2019_Nov1-FiguresRearranged_IMPC_variance_and_sex_difference.Rmd
---
title: "IMPC Mouse data - Variance in sex differences"
author: "Susanne Zajitschek, Felix Zajitschek, Russell Bonduriansky,Robert Brooks, Will Cornwell, Daniel Falster, Malgortaza Lagisz, Jeremy Mason, Daniel Noble, Alistair Senior & Shinichi Nakagawa"
date: "August 2019"
output:
html_document:
code_download: true
code_folding: hide
depth: 4
number_sections: no
theme: flatly
toc: yes
toc_depth: 4
toc_float: yes
html_notebook:
toc: yes
pdf_document:
toc: yes
toc_depth: '4'
subtitle: Electronic Supplementary Material
---
# Set-up
## Load packages & functions
```{r, include=FALSE}
knitr::opts_chunk$set(
echo = TRUE,
warning = FALSE,
message = FALSE,
cache = TRUE,
tidy = TRUE
)
```
```{r}
library(readr)
library(dplyr)
library(metafor)
library(devtools)
library(purrr)
library(tidyverse)
library(tibble)
library(kableExtra)
library(robumeta)
library(ggpubr)
library(ggplot2)
library(here)
```
Functions for preparing the data for meta analyses
1) "Population statistics"
```{r}
calculate_population_stats <- function(mydata, min_individuals = 5) {
mydata %>%
group_by(population, strain_name, production_center, sex) %>%
summarise(
trait = parameter_name[1],
x_bar = mean(data_point),
x_sd = sd(data_point),
n_ind = n()
) %>%
ungroup() %>%
filter(n_ind > min_individuals) %>%
# Check both sexes present & filter those missing
group_by(population) %>%
mutate(
n_sex = n_distinct(sex)
) %>%
ungroup() %>%
filter(n_sex == 2) %>%
select(-n_sex) %>%
arrange(production_center, strain_name, population, sex)
}
```
2) Extraction of effect sizes and sample variances
```{r}
create_meta_analysis_effect_sizes <- function(mydata) {
i <- seq(1, nrow(mydata), by = 2)
input <- data.frame(
n1i = mydata$n_ind[i],
n2i = mydata$n_ind[i + 1],
x1i = mydata$x_bar[i],
x2i = mydata$x_bar[i + 1],
sd1i = mydata$x_sd[i],
sd2i = mydata$x_sd[i + 1]
)
mydata[i, ] %>%
select(strain_name, production_center, trait) %>%
mutate(
effect_size_CVR = calculate_lnCVR(CMean = input$x1i, CSD = input$sd1i, CN = input$n1i, EMean = input$x2i, ESD = input$sd2i, EN = input$n2i),
sample_variance_CVR = calculate_var_lnCVR(CMean = input$x1i, CSD = input$sd1i, CN = input$n1i, EMean = input$x2i, ESD = input$sd2i, EN = input$n2i),
effect_size_VR = calculate_lnVR(CSD = input$sd1i, CN = input$n1i, ESD = input$sd2i, EN = input$n2i),
sample_variance_VR = calculate_var_lnVR(CN = input$n1i, EN = input$n2i),
effect_size_RR = calculate_lnRR(CMean = input$x1i, CSD = input$sd1i, CN = input$n1i, EMean = input$x2i, ESD = input$sd2i, EN = input$n2i),
sample_variance_RR = calculate_var_lnRR(CMean = input$x1i, CSD = input$sd1i, CN = input$n1i, EMean = input$x2i, ESD = input$sd2i, EN = input$n2i),
err = as.factor(seq_len(n()))
)
}
```
3) Calculate meta-analysis statistics
Based on function created by A M Senior @ the University of Otago NZ 03/01/2014:
* Calculates effect sizes for meta-analysis of variance. All functions take the mean, sd and n from the control and experimental groups.
* The first function, calculate_lnCVR, calculates the the log response-ratio of the coefficient of variance (lnCVR) - see Nakagawa et al 2015.
* The second function calculates the measurement error variance for lnCVR. As well as the aforementioned parameters, this function also takes Equal_E_C_Corr (default = T), which must be True or False. If true, the function assumes that the correlation between mean and sd (Taylor's Law) is equal for the mean and control groups, and, thus these data are pooled. If False the mean-SD correlation for the experimental and control groups are calculated separately from one another.
* Similar functions are then implemented for lnVR (for comparison of standard deviations) and ln RR (for comparison of means)
```{r}
calculate_lnCVR <- function(CMean, CSD, CN, EMean, ESD, EN) {
log(ESD) - log(EMean) + 1 / (2 * (EN - 1)) - (log(CSD) - log(CMean) + 1 / (2 * (CN - 1)))
}
calculate_var_lnCVR <- function(CMean, CSD, CN, EMean, ESD, EN, Equal_E_C_Corr = T) {
if (Equal_E_C_Corr == T) {
mvcorr <- 0 # cor.test(log(c(CMean, EMean)), log(c(CSD, ESD)))$estimate old, slightly incorrect
S2 <- CSD^2 / (CN * (CMean^2)) + 1 / (2 * (CN - 1)) - 2 * mvcorr * sqrt((CSD^2 / (CN * (CMean^2))) * (1 / (2 * (CN - 1)))) + ESD^2 / (EN * (EMean^2)) + 1 / (2 * (EN - 1)) - 2 * mvcorr * sqrt((ESD^2 / (EN * (EMean^2))) * (1 / (2 * (EN - 1))))
}
else {
Cmvcorr <- cor.test(log(CMean), log(CSD))$estimate
Emvcorr <- cor.test(log(EMean), (ESD))$estimate
S2 <- CSD^2 / (CN * (CMean^2)) + 1 / (2 * (CN - 1)) - 2 * Cmvcorr * sqrt((CSD^2 / (CN * (CMean^2))) * (1 / (2 * (CN - 1)))) + ESD^2 / (EN * (EMean^2)) + 1 / (2 * (EN - 1)) - 2 * Emvcorr * sqrt((ESD^2 / (EN * (EMean^2))) * (1 / (2 * (EN - 1))))
}
S2
}
calculate_lnVR <- function(CSD, CN, ESD, EN) {
log(ESD) - log(CSD) + 1 / (2 * (EN - 1)) - 1 / (2 * (CN - 1))
}
calculate_var_lnVR <- function(CN, EN) {
1 / (2 * (EN - 1)) + 1 / (2 * (CN - 1))
}
calculate_lnRR <- function(CMean, CSD, CN, EMean, ESD, EN) {
log(EMean) - log(CMean)
}
calculate_var_lnRR <- function(CMean, CSD, CN, EMean, ESD, EN) {
CSD^2 / (CN * CMean^2) + ESD^2 / (EN * EMean^2)
}
```
## Load & clean data
Having loaded the necessary functions, we can get started on the dataset.
We here provide the cleaned dataset, which we have saved in a folder called `export`, as easy starting point. However, the full dataset can be loaded and cleaned using the data cleaning function below. We created this as it much smaller than the .csv.
1) Data loading and cleaning of the csv file
This step we have already done and provide a cleaned up file which is less computing intensive. However, the cvs is provided in case this is preferred to be attempted, following the steps below:
```{r clean, eval=FALSE, include=TRUE}
# loads the raw data, setting some default types for various columns
load_raw <- function(filename) {
read_csv(filename,
col_types = cols(
.default = col_character(),
project_id = col_character(),
id = col_character(),
parameter_id = col_character(),
age_in_days = col_integer(),
date_of_experiment = col_datetime(format = ""),
weight = col_double(),
phenotyping_center_id = col_character(),
production_center_id = col_character(),
weight_date = col_datetime(format = ""),
date_of_birth = col_datetime(format = ""),
procedure_id = col_character(),
pipeline_id = col_character(),
biological_sample_id = col_character(),
biological_model_id = col_character(),
weight_days_old = col_integer(),
datasource_id = col_character(),
experiment_id = col_character(),
data_point = col_double(),
age_in_weeks = col_integer(),
`_version_` = col_character()
)
)
}
# Apply some standard cleaning to the data
clean_raw_data <- function(mydata) {
group <- read_csv(here("data", "ParameterGrouping.csv"))
tmp <-
mydata %>%
# Filter to IMPC source (recommend by Jeremey in email to Susi on 20 Aug 2018)
filter(datasource_name == "IMPC") %>%
# standardise trait names
mutate(parameter_name = tolower(parameter_name)) %>%
# remove extreme ages
filter(age_in_days > 0 & age_in_days < 500) %>%
# remove NAs
filter(!is.na(data_point)) %>%
# subset to reasonable set of variables
# date_of_experiment: Jeremy suggested using as an indicator of batch-level effects
select(production_center, strain_name, strain_accession_id, biological_sample_id, pipeline_stable_id, procedure_group, procedure_name, sex, date_of_experiment, age_in_days, weight, parameter_name, data_point) %>%
# sort
arrange(production_center, biological_sample_id, age_in_days)
# filter to groups with > 1 centre
# **Review** - retaining merge here to retain ordering of data used in previous version
# usually i would use mutate instead of creating sperate dataset
merge(tmp,
tmp %>% group_by(parameter_name) %>%
summarise(center_per_trait = length(unique(production_center, na.rm = TRUE)))
)%>%
filter(center_per_trait >= 2) %>%
# Define population variable
mutate(population = sprintf("%s-%s", production_center, strain_name)) %>%
# add grouping variable: these were decided based on functional groups and procedures
# **Review** - retaining match here to retain ordering of data used in rpevious version
mutate(parameter_group = group$parameter_group[match(parameter_name, group$parameter_name)] ) %>%
# usually i would use left_join
# left_join(by="parameter_name",
# read_csv(here("data", "ParameterGrouping.csv")) %>%
# select(-id)
# ) %>%
# Assign unique IDs (per trait)
# each unique parameter_name (=trait,use trait variable) gets a unique number ('id')
# We add a new variable, where redundant traits are combined
#[note however, at this stage the dataset still contains nonsensical traits, i.e. traits that may not contain any information on variance]
mutate(id = match(parameter_name, unique(parameter_name))) %>%
as_tibble()
}
# Load raw data - save cleaned dataset as RDS for reuse
data_raw <- load_raw(here("data","dr7.0_all_control_data.csv.gz"))
dir.create("export", F, F)
data <- data_raw %>%
clean_raw_data()
saveRDS(data, "export/data_clean.rds")
```
For analysis we load the RDS created above and other datasets:
```{r load}
data <- readRDS(here("export", "data_clean.rds"))
procedures <- read_csv(here("data", "procedures.csv"))
```
Check length of different variables:
```{r}
length(unique(data$parameter_name)) # 232
length(unique(data$parameter_group)) # 161
length(unique(data$procedure_name)) # 26
```
# Phase 1: across all traits
Create function for sub-setting the data to choose only one data point per individual per trait. This is a necessary step for the loop across all traits
```{r}
data_subset_parameterid_individual_by_age <- function(mydata, parameter, age_min=0, age_center=100) {
tmp <- mydata %>%
filter(
age_in_days >= age_min,
id == parameter
) %>%
# take results for single individual closest to age_center
mutate(age_diff = abs(age_center - age_in_days)) %>%
group_by(biological_sample_id) %>%
filter(age_diff == min(age_diff)) %>%
select(-age_diff)# %>%
# filter(!duplicated(biological_sample_id))
# still some individuals with multiple records (because same individual appears under different procedures, so filter to one record)
j <- match(unique(tmp$biological_sample_id), tmp$biological_sample_id)
tmp[j, ]
}
```
Loop running meta-analysis on all traits
* The loop combines the functions mentioned above and fills the data matrix with results from our meta analysis.
