA> 1 male s… Head M 1 incon possib…
6 cebid… Alouat… pallia… 1 F: les… Head, … F 1 incon incons…
# … with 18 more variables: Sexual_dichromatism <dbl>,
# Sexual_dichromatism_type <chr>, Where <chr>, Darker <chr>,
# SDC_description <chr>, Size_Dimorphism <dbl>, Simple_Natal_Coat_Type <chr>,
# Natal_Coat_Conspicuous <dbl>, Natal_Coat_Inconspicuous <dbl>,
# Natal_Coat_Present <dbl>, Maturation_Color_Change <chr>,
# Maturation_Males_Only <dbl>, Maturation_Females_Only <dbl>,
# Maturation_Both <dbl>, Maturation_None <dbl>, …# get the order of the tip labels
tip_order <- pruned.tree$tip.label
# Match the order of species in the dataframe to the order of tip labels in the tree
ordered_indices <- match(tip_order, data_pruned$species)
# Reorder the dataframe based on the indices obtained
data_pruned_ordered <- Binary_traits_combined[ordered_indices, ]#put data into useful form for phylolm
colnames(data_pruned_ordered) = gsub(" ", "_", colnames(data_pruned))
data_pruned_rownames = column_to_rownames(data_pruned_ordered, var = "species")
head(data_pruned_rownames) family subspecies Sexual_dimorphism
Simias_concolor cercopithecidae <NA> 0
Miopithecus_talapoin cercopithecidae <NA> 0
Lophocebus_albigena cercopithecidae <NA> 0
Galago_senegalensis galagonidae <NA> 0
Galago_gallarum galagonidae <NA> 0
Galago_matschiei galagonidae <NA> 0
Sexual_Dimorph_type Location Direction Natal_coat
Simias_concolor <NA> <NA> <NA> 1
Miopithecus_talapoin <NA> <NA> <NA> 1
Lophocebus_albigena <NA> <NA> <NA> 1
Galago_senegalensis <NA> <NA> <NA> 0
Galago_gallarum <NA> <NA> <NA> 0
Galago_matschiei <NA> <NA> <NA> 0
Natal_Coat_Type
Simias_concolor incon
Miopithecus_talapoin incon
Lophocebus_albigena incon
Galago_senegalensis <NA>
Galago_gallarum <NA>
Galago_matschiei <NA>
NC_description
Simias_concolor lighter face in infants
Miopithecus_talapoin no treves 31,33,39, juveniles lack the black maxillary patches and have less yellow in the pelage hill
Lophocebus_albigena l.a.johnstoni no treves 28,33,43, in hill this subspecies was uniformly black and got more brown as it aged, infant is darker in zenkeri subspecies, overall the infants are darker with less color variation
Galago_senegalensis no treves 67
Galago_gallarum <NA>
Galago_matschiei <NA>
Sexual_dichromatism Sexual_dichromatism_type Where
Simias_concolor 0 <NA> <NA>
Miopithecus_talapoin 1 Partial Body
Lophocebus_albigena 1 Partial Multiple
Galago_senegalensis 0 <NA> <NA>
Galago_gallarum 0 <NA> <NA>
Galago_matschiei 0 <NA> <NA>
Darker
Simias_concolor <NA>
Miopithecus_talapoin M
Lophocebus_albigena M
Galago_senegalensis <NA>
Galago_gallarum <NA>
Galago_matschiei <NA>
SDC_description
Simias_concolor maybe? rowe 838, 80
Miopithecus_talapoin females are less richly colored hill
Lophocebus_albigena F: paler around ears, hind-neck, and mantle, fewer white rings on mantle hairs, underparts reddish black hill
Galago_senegalensis <NA>
Galago_gallarum <NA>
Galago_matschiei <NA>
Size_Dimorphism Simple_Natal_Coat_Type
Simias_concolor 1 inconspicuous
Miopithecus_talapoin 1 inconspicuous
Lophocebus_albigena 1 inconspicuous
Galago_senegalensis 1 none
Galago_gallarum 0 none
Galago_matschiei 0 none
Natal_Coat_Conspicuous Natal_Coat_Inconspicuous
Simias_concolor 0 1
Miopithecus_talapoin 0 1
Lophocebus_albigena 0 1
Galago_senegalensis 0 0
Galago_gallarum 0 0
Galago_matschiei 0 0
Natal_Coat_Present Maturation_Color_Change