* Error messages indicate traits that either did not reach convergence, or that did not return meaningful results in the meta-analysis, due to absence of variance. Those traits will be removed in later steps, outlined below.
```{r}
(n <- length(unique(data$id)))
# Create dataframe to store results
results_alltraits_grouping <-
tibble(id = 1:n, lnCVR=0, lnCVR_lower=0, lnCVR_upper=0,
lnCVR_se=0, lnVR=0, lnVR_lower=0, lnVR_upper=0,
lnVR_se=0, lnRR=0, lnRR_lower=0, lnRR_upper=0, lnRR_se=0, sampleSize=0, trait=0)
for (t in 1:n) {
tryCatch(
{
results <- data %>%
data_subset_parameterid_individual_by_age(t) %>%
calculate_population_stats() %>%
create_meta_analysis_effect_sizes()
# lnCVR, log repsonse-ratio of the coefficient of variance
cvr <- metafor::rma.mv(yi = effect_size_CVR, V = sample_variance_CVR,
random = list(~ 1 | strain_name, ~ 1 | production_center, ~ 1 | err),
control = list(optimizer = "optim", optmethod = "Nelder-Mead",
maxit = 1000), verbose = F, data = results)
# lnVR, comparison of standard deviations
cv <- metafor::rma.mv(yi = effect_size_VR, V = sample_variance_VR,
random = list(~ 1 | strain_name, ~ 1 | production_center, ~ 1 | err),
control = list(optimizer = "optim", optmethod = "Nelder-Mead",
maxit = 1000), verbose = F, data = results)
# for means, lnRR
means <- metafor::rma.mv(yi = effect_size_RR, V = sample_variance_RR,
random = list(~ 1 | strain_name, ~ 1 | production_center, ~ 1 | err),
control = list(optimizer = "optim", optmethod = "Nelder-Mead",
maxit = 1000), verbose = F, data = results)
f <- function(x) unlist(x[c("b", "ci.lb", "ci.ub", "se")])
results_alltraits_grouping[t, 2:14] <- c(f(cvr), f(cv), f(means), means$k)
results_alltraits_grouping[t, 15] <- unique(results$trait)
},
error = function(e) {
cat("ERROR :", t, conditionMessage(e), "\n")
}
)
}
```
--------
**REVIEW**: The above loop gives some errors, can these be fixed?
ERROR : 84 Optimizer (optim) did not achieve convergence (convergence = 10).
ERROR : 158 Optimizer (optim) did not achieve convergence (convergence = 10).
ERROR : 160 NA/NaN/Inf in 'y'
ERROR : 161 NA/NaN/Inf in 'y'
ERROR : 162 NA/NaN/Inf in 'y'
ERROR : 163 NA/NaN/Inf in 'y'
ERROR : 165 NA/NaN/Inf in 'y'
ERROR : 166 NA/NaN/Inf in 'y'
ERROR : 168 NA/NaN/Inf in 'y'
ERROR : 231 NA/NaN/Inf in 'y'
Also a bunch of warnings, are any of these a concern?
> warnings()
Warning messages:
1: In metafor::rma.mv(yi = effect_size_CVR, V = sample_variance_CVR, ... :
Rows with NAs omitted from model fitting.
...
13: In metafor::rma.mv(yi = effect_size_RR, V = sample_variance_RR, ... :
There are outcomes with non-positive sampling variances.
14: In metafor::rma.mv(yi = effect_size_RR, V = sample_variance_RR, ... :
'V' appears to be not positive definite.
16: In metafor::rma.mv(yi = effect_size_CVR, V = sample_variance_CVR, ... :
Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.
...
50: In metafor::rma.mv(yi = effect_size_RR, V = sample_variance_RR, ... :
'V' appears to be not positive definite
------
Now that we have a "results" table with each of the meta-analytic means for all effect sizes of interest, we can use this table as part of the Shiny App, which will then be able to back calculate the percentage differences between males and females for mean, variance and coefficient of variance. We'll export and use this in the Shiny App. **Note that I have not dealt with convergence issues in some of these models, and so, this will need to be done down the road**
(Note Susi 31/7/2019: This dataset contains dublicated values, plus no info on what the "traits" mean. I will change Dan N's to one further belwo, that have been cleaned up already
FILE TO USE: METACOMBO (around line 500))
### Merging datasets & removal of non-converged traits
Procedure names, grouping variables etc. are merged back together with the results from the metafor analysis above.This requires loading of another excel sheet, "procedures.csv"
```{r}
results_alltraits_grouping2 <-
results_alltraits_grouping %>%
left_join(by="id",
data %>% select(id, parameter_group, procedure = procedure_name, parameter_name) %>%
# REVIEW -- this bext line replciates precious code, but removes some procedures, is that right?
filter(!duplicated(id))
) %>%
left_join(by="procedure",
procedures %>% distinct()
)
n <- length(unique(results_alltraits_grouping2$parameter_name)) # 232
```
Removal of traits that did not achieve convergence, are nonsensical for analysis of variance (such as traits that show variation, such as number of ribs, digits, etc). 14 traits from the originally 232 that had been included are removed.
**Review**: How did we determine this the ones with problems?
```{r}
has_problems <- c(84, 144, 158, 160, 161, 162, 163, 165, 166, 167, 168, 221, 222, 231)
meta_clean <- results_alltraits_grouping2 %>% filter(!id %in% has_problems)
meta_problem <- results_alltraits_grouping2 %>% filter(id %in% has_problems)
```
**Reveiw**: check against old script -- identical, remove once fixed
```{r, eval=FALSE}
meta_clean.test <- readRDS("../meta_clean.test.rds")
all.equal(meta_clean, meta_clean.test)
all.equal(meta_clean %>% select(-parameter_group), meta_clean.test %>% mutate(id=as.integer(id), GroupingTerm = as.character(GroupingTerm)))
```
## Meta-analysis, Phase 2: non-independent traits
### Dealing with Correlated Parameters, preparation
This dataset contained a number of highly correlated traits, such as different kinds of cell counts (for example, hierarchical parameterization within immunological assays). As those data-points are not independent of each other, we conducted a meta analyses on these correlated parameters to collapse the number of levels.
#### Collapsing and merging correlated parameters
Here we double check numbers of trait parameters in the dataset
```{r}
meta1 <- meta_clean
length(unique(meta1$procedure)) #18
length(unique(meta1$GroupingTerm)) #9
# Review: next line now 155 not 148
length(unique(meta1$parameter_group)) # 148 levels. To be used as grouping factor for meta-meta analysis / collapsing down based on things that are classified identically in "parameter_group" but have different "parameter_name"
length(unique(meta1$parameter_name)) #218
```
#### Count of number of parameter names (correlated sub-traits) in each parameter group (par_group_size)
This serves to identify and separate the traits that are correlated from the full dataset that can be processed as is. If the sample size (n) for a given "parameter group" equals 1, the trait is unique and uncorrelated. All instances, where there are 2 or more traits associated with the same parameter group (90 cases), are selected for a "mini-meta analysis", which removes the issue of correlation.
```{r}
kable(cbind(meta1 %>% count(parameter_group))) %>%
kable_styling() %>%
scroll_box(width = "100%", height = "200px")
```
```{r}
meta1_sub <- meta1 %>%
# add summary of number of parameter names in each parameter group
group_by(parameter_group) %>%
mutate(par_group_size = length(unique(parameter_name)),
sampleSize = as.numeric(sampleSize)) %>%
ungroup() %>%
# Create subsets with > 1 count (par_group_size > 1)
filter(par_group_size > 1) # 90 observations
```
#### Meta-analyses on correlated (sub-)traits, using robumeta`
The subset of the data is prepared (nested), and in this first step the model of the meta analysis effect sizes are calculated
```{r}
meta1b <-
meta1 %>%
group_by(parameter_group) %>%
summarize(par_group_size = length(unique(parameter_name, na.rm = TRUE)))
#this gives a summary of number of parameter names in each parameter group, now it neeeds to get merged it back together
meta1$par_group_size <- meta1b$par_group_size[match(meta1$parameter_group, meta1b$parameter_group)]
# Create subsets with > 1 count (par_group_size > 1)
meta1_sub<-subset(meta1,par_group_size >1) # 90 observations
meta1_sub$sampleSize <- as.numeric(meta1_sub$sampleSize)
# nesting
n_count <- meta1_sub %>%
group_by(parameter_group) %>%
mutate(raw_N = sum(sampleSize)) %>%
nest() %>%
ungroup()
model_count <- n_count %>%
mutate(
model_lnRR = map(data, ~ robu(.x$lnRR ~ 1, data = .x, studynum = .x$id, modelweights = c("CORR"), rho = 0.8, small = TRUE, var.eff.size = (.x$lnRR_se)^2)),
model_lnVR = map(data, ~ robu(.x$lnVR ~ 1, data = .x, studynum = .x$id, modelweights = c("CORR"), rho = 0.8, small = TRUE, var.eff.size = (.x$lnVR_se)^2)),
model_lnCVR = map(data, ~ robu(.x$lnCVR ~ 1, data = .x, studynum = .x$id, modelweights = c("CORR"), rho = 0.8, small = TRUE, var.eff.size = (.x$lnCVR_se)^2))
)
```
Extract and save parameter estimates:
Function to collect the outcomes of the "mini" meta analysis
```{r}
count_fun <- function(mod_sub) {
return(c(mod_sub$reg_table$b.r, mod_sub$reg_table$CI.L, mod_sub$reg_table$CI.U, mod_sub$reg_table$SE))
} # estimate, lower ci, upper ci, SE
```
Extraction of values created during Meta analysis using robu meta:
```{r}
robusub_RR <- model_count %>%
transmute(parameter_group, estimatelnRR = map(model_lnRR, count_fun)) %>%
mutate(r = map(estimatelnRR, ~ data.frame(t(.)))) %>%
unnest(r) %>%
select(-estimatelnRR) %>%