Simias_concolor 1 None
Miopithecus_talapoin 1 None
Lophocebus_albigena 1 None
Galago_senegalensis 0 None
Galago_gallarum 0 None
Galago_matschiei 0 None
Maturation_Males_Only Maturation_Females_Only
Simias_concolor 0 0
Miopithecus_talapoin 0 0
Lophocebus_albigena 0 0
Galago_senegalensis 0 0
Galago_gallarum 0 0
Galago_matschiei 0 0
Maturation_Both Maturation_None
Simias_concolor 0 1
Miopithecus_talapoin 0 1
Lophocebus_albigena 0 1
Galago_senegalensis 0 1
Galago_gallarum 0 1
Galago_matschiei 0 1
Sexual_Dichromatism_Complete Sexual_Dichromatism_Partial
Simias_concolor NA NA
Miopithecus_talapoin 0 1
Lophocebus_albigena 0 1
Galago_senegalensis NA NA
Galago_gallarum NA NA
Galago_matschiei NA NA
Sexual_Dichromatism_Present
Simias_concolor 0
Miopithecus_talapoin 1
Lophocebus_albigena 1
Galago_senegalensis 0
Galago_gallarum 0
Galago_matschiei 0write_csv(data_pruned_rownames, "data/data_formatted_phylolm.csv")Run the Logistic Regressions
# Create the phylolm function
run_phylolm_analyses <- function(data, phylo_tree, independent_vars, dependent_vars){
results <- list()
for (ind_var in independent_vars){
for (dep_var in dependent_vars){
formula <- as.formula(paste(dep_var, "~", ind_var))
model <- phyloglm(formula, data=data, phy=phylo_tree, method = "logistic_MPLE")
results[[paste(ind_var, dep_var, sep = "_vs_")]] <- summary(model)
}
}
return(results)
}
#Function to extract model stats, odds ratio, p-value
extract_model_stats <- function(results_list, independent_vars, dependent_vars) {
# Initialize a matrix to store the odds ratios
odds_ratios <- matrix(NA,
nrow = length(dependent_vars),
ncol = length(independent_vars),
dimnames = list(dependent_vars, independent_vars))
p_values <- matrix(NA,
nrow = length(dependent_vars),
ncol = length(independent_vars),
dimnames = list(dependent_vars, independent_vars))
# Iterate through the results to extract coefficients
for (dep_var in dependent_vars) {
for (ind_var in independent_vars) {
# Construct the result name used as the key in the results list
result_key <- paste(ind_var, dep_var, sep = "_vs_")
# Check if the result exists and extract the coefficients
if (result_key %in% names(results_list)) {
# Extract the model summary
model_summary <- results_list[[result_key]]
# Check if the model summary is indeed a list with a coefficients data frame
if (is.list(model_summary) && "coefficients" %in% names(model_summary)) {
# Extract the estimate for the independent variable
if (ind_var %in% rownames(model_summary$coefficients)) {
estimate <- model_summary$coefficients[ind_var, "Estimate"]
p_value <- model_summary$coefficients[ind_var, "p.value"]
odds_ratios[dep_var, ind_var] <- exp(estimate)
p_values[dep_var, ind_var] <- p_value
}
}
}
}
}
return(list(odds_ratios = odds_ratios, p_values = p_values))
}data <- data_pruned_rownames
phylo_tree <- pruned.tree
independent_vars <- c("Natal_Coat_Conspicuous", "Natal_Coat_Inconspicuous", "Natal_Coat_Present")
dependent_vars <- c("Sexual_Dichromatism_Complete", "Sexual_Dichromatism_Partial", "Sexual_Dichromatism_Present", "Maturation_Males_Only", "Maturation_Females_Only", "Maturation_Both")
Natal_on_Dichromatism_results <- run_phylolm_analyses(data,phylo_tree, independent_vars, dependent_vars)
Natal_on_Dichromatism_model_stats <- extract_model_stats(Natal_on_Dichromatism_results, independent_vars, dependent_vars)