purrr::set_names(c("parameter_group", "lnRR", "lnRR_lower", "lnRR_upper", "lnRR_se"))
robusub_CVR <- model_count %>%
transmute(parameter_group, estimatelnCVR = map(model_lnCVR, count_fun)) %>%
mutate(r = map(estimatelnCVR, ~ data.frame(t(.)))) %>%
unnest(r) %>%
select(-estimatelnCVR) %>%
purrr::set_names(c("parameter_group", "lnCVR", "lnCVR_lower", "lnCVR_upper", "lnCVR_se"))
robusub_VR <- model_count %>%
transmute(parameter_group, estimatelnVR = map(model_lnVR, count_fun)) %>%
mutate(r = map(estimatelnVR, ~ data.frame(t(.)))) %>%
unnest(r) %>%
select(-estimatelnVR) %>%
purrr::set_names(c("parameter_group", "lnVR", "lnVR_lower", "lnVR_upper", "lnVR_se"))
robu_all <- full_join(robusub_CVR, robusub_VR) %>% full_join(., robusub_RR)
```
```{r}
kable(cbind(robu_all, robu_all)) %>%
kable_styling() %>%
scroll_box(width = "100%", height = "200px")
```
Merge the two data sets (the new [robu_all] and the initial [uncorrelated sub-traits with count = 1])
```{r}
meta_all <- meta1 %>%
filter(par_group_size == 1) %>%
as_tibble()
# str(meta_all)
# str(robu_all)
# which(is.na(match(names(meta_all),names(robu_all)))) # check
```
#### Combine data
```{r}
# Step1
combinedmeta <- bind_rows(robu_all, meta_all)
# glimpse(combinedmeta)
# Steps 2&3
metacombo <- combinedmeta
metacombo$counts <- meta1$par_group_size[match(metacombo$parameter_group, meta1$parameter_group)]
metacombo$procedure2 <- meta1$procedure[match(metacombo$parameter_group, meta1$parameter_group)]
metacombo$GroupingTerm2 <- meta1$GroupingTerm[match(metacombo$parameter_group, meta1$parameter_group)]
kable(cbind(metacombo, metacombo)) %>%
kable_styling() %>%
scroll_box(width = "100%", height = "200px")
```
Clean-up and rename
```{r}
metacombo <- metacombo[, c(1, 21:23, 2:13)]
names(metacombo)[3] <- "procedure"
names(metacombo)[4] <- "GroupingTerm"
# Quick pre-check before doing plots
compare <- metacombo %>%
group_by(GroupingTerm) %>%
dplyr::summarize(MeanCVR = mean(lnCVR), MeanVR = mean(lnVR), MeanRR = mean(lnRR))
# compare
```
```{r}
# SHINY APP # Now that we have a corrected "results" table with each of the meta-analytic means for all effect sizes of interest, we can use this table as part of the Shiny App, which will then be able to back calculate the percentage differences between males and females for mean, variance and coefficient of variance. We'll export and use this in the Shiny App. **Note that I have not dealt with convergence issues in some of these models, and so, this will need to be done down the road**
## Note Susi 31/7/2019: This has been cleaned up already
# FILE TO USE: METACOMBO
### note: to use
# trait_meta_results <- write.csv(metacombo, file = "export/trait_meta_results.csv")
```
## Meta-analysis, Phase 3: Second-order meta analysis for functional groups
#### Perform meta-analyses (3 for each of the 9 grouping terms: lnCVR, lnVR, lnRR)
This is the full result dataset
```{r}
kable(cbind(metacombo, metacombo)) %>%
kable_styling() %>%
scroll_box(width = "100%", height = "200px")
```
#### Prepare data
Nesting, calculating the number of parameters within each grouping term, and running the meta-analysis
```{r}
metacombo_final <- metacombo %>%
group_by(GroupingTerm) %>%
nest()
# **calculate number of parameters per grouping term
metacombo_final <- metacombo_final %>% mutate(para_per_GroupingTerm = map_dbl(data, nrow))
# For all grouping terms
metacombo_final_all <- metacombo %>%
nest()
# **Final fixed effects meta-analyses within grouping terms, with SE of the estimate
overall1 <- metacombo_final %>%
mutate(
model_lnCVR = map(data, ~ metafor::rma.uni(
yi = .x$lnCVR, sei = (.x$lnCVR_upper - .x$lnCVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)),
model_lnVR = map(data, ~ metafor::rma.uni(
yi = .x$lnVR, sei = (.x$lnVR_upper - .x$lnVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)),
model_lnRR = map(data, ~ metafor::rma.uni(
yi = .x$lnRR, sei = (.x$lnRR_upper - .x$lnRR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
))
)
# **Final fixed effects meta-analyses ACROSS grouping terms, with SE of the estimate
overall_all1 <- metacombo_final_all %>%
mutate(
model_lnCVR = map(data, ~ metafor::rma.uni(
yi = .x$lnCVR, sei = (.x$lnCVR_upper - .x$lnCVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)),
model_lnVR = map(data, ~ metafor::rma.uni(
yi = .x$lnVR, sei = (.x$lnVR_upper - .x$lnVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)),
model_lnRR = map(data, ~ metafor::rma.uni(
yi = .x$lnRR, sei = (.x$lnRR_upper - .x$lnRR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
))
)
```
Re-structure data for each grouping term; delete unused variables
```{r}
Behaviour <- as.data.frame(overall1 %>% filter(., GroupingTerm == "Behaviour") %>% mutate(
lnCVR = .[[4]][[1]]$b, lnCVR_lower = .[[4]][[1]]$ci.lb, lnCVR_upper = .[[4]][[1]]$ci.ub, lnCVR_se = .[[4]][[1]]$se,
lnVR = .[[5]][[1]]$b, lnVR_lower = .[[5]][[1]]$ci.lb, lnVR_upper = .[[5]][[1]]$ci.ub, lnVR_se = .[[5]][[1]]$se,
lnRR = .[[6]][[1]]$b, lnRR_lower = .[[6]][[1]]$ci.lb, lnRR_upper = .[[6]][[1]]$ci.ub, lnRR_se = .[[6]][[1]]$se
))[, c(1, 7:18)]
Immunology <- as.data.frame(overall1 %>% filter(., GroupingTerm == "Immunology") %>% mutate(
lnCVR = .[[4]][[1]]$b, lnCVR_lower = .[[4]][[1]]$ci.lb, lnCVR_upper = .[[4]][[1]]$ci.ub, lnCVR_se = .[[4]][[1]]$se,
lnVR = .[[5]][[1]]$b, lnVR_lower = .[[5]][[1]]$ci.lb, lnVR_upper = .[[5]][[1]]$ci.ub, lnVR_se = .[[5]][[1]]$se,
lnRR = .[[6]][[1]]$b, lnRR_lower = .[[6]][[1]]$ci.lb, lnRR_upper = .[[6]][[1]]$ci.ub, lnRR_se = .[[6]][[1]]$se
))[, c(1, 7:18)]
Hematology <- as.data.frame(overall1 %>% filter(., GroupingTerm == "Hematology") %>% mutate(
lnCVR = .[[4]][[1]]$b, lnCVR_lower = .[[4]][[1]]$ci.lb, lnCVR_upper = .[[4]][[1]]$ci.ub, lnCVR_se = .[[4]][[1]]$se,
lnVR = .[[5]][[1]]$b, lnVR_lower = .[[5]][[1]]$ci.lb, lnVR_upper = .[[5]][[1]]$ci.ub, lnVR_se = .[[5]][[1]]$se,
lnRR = .[[6]][[1]]$b, lnRR_lower = .[[6]][[1]]$ci.lb, lnRR_upper = .[[6]][[1]]$ci.ub, lnRR_se = .[[6]][[1]]$se
))[, c(1, 7:18)]
Hearing <- as.data.frame(overall1 %>% filter(., GroupingTerm == "Hearing") %>% mutate(
lnCVR = .[[4]][[1]]$b, lnCVR_lower = .[[4]][[1]]$ci.lb, lnCVR_upper = .[[4]][[1]]$ci.ub, lnCVR_se = .[[4]][[1]]$se,
lnVR = .[[5]][[1]]$b, lnVR_lower = .[[5]][[1]]$ci.lb, lnVR_upper = .[[5]][[1]]$ci.ub, lnVR_se = .[[5]][[1]]$se,
lnRR = .[[6]][[1]]$b, lnRR_lower = .[[6]][[1]]$ci.lb, lnRR_upper = .[[6]][[1]]$ci.ub, lnRR_se = .[[6]][[1]]$se
))[, c(1, 7:18)]
Physiology <- as.data.frame(overall1 %>% filter(., GroupingTerm == "Physiology") %>% mutate(
lnCVR = .[[4]][[1]]$b, lnCVR_lower = .[[4]][[1]]$ci.lb, lnCVR_upper = .[[4]][[1]]$ci.ub, lnCVR_se = .[[4]][[1]]$se,
lnVR = .[[5]][[1]]$b, lnVR_lower = .[[5]][[1]]$ci.lb, lnVR_upper = .[[5]][[1]]$ci.ub, lnVR_se = .[[5]][[1]]$se,
lnRR = .[[6]][[1]]$b, lnRR_lower = .[[6]][[1]]$ci.lb, lnRR_upper = .[[6]][[1]]$ci.ub, lnRR_se = .[[6]][[1]]$se
))[, c(1, 7:18)]
Metabolism <- as.data.frame(overall1 %>% filter(., GroupingTerm == "Metabolism") %>% mutate(
lnCVR = .[[4]][[1]]$b, lnCVR_lower = .[[4]][[1]]$ci.lb, lnCVR_upper = .[[4]][[1]]$ci.ub, lnCVR_se = .[[4]][[1]]$se,
lnVR = .[[5]][[1]]$b, lnVR_lower = .[[5]][[1]]$ci.lb, lnVR_upper = .[[5]][[1]]$ci.ub, lnVR_se = .[[5]][[1]]$se,
lnRR = .[[6]][[1]]$b, lnRR_lower = .[[6]][[1]]$ci.lb, lnRR_upper = .[[6]][[1]]$ci.ub, lnRR_se = .[[6]][[1]]$se
))[, c(1, 7:18)]
Morphology <- as.data.frame(overall1 %>% filter(., GroupingTerm == "Morphology") %>% mutate(
lnCVR = .[[4]][[1]]$b, lnCVR_lower = .[[4]][[1]]$ci.lb, lnCVR_upper = .[[4]][[1]]$ci.ub, lnCVR_se = .[[4]][[1]]$se,
lnVR = .[[5]][[1]]$b, lnVR_lower = .[[5]][[1]]$ci.lb, lnVR_upper = .[[5]][[1]]$ci.ub, lnVR_se = .[[5]][[1]]$se,
lnRR = .[[6]][[1]]$b, lnRR_lower = .[[6]][[1]]$ci.lb, lnRR_upper = .[[6]][[1]]$ci.ub, lnRR_se = .[[6]][[1]]$se
))[, c(1, 7:18)]
Heart <- as.data.frame(overall1 %>% filter(., GroupingTerm == "Heart") %>% mutate(
lnCVR = .[[4]][[1]]$b, lnCVR_lower = .[[4]][[1]]$ci.lb, lnCVR_upper = .[[4]][[1]]$ci.ub, lnCVR_se = .[[4]][[1]]$se,
lnVR = .[[5]][[1]]$b, lnVR_lower = .[[5]][[1]]$ci.lb, lnVR_upper = .[[5]][[1]]$ci.ub, lnVR_se = .[[5]][[1]]$se,
lnRR = .[[6]][[1]]$b, lnRR_lower = .[[6]][[1]]$ci.lb, lnRR_upper = .[[6]][[1]]$ci.ub, lnRR_se = .[[6]][[1]]$se
))[, c(1, 7:18)]
Eye <- as.data.frame(overall1 %>% filter(., GroupingTerm == "Eye") %>% mutate(
lnCVR = .[[4]][[1]]$b, lnCVR_lower = .[[4]][[1]]$ci.lb, lnCVR_upper = .[[4]][[1]]$ci.ub, lnCVR_se = .[[4]][[1]]$se,
lnVR = .[[5]][[1]]$b, lnVR_lower = .[[5]][[1]]$ci.lb, lnVR_upper = .[[5]][[1]]$ci.ub, lnVR_se = .[[5]][[1]]$se,
lnRR = .[[6]][[1]]$b, lnRR_lower = .[[6]][[1]]$ci.lb, lnRR_upper = .[[6]][[1]]$ci.ub, lnRR_se = .[[6]][[1]]$se
))[, c(1, 7:18)]
All <- as.data.frame(overall_all1 %>% mutate(
lnCVR = .[[2]][[1]]$b, lnCVR_lower = .[[2]][[1]]$ci.lb, lnCVR_upper = .[[2]][[1]]$ci.ub, lnCVR_se = .[[2]][[1]]$se, lnVR = .[[3]][[1]]$b, lnVR_lower = .[[3]][[1]]$ci.lb, lnVR_upper = .[[3]][[1]]$ci.ub, lnVR_se = .[[3]][[1]]$se,
lnRR = .[[4]][[1]]$b, lnRR_lower = .[[4]][[1]]$ci.lb, lnRR_upper = .[[4]][[1]]$ci.ub, lnRR_se = .[[4]][[1]]$se
))[, c(5:16)]
All$lnCVR <- as.numeric(All$lnCVR)
All$lnVR <- as.numeric(All$lnVR)
All$lnRR <- as.numeric(All$lnRR)