Natal_on_Dichromatism_odds_ratio_matrix <- Natal_on_Dichromatism_model_stats$odds_ratios
Natal_on_Dichromatism_p_value_matrix <- Natal_on_Dichromatism_model_stats$p_valuesdata <- data_pruned_rownames
phylo_tree <- pruned.tree
independent_vars <- c("Sexual_Dichromatism_Complete", "Sexual_Dichromatism_Partial", "Sexual_Dichromatism_Present", "Maturation_Males_Only", "Maturation_Females_Only", "Maturation_Both")
dependent_vars <- c("Natal_Coat_Conspicuous", "Natal_Coat_Inconspicuous", "Natal_Coat_Present")
Dichromatism_on_Natal_results <- run_phylolm_analyses(data,phylo_tree, independent_vars, dependent_vars)
Dichromatism_on_Natal_model_stats <- extract_model_stats(Dichromatism_on_Natal_results, independent_vars, dependent_vars)
Dichromatism_on_Natal_odds_ratio_matrix <- Dichromatism_on_Natal_model_stats$odds_ratios
Dichromatism_on_Natal_p_value_matrix <- Dichromatism_on_Natal_model_stats$p_valuesdata <- data_pruned_rownames
phylo_tree <- pruned.tree
independent_vars <- c("Sexual_dimorphism", "Size_Dimorphism")
dependent_vars <- c("Sexual_Dichromatism_Complete", "Sexual_Dichromatism_Partial", "Sexual_Dichromatism_Present", "Maturation_Males_Only", "Maturation_Females_Only", "Maturation_Both","Natal_Coat_Conspicuous", "Natal_Coat_Inconspicuous", "Natal_Coat_Present")
Dimorphism_on_Natal_and_Dichrom_results <- run_phylolm_analyses(data,phylo_tree, independent_vars, dependent_vars)
Dimorphism_on_Natal_and_Dichrom_model_stats <- extract_model_stats(Dimorphism_on_Natal_and_Dichrom_results, independent_vars, dependent_vars)
Dimorphism_on_Natal_and_Dichrom_odds_ratio_matrix <- Dimorphism_on_Natal_and_Dichrom_model_stats$odds_ratios
Dimorphism_on_Natal_and_Dichrom_p_value_matrix <- Dimorphism_on_Natal_and_Dichrom_model_stats$p_valuesVisualizations
# Function to determine significance symbols based on p-values
get_significance_symbol <- function(p_value) {
ifelse(p_value < 0.001, '***',
ifelse(p_value < 0.01, '**',
ifelse(p_value < 0.05, '*', '')))
}
# Function to create a heatmap with significance symbols
create_heatmap <- function(odds_ratio_matrix, p_value_matrix, title_prefix) {
# Melt the odds ratio matrix and p-value matrix into data frames
df_odds <- melt(odds_ratio_matrix)
df_pvals <- melt(p_value_matrix)
# Add column names for merging
colnames(df_odds) <- c("RowTraits", "ColTraits", "value")
colnames(df_pvals) <- c("RowTraits", "ColTraits", "p_value")
# Merge the data frames
df_merged <- merge(df_odds, df_pvals, by = c("RowTraits", "ColTraits"))
# Apply logarithmic transformation to the odds ratio values
df_merged$value_log <- log(df_merged$value + 1)
# Calculate significance symbols
df_merged$significance <- get_significance_symbol(df_merged$p_value)
# Create the heatmap
heatmap <- ggplot(df_merged, aes(RowTraits, ColTraits, fill = value_log)) +
geom_tile() +
scale_fill_gradient2(low = "white", high = "red", mid = "blue", midpoint = log(1 + 1), space = "Lab", name="Log Odds Ratio") +
geom_text(aes(label = sprintf("%.2f", value)), size = 3, vjust = -1) +
geom_text(aes(label = significance), size = 3, vjust = 1) +
theme_minimal() +
labs(title = paste(title_prefix, "Log Scale"), x = "Column Traits", y = "Row Traits") +
theme(axis.text.x = element_text(angle = 45, hjust = 1), axis.text.y = element_text(angle = 45, vjust = 1))
return(heatmap)
}
# usage:
heatmap1 <- create_heatmap(Natal_on_Dichromatism_odds_ratio_matrix, Natal_on_Dichromatism_p_value_matrix, "Effect of Natal Coat on Sexual Dichromatism")