All <- All %>% mutate(GroupingTerm = "All")
overall2 <- bind_rows(Behaviour, Morphology, Metabolism, Physiology, Immunology, Hematology, Heart, Hearing, Eye, All)
```
## Visualisation
#### Preparation for plots: Count data, based on First-order meta analysis results
Re-order grouping terms
```{r}
meta_clean$GroupingTerm <- factor(meta_clean$GroupingTerm, levels = c("Behaviour", "Morphology", "Metabolism", "Physiology", "Immunology", "Hematology", "Heart", "Hearing", "Eye"))
meta_clean$GroupingTerm <- factor(meta_clean$GroupingTerm, rev(levels(meta_clean$GroupingTerm)))
# *Prepare data for all traits
meta.plot2.all <- meta_clean %>%
select(lnCVR, lnVR, lnRR, GroupingTerm) %>%
arrange(GroupingTerm)
meta.plot2.all.b <- gather(meta.plot2.all, trait, value, c(lnCVR, lnRR)) # lnVR,
meta.plot2.all.b$trait <- factor(meta.plot2.all.b$trait, levels = c("lnCVR", "lnRR")) # "lnVR",
meta.plot2.all.c <- meta.plot2.all.b %>%
group_by_at(vars(trait, GroupingTerm)) %>%
summarise(
malebias = sum(value > 0), femalebias = sum(value <= 0), total = malebias + femalebias,
malepercent = malebias * 100 / total, femalepercent = femalebias * 100 / total
)
meta.plot2.all.c$label <- "All traits"
# restructure to create stacked bar plots
meta.plot2.all.d <- as.data.frame(meta.plot2.all.c)
meta.plot2.all.e <- gather(meta.plot2.all.d, key = sex, value = percent, malepercent:femalepercent, factor_key = TRUE)
# create new sample size variable
meta.plot2.all.e$samplesize <- with(meta.plot2.all.e, ifelse(sex == "malepercent", malebias, femalebias))
malebias_Fig2_alltraits <-
ggplot(meta.plot2.all.e) +
aes(x = GroupingTerm, y = percent, fill = sex) +
geom_col() +
geom_hline(yintercept = 50, linetype = "dashed", color = "gray40") +
geom_text(
data = subset(meta.plot2.all.e, samplesize != 0), aes(label = samplesize), position = position_stack(vjust = .5),
color = "white", size = 3.5
) +
facet_grid(
cols = vars(trait), rows = vars(label), labeller = label_wrap_gen(width = 18),
scales = "free", space = "free"
) +
scale_fill_brewer(palette = "Set2") +
theme_bw(base_size = 18) +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.position = "none",
axis.title.x = element_blank(),
axis.title.y = element_blank()
) +
coord_flip()
# malebias_Fig2_alltraits #(panel A in Figure 4 in ms)
```
#### Prepare data for traits with CI not overlapping 0
create column with 1= different from zero, 0= zero included in CI
```{r}
meta.plot2.sig <- meta_clean %>%
mutate(
lnCVRsig = ifelse(lnCVR_lower * lnCVR_upper > 0, 1, 0), lnVRsig = ifelse(lnVR_lower * lnVR_upper > 0, 1, 0),
lnRRsig = ifelse(lnRR_lower * lnRR_upper > 0, 1, 0)
)
meta.plot2.sig.b <- meta.plot2.sig[, c("lnCVR", "lnRR", "lnCVRsig", "lnVRsig", "lnRRsig", "GroupingTerm")] # "lnVR",
meta.plot2.sig.c <- gather(meta.plot2.sig.b, trait, value, lnCVR:lnRR)
meta.plot2.sig.c$sig <- "placeholder"
meta.plot2.sig.c$trait <- factor(meta.plot2.sig.c$trait, levels = c("lnCVR", "lnRR")) # "lnVR",
meta.plot2.sig.c$sig <- ifelse(meta.plot2.sig.c$trait == "lnCVR", meta.plot2.sig.c$lnCVRsig,
ifelse(meta.plot2.sig.c$trait == "lnVR", meta.plot2.sig.c$lnVRsig, meta.plot2.sig.c$lnRRsig)
)
# choosing sex biased ln-ratios significantly larger than 0
meta.plot2.sig.malebias <- meta.plot2.sig.c %>%
group_by_at(vars(trait, GroupingTerm)) %>%
filter(sig == 1) %>%
summarise(male_sig = sum(value > 0), female_sig = sum(value < 0), total = male_sig + female_sig)
meta.plot2.sig.malebias <- ungroup(meta.plot2.sig.malebias) %>%
add_row(trait = "lnCVR", GroupingTerm = "Hearing", male_sig = 0, female_sig = 0, .before = 4) %>% # add "Hearing" for lnCVR (not filtered as only zeros)
mutate(malepercent = male_sig * 100 / total, femalepercent = female_sig * 100 / total)
meta.plot2.sig.malebias$label <- "CI not overlapping zero"
# restructure to create stacked bar plots
meta.plot2.sig.bothsexes <- as.data.frame(meta.plot2.sig.malebias)
meta.plot2.sig.bothsexes.b <- gather(meta.plot2.sig.bothsexes, key = sex, value = percent, malepercent:femalepercent, factor_key = TRUE)
# create new sample size variable
meta.plot2.sig.bothsexes.b$samplesize <- with(meta.plot2.sig.bothsexes.b, ifelse(sex == "malepercent", male_sig, female_sig))
# *Plot Fig2 all significant results (CI not overlapping zero):
# no sig. lnCVR for 'Hearing' in either sex; no sig. male-biased lnCVR for 'Immunology' and 'Eye, and no sig. male-biased lnVR for 'Eye'
malebias_Fig2_sigtraits <-
ggplot(meta.plot2.sig.bothsexes.b) +
aes(x = GroupingTerm, y = percent, fill = sex) +
geom_col() +
geom_hline(yintercept = 50, linetype = "dashed", color = "gray40") +
geom_text(
data = subset(meta.plot2.sig.bothsexes.b, samplesize != 0), aes(label = samplesize), position = position_stack(vjust = .5),
color = "white", size = 3.5
) +
facet_grid(
cols = vars(trait), rows = vars(label), labeller = label_wrap_gen(width = 18),
scales = "free", space = "free"
) +
scale_fill_brewer(palette = "Set2") +
theme_bw(base_size = 18) +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.position = "none",
axis.title.x = element_blank(),
axis.title.y = element_blank()
) +
coord_flip()
```
Prepare data for traits with effect size ratios > 10% larger in males
```{r}
meta.plot2.over10 <- meta_clean %>%
select(lnCVR, lnRR, GroupingTerm) %>%
arrange(GroupingTerm) # lnVR,
meta.plot2.over10.b <- gather(meta.plot2.over10, trait, value, c(lnCVR, lnRR)) # lnVR,
meta.plot2.over10.b$trait <- factor(meta.plot2.over10.b$trait, levels = c("lnCVR", "lnRR")) # "lnVR",
meta.plot2.over10.c <- meta.plot2.over10.b %>%
group_by_at(vars(trait, GroupingTerm)) %>%
summarise(
malebias = sum(value > log(11 / 10)), femalebias = sum(value < log(9 / 10)), total = malebias + femalebias,
malepercent = malebias * 100 / total, femalepercent = femalebias * 100 / total
)
meta.plot2.over10.c$label <- "Sex difference in m/f ratios > 10%"
# restructure to create stacked bar plots
meta.plot2.over10.c <- as.data.frame(meta.plot2.over10.c)
meta.plot2.over10.d <- gather(meta.plot2.over10.c, key = sex, value = percent, malepercent:femalepercent, factor_key = TRUE)
# create new sample size variable
meta.plot2.over10.d$samplesize <- with(meta.plot2.over10.d, ifelse(sex == "malepercent", malebias, femalebias))
# *Plot Fig2 Sex difference in m/f ratio > 10%
malebias_Fig2_over10 <-
ggplot(meta.plot2.over10.d) +
aes(x = GroupingTerm, y = percent, fill = sex) +
geom_col() +
geom_hline(yintercept = 50, linetype = "dashed", color = "gray40") +
geom_text(
data = subset(meta.plot2.over10.d, samplesize != 0), aes(label = samplesize), position = position_stack(vjust = .5),
color = "white", size = 3.5
) +
facet_grid(
cols = vars(trait), rows = vars(label), labeller = label_wrap_gen(width = 18),
scales = "free", space = "free"
) +
scale_fill_brewer(palette = "Set2") +
theme_bw(base_size = 18) +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_blank(),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.position = "none",
axis.title.x = element_blank(),
axis.title.y = element_blank()
) +
coord_flip()
# malebias_Fig2_over10 (Panel C in Fig 5 in ms)
```
### Overall results of second order meta analysis (Figure 4: overall, Figure 5: sex-bias)
#### Restructure data for plotting
Data are restructured, and grouping terms are being re-ordered
```{r}
overall3 <- gather(overall2, parameter, value, c(lnCVR, lnRR), factor_key = TRUE) # lnVR,
lnCVR.ci <- overall3 %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
lnVR.ci <- overall3 %>%
filter(parameter == "lnVR") %>%
mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3 %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4 <- bind_rows(lnCVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high) # lnVR.ci,
# re-order Grouping Terms
overall4$GroupingTerm <- factor(overall4$GroupingTerm, levels = c("Behaviour", "Morphology", "Metabolism", "Physiology", "Immunology", "Hematology", "Heart", "Hearing", "Eye", "All"))
overall4$GroupingTerm <- factor(overall4$GroupingTerm, rev(levels(overall4$GroupingTerm)))
overall4$label <- "All traits"
kable(cbind(overall4, overall4)) %>%
kable_styling() %>%
scroll_box(width = "100%", height = "200px")
```
#### Preparation for Plots FIGURE 4B & 5B, 5D (Second-order meta analysis results)
Preparation: Sub-Plot for Figure 3: all traits (4B)
```{r}
Metameta_Fig3_alltraits <- overall4 %>%
ggplot(aes(y = GroupingTerm, x = value)) +
geom_errorbarh(aes(
xmin = ci.low,
xmax = ci.high
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(shape = parameter),
fill = "black",
color = "black", size = 2.2,
show.legend = FALSE
) +
scale_x_continuous(
limits = c(-0.24, 0.25),
breaks = c(-0.2, -0.1, 0, 0.1, 0.2),
name = "Effect size"
) +
geom_vline(
xintercept = 0,
color = "black",
linetype = "dashed"
) +
facet_grid(
cols = vars(parameter), rows = vars(label),
labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_text(hjust = 0.5, size = 14),
axis.title.y = element_blank()
)
# Metameta_Fig3_alltraits
```
#### Figure 5 - traits with CI not overlapping 0
Prepare data
create column with 1= different from zero, 0= zero included in CI
Male-biased (significant) traits
```{r}
meta.male.plot3.sig <- metacombo %>%
mutate(
sigCVR = ifelse(lnCVR_lower > 0, 1, 0),
sigVR = ifelse(lnVR_lower > 0, 1, 0),
sigRR = ifelse(lnRR_lower > 0, 1, 0)
)
# Significant subset for lnCVR
metacombo_male.plot3.CVR <- meta.male.plot3.sig %>%
filter(sigCVR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_male.plot3.CVR.all <- meta.male.plot3.sig %>%
filter(sigCVR == 1) %>%
nest()
# Significant subset for lnVR
metacombo_male.plot3.VR <- meta.male.plot3.sig %>%
filter(sigVR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_male.plot3.VR.all <- meta.male.plot3.sig %>%
filter(sigVR == 1) %>%
nest()
# Significant subset for lnRR
metacombo_male.plot3.RR <- meta.male.plot3.sig %>%
filter(sigRR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_male.plot3.RR.all <- meta.male.plot3.sig %>%
filter(sigRR == 1) %>%
nest()
# **Final fixed effects meta-analyses within grouping terms, with SE of the estimate
plot3.male.meta.CVR <- metacombo_male.plot3.CVR %>%
mutate(model_lnCVR = map(data, ~ metafor::rma.uni(
yi = .x$lnCVR, sei = (.x$lnCVR_upper - .x$lnCVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.male.meta.VR <- metacombo_male.plot3.VR %>%
mutate(model_lnVR = map(data, ~ metafor::rma.uni(
yi = .x$lnVR, sei = (.x$lnVR_upper - .x$lnVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.male.meta.RR <- metacombo_male.plot3.RR %>%
mutate(model_lnRR = map(data, ~ metafor::rma.uni(
yi = .x$lnRR, sei = (.x$lnRR_upper - .x$lnRR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
# Across all grouping terms #
plot3.male.meta.CVR.all <- metacombo_male.plot3.CVR.all %>%
mutate(model_lnCVR = map(data, ~ metafor::rma.uni(
yi = .x$lnCVR, sei = (.x$lnCVR_upper - .x$lnCVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.male.meta.CVR.all <- plot3.male.meta.CVR.all %>% mutate(GroupingTerm = "All")
plot3.male.meta.VR.all <- metacombo_male.plot3.VR.all %>%
mutate(model_lnVR = map(data, ~ metafor::rma.uni(
yi = .x$lnVR, sei = (.x$lnVR_upper - .x$lnVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.male.meta.VR.all <- plot3.male.meta.VR.all %>% mutate(GroupingTerm = "All")
plot3.male.meta.RR.all <- metacombo_male.plot3.RR.all %>%
mutate(model_lnRR = map(data, ~ metafor::rma.uni(
yi = .x$lnRR, sei = (.x$lnRR_upper - .x$lnRR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.male.meta.RR.all <- plot3.male.meta.RR.all %>% mutate(GroupingTerm = "All")
# Combine with separate grouping term results
plot3.male.meta.CVR <- bind_rows(plot3.male.meta.CVR, plot3.male.meta.CVR.all)
plot3.male.meta.VR <- bind_rows(plot3.male.meta.VR, plot3.male.meta.VR.all)
plot3.male.meta.RR <- bind_rows(plot3.male.meta.RR, plot3.male.meta.RR.all)
# **Re-structure data for each grouping term; delete un-used variables
plot3.male.meta.CVR.b <- as.data.frame(plot3.male.meta.CVR %>% group_by(GroupingTerm) %>%
mutate(
lnCVR = map_dbl(model_lnCVR, pluck(2)), lnCVR_lower = map_dbl(model_lnCVR, pluck(6)),
lnCVR_upper = map_dbl(model_lnCVR, pluck(7)), lnCVR_se = map_dbl(model_lnCVR, pluck(3))
))[, c(1, 4:7)]
add.row.hearing <- as.data.frame(t(c("Hearing", NA, NA, NA, NA))) %>% setNames(names(plot3.male.meta.CVR.b))
plot3.male.meta.CVR.b <- bind_rows(plot3.male.meta.CVR.b, add.row.hearing)
plot3.male.meta.CVR.b <- plot3.male.meta.CVR.b[order(plot3.male.meta.CVR.b$GroupingTerm), ]
plot3.male.meta.VR.b <- as.data.frame(plot3.male.meta.VR %>% group_by(GroupingTerm) %>%
mutate(
lnVR = map_dbl(model_lnVR, pluck(2)), lnVR_lower = map_dbl(model_lnVR, pluck(6)),
lnVR_upper = map_dbl(model_lnVR, pluck(7)), lnVR_se = map_dbl(model_lnVR, pluck(3))
))[, c(1, 4:7)]
plot3.male.meta.VR.b <- plot3.male.meta.VR.b[order(plot3.male.meta.VR.b$GroupingTerm), ]
plot3.male.meta.RR.b <- as.data.frame(plot3.male.meta.RR %>% group_by(GroupingTerm) %>%
mutate(
lnRR = map_dbl(model_lnRR, pluck(2)), lnRR_lower = map_dbl(model_lnRR, pluck(6)),
lnRR_upper = map_dbl(model_lnRR, pluck(7)), lnRR_se = map_dbl(model_lnRR, pluck(3))
))[, c(1, 4:7)]
plot3.male.meta.RR.b <- plot3.male.meta.RR.b[order(plot3.male.meta.RR.b$GroupingTerm), ]
overall.male.plot3 <- full_join(plot3.male.meta.CVR.b, plot3.male.meta.VR.b)
overall.male.plot3 <- full_join(overall.male.plot3, plot3.male.meta.RR.b)
overall.male.plot3$GroupingTerm <- factor(overall.male.plot3$GroupingTerm, levels = c("Behaviour", "Morphology", "Metabolism", "Physiology", "Immunology", "Hematology", "Heart", "Hearing", "Eye", "All"))
overall.male.plot3$GroupingTerm <- factor(overall.male.plot3$GroupingTerm, rev(levels(overall.male.plot3$GroupingTerm)))
# add missing GroupingTerms for plot
overall.male.plot3 <- add_row(overall.male.plot3, GroupingTerm = "Behaviour")
overall.male.plot3 <- add_row(overall.male.plot3, GroupingTerm = "Immunology")
overall.male.plot3 <- add_row(overall.male.plot3, GroupingTerm = "Eye")
overall.male.plot3$GroupingTerm <- factor(overall.male.plot3$GroupingTerm, levels = c("Behaviour", "Morphology", "Metabolism", "Physiology", "Immunology", "Hematology", "Heart", "Hearing", "Eye", "All"))
overall.male.plot3$GroupingTerm <- factor(overall.male.plot3$GroupingTerm, rev(levels(overall.male.plot3$GroupingTerm)))
# str(overall.male.plot3)
```
Restructure MALE data for plotting
```{r}
overall3.male.sig <- gather(overall.male.plot3, parameter, value, c(lnCVR, lnRR), factor_key = TRUE) # lnVR,
lnCVR.ci <- overall3.male.sig %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
# lnVR.ci <- overall3.male.sig %>% filter(parameter == "lnVR") %>% mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3.male.sig %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4.male.sig <- bind_rows(lnCVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high) # lnVR.ci,
overall4.male.sig$label <- "CI not overlapping zero"
```
Plot Fig5b all significant results (CI not overlapping zero) for males
```{r}
Metameta_Fig3_male.sig <- overall4.male.sig %>%
ggplot(aes(y = GroupingTerm, x = value)) +
geom_errorbarh(aes(
xmin = ci.low,
xmax = ci.high
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(shape = parameter),
fill = "mediumaquamarine", color = "mediumaquamarine", size = 2.2,
show.legend = FALSE
) +
scale_x_continuous(
limits = c(0, 0.4),
breaks = c(0, 0.3),
name = "Effect size"
) +
geom_vline(
xintercept = 0,
color = "black",
linetype = "dashed"
) +
facet_grid(
cols = vars(parameter), rows = vars(label),
labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank()
)
# Metameta_Fig3_male.sig
```
#### Female Figure, significant traits
Female Fig5B sig
Prepare data for traits with CI not overlapping 0
create column with 1= different from zero, 0= zero included in CI
```{r}
# female-biased traits
meta.female.plot3.sig <- metacombo %>%
mutate(
sigCVR = ifelse(lnCVR_upper < 0, 1, 0),
sigVR = ifelse(lnVR_upper < 0, 1, 0),
sigRR = ifelse(lnRR_upper < 0, 1, 0)
)
# Significant subset for lnCVR
metacombo_female.plot3.CVR <- meta.female.plot3.sig %>%
filter(sigCVR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_female.plot3.CVR.all <- meta.female.plot3.sig %>%
filter(sigCVR == 1) %>%
nest()
# Significant subset for lnVR
metacombo_female.plot3.VR <- meta.female.plot3.sig %>%
filter(sigVR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_female.plot3.VR.all <- meta.female.plot3.sig %>%
filter(sigVR == 1) %>%
nest()
# Significant subset for lnRR
metacombo_female.plot3.RR <- meta.female.plot3.sig %>%
filter(sigRR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_female.plot3.RR.all <- meta.female.plot3.sig %>%
filter(sigRR == 1) %>%
nest()
# **Final fixed effects meta-analyses within grouping terms, with SE of the estimate
plot3.female.meta.CVR <- metacombo_female.plot3.CVR %>%
mutate(model_lnCVR = map(data, ~ metafor::rma.uni(
yi = .x$lnCVR, sei = (.x$lnCVR_upper - .x$lnCVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.female.meta.VR <- metacombo_female.plot3.VR %>%
mutate(model_lnVR = map(data, ~ metafor::rma.uni(
yi = .x$lnVR, sei = (.x$lnVR_upper - .x$lnVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.female.meta.RR <- metacombo_female.plot3.RR %>%
mutate(model_lnRR = map(data, ~ metafor::rma.uni(
yi = .x$lnRR, sei = (.x$lnRR_upper - .x$lnRR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
# Across all grouping terms #
plot3.female.meta.CVR.all <- metacombo_female.plot3.CVR.all %>%
mutate(model_lnCVR = map(data, ~ metafor::rma.uni(
yi = .x$lnCVR, sei = (.x$lnCVR_upper - .x$lnCVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.female.meta.CVR.all <- plot3.female.meta.CVR.all %>% mutate(GroupingTerm = "All")
plot3.female.meta.VR.all <- metacombo_female.plot3.VR.all %>%
mutate(model_lnVR = map(data, ~ metafor::rma.uni(
yi = .x$lnVR, sei = (.x$lnVR_upper - .x$lnVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.female.meta.VR.all <- plot3.female.meta.VR.all %>% mutate(GroupingTerm = "All")
plot3.female.meta.RR.all <- metacombo_female.plot3.RR.all %>%
mutate(model_lnRR = map(data, ~ metafor::rma.uni(
yi = .x$lnRR, sei = (.x$lnRR_upper - .x$lnRR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.female.meta.RR.all <- plot3.female.meta.RR.all %>% mutate(GroupingTerm = "All")