heatmap2 <- create_heatmap(Dichromatism_on_Natal_odds_ratio_matrix, Dichromatism_on_Natal_p_value_matrix, "Effect of Sexual Dichromatism on Natal Coat")
heatmap3 <- create_heatmap( Dimorphism_on_Natal_and_Dichrom_odds_ratio_matrix, Dimorphism_on_Natal_and_Dichrom_p_value_matrix, "Sexual Dimorphism Impacting other Characteristics")
# Print heatmaps side by side
grid.arrange(heatmap1, heatmap2, heatmap3, ncol = 3)
# Define the traits
set_attributes <- c(
'Natal_Coat_Conspicuous',
'Natal_Coat_Inconspicuous',
'Natal_Coat_Present',
'Sexual_Dichromatism_Complete',
'Sexual_Dichromatism_Partial',
'Sexual_Dichromatism_Present',
'Maturation_Males_Only',
'Maturation_Females_Only',
'Maturation_Both',
'Sexual_dimorphism')
# Create the plot
upset(
data_pruned_rownames,
set_attributes,
base_annotations=list(
'Intersection size'=intersection_size(
counts=TRUE,
mapping=aes(fill=family)
)
),
width_ratio=0.1
)Warning in upset_data(data, intersect, mode = mode, encode_sets = encode_sets,
: Converting non-logical columns to binary: Natal_Coat_Conspicuous,
Natal_Coat_Inconspicuous, Natal_Coat_Present, Sexual_Dichromatism_Complete,
Sexual_Dichromatism_Partial, Sexual_Dichromatism_Present,
Maturation_Males_Only, Maturation_Females_Only, Maturation_Both,
Sexual_dimorphismWarning in upset_data(data, intersect, mode = mode, encode_sets = encode_sets,
: Detected missing values in the columns indicating sets, coercing to FALSE
sessionInfo()R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ComplexUpset_1.3.3 reshape2_1.4.4 gridExtra_2.3 phytools_2.0-3
[5] maps_3.4.1 ggtree_3.6.2 phylolm_2.6.2 lubridate_1.9.2
[9] forcats_1.0.0 stringr_1.5.0 purrr_1.0.1 tidyr_1.3.0
[13] tibble_3.1.8 ggplot2_3.4.4 tidyverse_2.0.0 ape_5.7
[17] readr_2.1.4 dplyr_1.1.0 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] nlme_3.1-160 fs_1.6.1 bit64_4.0.5
[4] doParallel_1.0.17 httr_1.4.4 rprojroot_2.0.4
[7] numDeriv_2016.8-1.1 tools_4.2.1 bslib_0.4.2
[10] utf8_1.2.2 R6_2.5.1 DBI_1.1.3
[13] lazyeval_0.2.2 colorspace_2.0-3 withr_2.5.0
[16] phangorn_2.11.1 mnormt_2.1.1 tidyselect_1.2.0
[19] processx_3.8.3 bit_4.0.5 compiler_4.2.1
[22] git2r_0.32.0 cli_3.6.2 expm_0.999-7
[25] labeling_0.4.2 sass_0.4.5 scales_1.2.1
[28] quadprog_1.5-8 callr_3.7.3 digest_0.6.30
[31] yulab.utils_0.0.6 rmarkdown_2.20 pkgconfig_2.0.3
[34] htmltools_0.5.7 parallelly_1.36.0 highr_0.10
[37] fastmap_1.1.0 rlang_1.1.2 rstudioapi_0.14
[40] optimParallel_1.0-2 farver_2.1.1 gridGraphics_0.5-1
[43] jquerylib_0.1.4 generics_0.1.3 combinat_0.0-8
[46] jsonlite_1.8.8 vroom_1.6.1 magrittr_2.0.3
[49] ggplotify_0.1.0 patchwork_1.1.2 Matrix_1.5-3
[52] Rcpp_1.0.11 munsell_0.5.0 fansi_1.0.3
[55] lifecycle_1.0.3 scatterplot3d_0.3-44 stringi_1.7.8
[58] whisker_0.4.1 yaml_2.3.7 clusterGeneration_1.3.8
[61] MASS_7.3-58.1 plyr_1.8.9 grid_4.2.1
[64] parallel_4.2.1 listenv_0.9.0 promises_1.2.1
[67] crayon_1.5.2 lattice_0.20-45 hms_1.1.2
[70] knitr_1.42 ps_1.7.2 pillar_1.8.1
[73] igraph_1.5.1 future.apply_1.11.0 codetools_0.2-18
[76] fastmatch_1.1-3 glue_1.6.2 evaluate_0.23
[79] getPass_0.2-2 ggfun_0.0.9 vctrs_0.5.2
[82] treeio_1.22.0 tzdb_0.3.0 httpuv_1.6.11
[85] foreach_1.5.2 gtable_0.3.1 future_1.33.0
[88] cachem_1.0.6 xfun_0.41 tidytree_0.4.2
[91] coda_0.19-4 later_1.3.1 iterators_1.0.14
[94] aplot_0.1.9 timechange_0.2.0 globals_0.16.2
[97] ellipsis_0.3.2