# Combine with separate grouping term results
plot3.female.meta.CVR <- bind_rows(plot3.female.meta.CVR, plot3.female.meta.CVR.all)
plot3.female.meta.VR <- bind_rows(plot3.female.meta.VR, plot3.female.meta.VR.all)
plot3.female.meta.RR <- bind_rows(plot3.female.meta.RR, plot3.female.meta.RR.all)
# **Re-structure data for each grouping term; delete un-used variables
plot3.female.meta.CVR.b <- as.data.frame(plot3.female.meta.CVR %>% group_by(GroupingTerm) %>%
mutate(
lnCVR = map_dbl(model_lnCVR, pluck(2)), lnCVR_lower = map_dbl(model_lnCVR, pluck(6)),
lnCVR_upper = map_dbl(model_lnCVR, pluck(7)), lnCVR_se = map_dbl(model_lnCVR, pluck(3))
))[, c(1, 4:7)]
add.row.hearing <- as.data.frame(t(c("Hearing", NA, NA, NA, NA))) %>% setNames(names(plot3.female.meta.CVR.b))
plot3.female.meta.CVR.b <- bind_rows(plot3.female.meta.CVR.b, add.row.hearing)
plot3.female.meta.CVR.b <- plot3.female.meta.CVR.b[order(plot3.female.meta.CVR.b$GroupingTerm), ]
plot3.female.meta.VR.b <- as.data.frame(plot3.female.meta.VR %>% group_by(GroupingTerm) %>%
mutate(
lnVR = map_dbl(model_lnVR, pluck(2)), lnVR_lower = map_dbl(model_lnVR, pluck(6)),
lnVR_upper = map_dbl(model_lnVR, pluck(7)), lnVR_se = map_dbl(model_lnVR, pluck(3))
))[, c(1, 4:7)]
plot3.female.meta.VR.b <- plot3.female.meta.VR.b[order(plot3.female.meta.VR.b$GroupingTerm), ]
plot3.female.meta.RR.b <- as.data.frame(plot3.female.meta.RR %>% group_by(GroupingTerm) %>%
mutate(
lnRR = map_dbl(model_lnRR, pluck(2)), lnRR_lower = map_dbl(model_lnRR, pluck(6)),
lnRR_upper = map_dbl(model_lnRR, pluck(7)), lnRR_se = map_dbl(model_lnRR, pluck(3))
))[, c(1, 4:7)]
plot3.female.meta.RR.b <- plot3.female.meta.RR.b[order(plot3.female.meta.RR.b$GroupingTerm), ]
overall.female.plot3 <- full_join(plot3.female.meta.CVR.b, plot3.female.meta.VR.b)
overall.female.plot3 <- full_join(overall.female.plot3, plot3.female.meta.RR.b)
overall.female.plot3$GroupingTerm <- factor(overall.female.plot3$GroupingTerm, levels = c("Behaviour", "Morphology", "Metabolism", "Physiology", "Immunology", "Hematology", "Heart", "Hearing", "Eye", "All"))
overall.female.plot3$GroupingTerm <- factor(overall.female.plot3$GroupingTerm, rev(levels(overall.female.plot3$GroupingTerm)))
```
Restructure data for plotting
```{r}
overall3.female.sig <- gather(overall.female.plot3, parameter, value, c(lnCVR, lnRR), factor_key = TRUE) # lnVR,
lnCVR.ci <- overall3.female.sig %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
# lnVR.ci <- overall3.female.sig %>% filter(parameter == "lnVR") %>% mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3.female.sig %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4.female.sig <- bind_rows(lnCVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high) # lnVR.ci,
overall4.female.sig$label <- "CI not overlapping zero"
```
Plot Fig5B all significant results (CI not overlapping zero, female )
```{r}
Metameta_Fig3_female.sig <- overall4.female.sig %>%
ggplot(aes(y = GroupingTerm, x = value)) +
geom_errorbarh(aes(
xmin = ci.low,
xmax = ci.high
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(shape = parameter),
fill = "salmon1", color = "salmon1", size = 2.2,
show.legend = FALSE
) +
scale_x_continuous(
limits = c(-0.4, 0),
breaks = c(-0.3, 0),
name = "Effect size"
) +
geom_vline(
xintercept = 0,
color = "black",
linetype = "dashed"
) +
facet_grid(
cols = vars(parameter), # rows = vars(label),
# labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank()
)
# Metameta_Fig3_female.sig (Figure 5B left panel)
```
#### Fig5 D >10%
Prepare data for traits with m/f difference > 10%
create column with 1= larger, 0= diff not larger than 10%
#### Male Fig 5D > 10% (male biased traits)
```{r}
meta.male.plot3.perc <- metacombo %>%
mutate(
percCVR = ifelse(lnCVR > log(11 / 10), 1, 0),
percVR = ifelse(lnVR > log(11 / 10), 1, 0),
percRR = ifelse(lnRR > log(11 / 10), 1, 0)
)
# Significant subset for lnCVR
metacombo_male.plot3.CVR.perc <- meta.male.plot3.perc %>%
filter(percCVR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_male.plot3.CVR.perc.all <- meta.male.plot3.perc %>%
filter(percCVR == 1) %>%
nest()
# Significant subset for lnVR
metacombo_male.plot3.VR.perc <- meta.male.plot3.perc %>%
filter(percVR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_male.plot3.VR.perc.all <- meta.male.plot3.perc %>%
filter(percVR == 1) %>%
nest()
# Significant subset for lnRR
metacombo_male.plot3.RR.perc <- meta.male.plot3.perc %>%
filter(percRR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_male.plot3.RR.perc.all <- meta.male.plot3.perc %>%
filter(percRR == 1) %>%
nest()
# **Final fixed effects meta-analyses within grouping terms and across grouping terms, with SE of the estimate
plot3.male.meta.CVR.perc <- metacombo_male.plot3.CVR.perc %>%
mutate(model_lnCVR = map(data, ~ metafor::rma.uni(
yi = .x$lnCVR, sei = (.x$lnCVR_upper - .x$lnCVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.male.meta.VR.perc <- metacombo_male.plot3.VR.perc %>%
mutate(model_lnVR = map(data, ~ metafor::rma.uni(
yi = .x$lnVR, sei = (.x$lnVR_upper - .x$lnVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.male.meta.RR.perc <- metacombo_male.plot3.RR.perc %>%
mutate(model_lnRR = map(data, ~ metafor::rma.uni(
yi = .x$lnRR, sei = (.x$lnRR_upper - .x$lnRR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
# Across all grouping terms #
plot3.male.meta.CVR.perc.all <- metacombo_male.plot3.CVR.perc.all %>%
mutate(model_lnCVR = map(data, ~ metafor::rma.uni(
yi = .x$lnCVR, sei = (.x$lnCVR_upper - .x$lnCVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.male.meta.CVR.perc.all <- plot3.male.meta.CVR.perc.all %>% mutate(GroupingTerm = "All")
plot3.male.meta.VR.perc.all <- metacombo_male.plot3.VR.perc.all %>%
mutate(model_lnVR = map(data, ~ metafor::rma.uni(
yi = .x$lnVR, sei = (.x$lnVR_upper - .x$lnVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.male.meta.VR.perc.all <- plot3.male.meta.VR.perc.all %>% mutate(GroupingTerm = "All")
plot3.male.meta.RR.perc.all <- metacombo_male.plot3.RR.perc.all %>%
mutate(model_lnRR = map(data, ~ metafor::rma.uni(
yi = .x$lnRR, sei = (.x$lnRR_upper - .x$lnRR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.male.meta.RR.perc.all <- plot3.male.meta.RR.perc.all %>% mutate(GroupingTerm = "All")
# Combine with separate grouping term results
plot3.male.meta.CVR.perc <- bind_rows(plot3.male.meta.CVR.perc, plot3.male.meta.CVR.perc.all)
plot3.male.meta.VR.perc <- bind_rows(plot3.male.meta.VR.perc, plot3.male.meta.VR.perc.all)
plot3.male.meta.RR.perc <- bind_rows(plot3.male.meta.RR.perc, plot3.male.meta.RR.perc.all)
# **Re-structure data for each grouping term; delete un-used variables: "Hearing missing for all 3 parameters"
plot3.male.meta.CVR.perc.b <- as.data.frame(plot3.male.meta.CVR.perc %>% group_by(GroupingTerm) %>%
mutate(
lnCVR = map_dbl(model_lnCVR, pluck(2)), lnCVR_lower = map_dbl(model_lnCVR, pluck(6)),
lnCVR_upper = map_dbl(model_lnCVR, pluck(7)), lnCVR_se = map_dbl(model_lnCVR, pluck(3))
))[, c(1, 4:7)]
add.row.hearing <- as.data.frame(t(c("Hearing", NA, NA, NA, NA))) %>% setNames(names(plot3.male.meta.CVR.perc.b))
plot3.male.meta.CVR.perc.b <- rbind(plot3.male.meta.CVR.perc.b, add.row.hearing)
plot3.male.meta.CVR.perc.b <- plot3.male.meta.CVR.perc.b[order(plot3.male.meta.CVR.perc.b$GroupingTerm), ]
plot3.male.meta.VR.perc.b <- as.data.frame(plot3.male.meta.VR.perc %>% group_by(GroupingTerm) %>%
mutate(
lnVR = map_dbl(model_lnVR, pluck(2)), lnVR_lower = map_dbl(model_lnVR, pluck(6)),
lnVR_upper = map_dbl(model_lnVR, pluck(7)), lnVR_se = map_dbl(model_lnVR, pluck(3))
))[, c(1, 4:7)]
add.row.hearing <- as.data.frame(t(c("Hearing", NA, NA, NA, NA))) %>% setNames(names(plot3.male.meta.VR.perc.b))
plot3.male.meta.VR.perc.b <- rbind(plot3.male.meta.VR.perc.b, add.row.hearing)
plot3.male.meta.VR.perc.b <- plot3.male.meta.VR.perc.b[order(plot3.male.meta.VR.perc.b$GroupingTerm), ]
plot3.male.meta.RR.perc.b <- as.data.frame(plot3.male.meta.RR.perc %>% group_by(GroupingTerm) %>%
mutate(
lnRR = map_dbl(model_lnRR, pluck(2)), lnRR_lower = map_dbl(model_lnRR, pluck(6)),
lnRR_upper = map_dbl(model_lnRR, pluck(7)), lnRR_se = map_dbl(model_lnRR, pluck(3))
))[, c(1, 4:7)]
add.row.hearing <- as.data.frame(t(c("Hearing", NA, NA, NA, NA))) %>%
setNames(names(plot3.male.meta.RR.perc.b))
plot3.male.meta.RR.perc.b <- rbind(plot3.male.meta.RR.perc.b, add.row.hearing)
add.row.eye <- as.data.frame(t(c("Eye", NA, NA, NA, NA))) %>%
setNames(names(plot3.male.meta.RR.perc.b))
plot3.male.meta.RR.perc.b <- rbind(plot3.male.meta.RR.perc.b, add.row.eye)
plot3.male.meta.RR.perc.b <- plot3.male.meta.RR.perc.b[order(plot3.male.meta.RR.perc.b$GroupingTerm), ]
plot3.male.meta.CVR.Vr.perc <- full_join(plot3.male.meta.CVR.perc.b, plot3.male.meta.VR.perc.b)
overall.male.plot3.perc <- full_join(plot3.male.meta.CVR.Vr.perc, plot3.male.meta.RR.perc.b)
overall.male.plot3.perc$GroupingTerm <- factor(overall.male.plot3.perc$GroupingTerm, levels = c("Behaviour", "Morphology", "Metabolism", "Physiology", "Immunology", "Hematology", "Heart", "Hearing", "Eye", "All"))
overall.male.plot3.perc$GroupingTerm <- factor(overall.male.plot3.perc$GroupingTerm, rev(levels(overall.male.plot3.perc$GroupingTerm)))
```
Restructure data for plotting : Male biased, 10% difference
```{r}
overall3.perc <- gather(overall.male.plot3.perc, parameter, value, c(lnCVR, lnRR), factor_key = TRUE) # lnVR,
lnCVR.ci <- overall3.perc %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
# lnVR.ci <- overall3.perc %>% filter(parameter == "lnVR") %>% mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3.perc %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4.male.perc <- bind_rows(lnCVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high) # lnVR.ci,
overall4.male.perc$label <- "Sex difference in m/f ratios > 10%"
overall4.male.perc$value <- as.numeric(overall4.male.perc$value)
overall4.male.perc$ci.low <- as.numeric(overall4.male.perc$ci.low)
overall4.male.perc$ci.high <- as.numeric(overall4.male.perc$ci.high)
```
Plot Fig5D all >10% difference (male bias)
```{r}
Metameta_Fig3_male.perc <- overall4.male.perc %>% # filter(., GroupingTerm != "Hearing") %>%
ggplot(aes(y = GroupingTerm, x = value)) +
geom_errorbarh(aes(
xmin = ci.low,
xmax = ci.high
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(
shape = parameter,
fill = parameter
),
color = "mediumaquamarine", size = 2.2,
show.legend = FALSE
) +
scale_x_continuous(
limits = c(-0.2, 0.62),
breaks = c(0, 0.3),
name = "Effect size"
) +
geom_vline(
xintercept = 0,
color = "black",
linetype = "dashed"
) +
facet_grid(
cols = vars(parameter), rows = vars(label),
labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_blank(),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_text(hjust = 0.5, size = 14),
axis.title.y = element_blank()
)
# Metameta_Fig3_male.perc (Figure 5D right panel)
```
#### Female Fig 5D >10%
```{r}
meta.plot3.perc <- metacombo %>%
mutate(
percCVR = ifelse(lnCVR < log(9 / 10), 1, 0),
percVR = ifelse(lnVR < log(9 / 10), 1, 0),
percRR = ifelse(lnRR < log(9 / 10), 1, 0)
)
# Significant subset for lnCVR
metacombo_plot3.CVR.perc <- meta.plot3.perc %>%
filter(percCVR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_plot3.CVR.perc.all <- meta.plot3.perc %>%
filter(percCVR == 1) %>%
nest()
# Significant subset for lnVR
metacombo_plot3.VR.perc <- meta.plot3.perc %>%
filter(percVR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_plot3.VR.perc.all <- meta.plot3.perc %>%
filter(percVR == 1) %>%
nest()
# Significant subset for lnRR
metacombo_plot3.RR.perc <- meta.plot3.perc %>%
filter(percRR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_plot3.RR.perc.all <- meta.plot3.perc %>%
filter(percRR == 1) %>%
nest()
# **Final fixed effects meta-analyses within grouping terms, with SE of the estimate
plot3.meta.CVR.perc <- metacombo_plot3.CVR.perc %>%
mutate(model_lnCVR = map(data, ~ metafor::rma.uni(
yi = .x$lnCVR, sei = (.x$lnCVR_upper - .x$lnCVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.meta.VR.perc <- metacombo_plot3.VR.perc %>%
mutate(model_lnVR = map(data, ~ metafor::rma.uni(
yi = .x$lnVR, sei = (.x$lnVR_upper - .x$lnVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.meta.RR.perc <- metacombo_plot3.RR.perc %>%
mutate(model_lnRR = map(data, ~ metafor::rma.uni(
yi = .x$lnRR, sei = (.x$lnRR_upper - .x$lnRR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
# Across all grouping terms #
plot3.meta.CVR.perc.all <- metacombo_plot3.CVR.perc.all %>%
mutate(model_lnCVR = map(data, ~ metafor::rma.uni(
yi = .x$lnCVR, sei = (.x$lnCVR_upper - .x$lnCVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.meta.CVR.perc.all <- plot3.meta.CVR.perc.all %>% mutate(GroupingTerm = "All")
plot3.meta.VR.perc.all <- metacombo_plot3.VR.perc.all %>%
mutate(model_lnVR = map(data, ~ metafor::rma.uni(
yi = .x$lnVR, sei = (.x$lnVR_upper - .x$lnVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.meta.VR.perc.all <- plot3.meta.VR.perc.all %>% mutate(GroupingTerm = "All")
plot3.meta.RR.perc.all <- metacombo_plot3.RR.perc.all %>%
mutate(model_lnRR = map(data, ~ metafor::rma.uni(
yi = .x$lnRR, sei = (.x$lnRR_upper - .x$lnRR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.meta.RR.perc.all <- plot3.meta.RR.perc.all %>% mutate(GroupingTerm = "All")
# Combine with separate grouping term results
plot3.meta.CVR.perc <- bind_rows(plot3.meta.CVR.perc, plot3.meta.CVR.perc.all)
plot3.meta.VR.perc <- bind_rows(plot3.meta.VR.perc, plot3.meta.VR.perc.all)
plot3.meta.RR.perc <- bind_rows(plot3.meta.RR.perc, plot3.meta.RR.perc.all)
# **Re-structure data for each grouping term; delete un-used variables: "Hearing missing for all 3 parameters"
plot3.meta.CVR.perc.b <- as.data.frame(plot3.meta.CVR.perc %>% group_by(GroupingTerm) %>%
mutate(
lnCVR = map_dbl(model_lnCVR, pluck(2)), lnCVR_lower = map_dbl(model_lnCVR, pluck(6)),
lnCVR_upper = map_dbl(model_lnCVR, pluck(7)), lnCVR_se = map_dbl(model_lnCVR, pluck(3))
))[, c(1, 4:7)]
add.row.hearing <- as.data.frame(t(c("Hearing", NA, NA, NA, NA))) %>% setNames(names(plot3.meta.CVR.perc.b))
plot3.meta.CVR.perc.b <- rbind(plot3.meta.CVR.perc.b, add.row.hearing)
plot3.meta.CVR.perc.b <- plot3.meta.CVR.perc.b[order(plot3.meta.CVR.perc.b$GroupingTerm), ]
plot3.meta.VR.perc.b <- as.data.frame(plot3.meta.VR.perc %>% group_by(GroupingTerm) %>%
mutate(
lnVR = map_dbl(model_lnVR, pluck(2)), lnVR_lower = map_dbl(model_lnVR, pluck(6)),
lnVR_upper = map_dbl(model_lnVR, pluck(7)), lnVR_se = map_dbl(model_lnVR, pluck(3))
))[, c(1, 4:7)]
add.row.hearing <- as.data.frame(t(c("Hearing", NA, NA, NA, NA))) %>% setNames(names(plot3.meta.VR.perc.b))
plot3.meta.VR.perc.b <- rbind(plot3.meta.VR.perc.b, add.row.hearing)
plot3.meta.VR.perc.b <- plot3.meta.VR.perc.b[order(plot3.meta.VR.perc.b$GroupingTerm), ]
plot3.meta.RR.perc.b <- as.data.frame(plot3.meta.RR.perc %>% group_by(GroupingTerm) %>%
mutate(
lnRR = map_dbl(model_lnRR, pluck(2)), lnRR_lower = map_dbl(model_lnRR, pluck(6)),
lnRR_upper = map_dbl(model_lnRR, pluck(7)), lnRR_se = map_dbl(model_lnRR, pluck(3))
))[, c(1, 4:7)]
add.row.hearing <- as.data.frame(t(c("Hearing", NA, NA, NA, NA))) %>% setNames(names(plot3.meta.RR.perc.b))
plot3.meta.RR.perc.b <- rbind(plot3.meta.RR.perc.b, add.row.hearing)
add.row.hematology <- as.data.frame(t(c("Hematology", NA, NA, NA, NA))) %>%
setNames(names(plot3.meta.RR.perc.b))
plot3.meta.RR.perc.b <- rbind(plot3.meta.RR.perc.b, add.row.hematology)
plot3.meta.RR.perc.b <- plot3.meta.RR.perc.b[order(plot3.meta.RR.perc.b$GroupingTerm), ]
plot3.meta.CVR.perc.c <- full_join(plot3.meta.CVR.perc.b, plot3.meta.VR.perc.b)
overall.plot3.perc <- full_join(plot3.meta.CVR.perc.c, plot3.meta.RR.perc.b)
overall.plot3.perc$GroupingTerm <- factor(overall.plot3.perc$GroupingTerm, levels = c("Behaviour", "Morphology", "Metabolism", "Physiology", "Immunology", "Hematology", "Heart", "Hearing", "Eye", "All"))
overall.plot3.perc$GroupingTerm <- factor(overall.plot3.perc$GroupingTerm, rev(levels(overall.plot3.perc$GroupingTerm)))
```
Restructure data for plotting
Female bias, 10 percent difference
```{r}
overall3.perc <- gather(overall.plot3.perc, parameter, value, c(lnCVR, lnRR), factor_key = TRUE) # lnVR,
lnCVR.ci <- overall3.perc %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
# lnVR.ci <- overall3.perc %>% filter(parameter == "lnVR") %>% mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3.perc %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4.perc <- bind_rows(lnCVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high) # lnVR.ci,
overall4.perc$label <- "Sex difference in m/f ratios > 10%"
overall4.perc$value <- as.numeric(overall4.perc$value)
overall4.perc$ci.low <- as.numeric(overall4.perc$ci.low)
overall4.perc$ci.high <- as.numeric(overall4.perc$ci.high)
```
Plot Fig5D all >10% difference (female)
```{r}
Metameta_Fig3_female.perc <- overall4.perc %>%
ggplot(aes(y = GroupingTerm, x = value)) +
geom_errorbarh(aes(
xmin = ci.low,
xmax = ci.high
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(shape = parameter),
fill = "salmon1", color = "salmon1", size = 2.2,
show.legend = FALSE
) +
# scale_shape_manual(values =
scale_x_continuous(
limits = c(-0.53, 0.2),
breaks = c(-0.3, 0),
name = "Effect size"
) +
geom_vline(
xintercept = 0,
color = "black",
linetype = "dashed"
) +
facet_grid(
cols = vars(parameter), # rows = vars(label),
# labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_blank(),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_text(hjust = 0.5, size = 14),
axis.title.y = element_blank()
)
# Metameta_Fig3_female.perc (Figure 5D left panel)
```
#### Plot Fig5: plots combined
```{r}
library(ggpubr)
Fig5b <- ggarrange(Metameta_Fig3_female.sig, Metameta_Fig3_male.sig,
ncol = 2, nrow = 1, widths = c(1, 1.20), heights = c(1, 1)
)
Fig5d <- ggarrange(Metameta_Fig3_female.perc, Metameta_Fig3_male.perc,
ncol = 2, nrow = 1, widths = c(1, 1.20), heights = c(1, 1)
)
# end combination Figure 5
Fig5 <- ggarrange(malebias_Fig2_sigtraits, malebias_Fig2_over10, Fig5b, Fig5d, ncol = 1, nrow = 4, heights = c(2.3, 2, 2.1, 2), labels = c("A", " ", "B", " "))
Fig5
```
## Heterogeneity
#### FIGURE 4 (Second-order meta analysis on heterogeneity)
Create matrix to store results for all traits
```{r}
results.allhetero.grouping <- as.data.frame(cbind(c(1:n), matrix(rep(0, n * 30), ncol = 30)))
names(results.allhetero.grouping) <- c(
"id", "sigma2_strain.CVR", "sigma2_center.CVR", "sigma2_error.CVR", "s.nlevels.strain.CVR",
"s.nlevels.center.CVR", "s.nlevels.error.CVR", "sigma2_strain.VR", "sigma2_center.VR", "sigma2_error.VR", "s.nlevels.strain.VR",
"s.nlevels.center.VR", "s.nlevels.error.VR", "sigma2_strain.RR", "sigma2_center.RR", "sigma2_error.RR", "s.nlevels.strain.RR",
"s.nlevels.center.RR", "s.nlevels.error.RR", "lnCVR", "lnCVR_lower", "lnCVR_upper", "lnCVR_se", "lnVR", "lnVR_lower", "lnVR_upper",
"lnVR_se", "lnRR", "lnRR_lower", "lnRR_upper", "lnRR_se"
)
```
LOOP
Parameters to extract from metafor (sigma2's, s.nlevels)
```{r}
for (t in 1:n) {
tryCatch(
{
data_par_age <- data_subset_parameterid_individual_by_age(data, t, age_min = 0, age_center = 100)
population_stats <- calculate_population_stats(data_par_age)
results <- create_meta_analysis_effect_sizes(population_stats)
# lnCVR, logaritm of the ratio of male and female coefficients of variance
cvr. <- metafor::rma.mv(yi = effect_size_CVR, V = sample_variance_CVR, random = list(
~ 1 | strain_name, ~ 1 | production_center,
~ 1 | err
), control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), data = results)
results.allhetero.grouping[t, 2] <- cvr.$sigma2[1]
results.allhetero.grouping[t, 3] <- cvr.$sigma2[2]
results.allhetero.grouping[t, 4] <- cvr.$sigma2[3]
results.allhetero.grouping[t, 5] <- cvr.$s.nlevels[1]
results.allhetero.grouping[t, 6] <- cvr.$s.nlevels[2]
results.allhetero.grouping[t, 7] <- cvr.$s.nlevels[3]
results.allhetero.grouping[t, 20] <- cvr.$b
results.allhetero.grouping[t, 21] <- cvr.$ci.lb
results.allhetero.grouping[t, 22] <- cvr.$ci.ub
results.allhetero.grouping[t, 23] <- cvr.$se
# lnVR, male to female variability ratio (logarithm of male and female standard deviations)
vr. <- metafor::rma.mv(yi = effect_size_VR, V = sample_variance_VR, random = list(
~ 1 | strain_name, ~ 1 | production_center,
~ 1 | err
), control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), data = results)
results.allhetero.grouping[t, 8] <- vr.$sigma2[1]
results.allhetero.grouping[t, 9] <- vr.$sigma2[2]
results.allhetero.grouping[t, 10] <- vr.$sigma2[3]
results.allhetero.grouping[t, 11] <- vr.$s.nlevels[1]
results.allhetero.grouping[t, 12] <- vr.$s.nlevels[2]
results.allhetero.grouping[t, 13] <- vr.$s.nlevels[3]
results.allhetero.grouping[t, 24] <- vr.$b
results.allhetero.grouping[t, 25] <- vr.$ci.lb
results.allhetero.grouping[t, 26] <- vr.$ci.ub
results.allhetero.grouping[t, 27] <- vr.$se
# lnRR, response ratio (logarithm of male and female means)
rr. <- metafor::rma.mv(yi = effect_size_RR, V = sample_variance_RR, random = list(
~ 1 | strain_name, ~ 1 | production_center,
~ 1 | err
), control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), data = results)
results.allhetero.grouping[t, 14] <- rr.$sigma2[1]
results.allhetero.grouping[t, 15] <- rr.$sigma2[2]
results.allhetero.grouping[t, 16] <- rr.$sigma2[3]
results.allhetero.grouping[t, 17] <- rr.$s.nlevels[1]
results.allhetero.grouping[t, 18] <- rr.$s.nlevels[2]
results.allhetero.grouping[t, 19] <- rr.$s.nlevels[3]
results.allhetero.grouping[t, 28] <- rr.$b
results.allhetero.grouping[t, 29] <- rr.$ci.lb
results.allhetero.grouping[t, 30] <- rr.$ci.ub
results.allhetero.grouping[t, 31] <- rr.$se
},
error = function(e) {
cat("ERROR :", conditionMessage(e), "\n")
}
)
}
```
#### Exclude traits, merge datasets
```{r}
results.allhetero.grouping2 <- results.allhetero.grouping[results.allhetero.grouping$s.nlevels.strain.VR != 0, ]
# nrow(results.allhetero.grouping2) #218
```
Merge data sets containing metafor results with procedure etc. names
```{r}
# procedures <- read.csv(here("export", "procedures.csv"))
results.allhetero.grouping2$parameter_group <- data$parameter_group[match(results.allhetero.grouping2$id, data$id)]
results.allhetero.grouping2$procedure <- data$procedure_name[match(results.allhetero.grouping2$id, data$id)]
results.allhetero.grouping2$GroupingTerm <- procedures$GroupingTerm[match(results.allhetero.grouping2$procedure, procedures$procedure)]
results.allhetero.grouping2$parameter_name <- data$parameter_name[match(results.allhetero.grouping2$id, data$id)]
```
#### Correlated parameters
```{r}
metahetero1 <- results.allhetero.grouping2
# length(unique(metahetero1$procedure)) #18
# length(unique(metahetero1$GroupingTerm)) #9
# length(unique(metahetero1$parameter_group)) # 149
# length(unique(metahetero1$parameter_name)) #218
# Count of number of parameter names (correlated sub-traits) in each parameter group (par_group_size)
metahetero1b <-
metahetero1 %>%
group_by(parameter_group) %>%
mutate(par_group_size = n_distinct(parameter_name))
metahetero1$par_group_size <- metahetero1b$par_group_size[match(metahetero1$parameter_group, metahetero1b$parameter_group)]
# Create subsets with > 1 count (par_group_size > 1)
metahetero1_sub <- subset(metahetero1, par_group_size > 1) # 90 observations
# str(metahetero1_sub)
# metahetero1_sub$sampleSize <- as.numeric(metahetero1_sub$sampleSize) #from previous analysis? don't think is used: : delete in final version
# Nest data
n_count. <- metahetero1_sub %>%
group_by(parameter_group) %>%
# mutate(raw_N = sum(sampleSize)) %>% #don't think is necessary: delete in final version
nest()
# meta-analysis preparation
model_count. <- n_count. %>%
mutate(
model_lnRR = map(data, ~ robu(.x$lnRR ~ 1,
data = .x, studynum = .x$id, modelweights = c("CORR"), rho = 0.8,
small = TRUE, var.eff.size = (.x$lnRR_se)^2
)),
model_lnVR = map(data, ~ robu(.x$lnVR ~ 1,
data = .x, studynum = .x$id, modelweights = c("CORR"), rho = 0.8,
small = TRUE, var.eff.size = (.x$lnVR_se)^2
)),
model_lnCVR = map(data, ~ robu(.x$lnCVR ~ 1,
data = .x, studynum = .x$id, modelweights = c("CORR"), rho = 0.8,
small = TRUE, var.eff.size = (.x$lnCVR_se)^2
))
)
# Robumeta object details:
# str(model_count.$model_lnCVR[[1]])
## *Perform meta-analyses on correlated sub-traits, using robumeta
# Shinichi: We think we want to use these for further analyses:
# residual variance: as.numeric(robu_fit$mod_info$term1) (same as 'mod_info$tau.sq')
# sample size: robu_fit$N
## **Extract and save parameter estimates
count_fun. <- function(mod_sub) {
return(c(as.numeric(mod_sub$mod_info$term1), mod_sub$N))
}
robusub_RR. <- model_count. %>%
transmute(parameter_group, estimatelnRR = map(model_lnRR, count_fun.)) %>%
mutate(r = map(estimatelnRR, ~ data.frame(t(.)))) %>%
unnest(r) %>%
select(-estimatelnRR) %>%
purrr::set_names(c("parameter_group", "var.RR", "N.RR"))
robusub_CVR. <- model_count. %>%
transmute(parameter_group, estimatelnCVR = map(model_lnCVR, count_fun.)) %>%
mutate(r = map(estimatelnCVR, ~ data.frame(t(.)))) %>%
unnest(r) %>%
select(-estimatelnCVR) %>%
purrr::set_names(c("parameter_group", "var.CVR", "N.CVR"))
robusub_VR. <- model_count. %>%
transmute(parameter_group, estimatelnVR = map(model_lnVR, count_fun.)) %>%
mutate(r = map(estimatelnVR, ~ data.frame(t(.)))) %>%
unnest(r) %>%
select(-estimatelnVR) %>%
purrr::set_names(c("parameter_group", "var.VR", "N.VR"))
robu_all. <- full_join(robusub_CVR., robusub_VR.) %>% full_join(., robusub_RR.)
```
Merge the two data sets (the new [robu_all.] and the initial [uncorrelated sub-traits with count = 1])
In this step, we
1) merge the N from robumeta and the N from metafor (s.nlevels.error) together into the same columns (N.RR, N.VR, N.CVR)
2) calculate the total variance for metafor models as the sum of random effect variances and the residual error, then add in the same columns together with the residual variances from robumeta
```{r}
metahetero_all <- metahetero1 %>%
filter(par_group_size == 1) %>%
as_tibble()
metahetero_all$N.RR <- metahetero_all$s.nlevels.error.RR
metahetero_all$N.CVR <- metahetero_all$s.nlevels.error.CVR
metahetero_all$N.VR <- metahetero_all$s.nlevels.error.VR
metahetero_all$var.RR <- log(sqrt(metahetero_all$sigma2_strain.RR + metahetero_all$sigma2_center.RR + metahetero_all$sigma2_error.RR))
metahetero_all$var.VR <- log(sqrt(metahetero_all$sigma2_strain.VR + metahetero_all$sigma2_center.VR + metahetero_all$sigma2_error.VR))
metahetero_all$var.CVR <- log(sqrt(metahetero_all$sigma2_strain.CVR + metahetero_all$sigma2_center.CVR + metahetero_all$sigma2_error.CVR))
# str(metahetero_all)
# str(robu_all.)
metahetero_all <- metahetero_all %>% mutate(
var.RR = if_else(var.RR == -Inf, -7, var.RR),
var.VR = if_else(var.VR == -Inf, -5, var.VR),
var.CVR = if_else(var.CVR == -Inf, -6, var.CVR)
)
# **Combine data
## Step1
combinedmetahetero <- bind_rows(robu_all., metahetero_all)
# glimpse(combinedmetahetero)
# Steps 2&3
metacombohetero <- combinedmetahetero
metacombohetero$counts <- metahetero1$par_group_size[match(metacombohetero$parameter_group, metahetero1$parameter_group)]
metacombohetero$procedure2 <- metahetero1$procedure[match(metacombohetero$parameter_group, metahetero1$parameter_group)]
metacombohetero$GroupingTerm2 <- metahetero1$GroupingTerm[match(metacombohetero$parameter_group, metahetero1$parameter_group)]
# **Clean-up and rename
metacombohetero <- metacombohetero[, c(1:7, 43:45)]
names(metacombohetero)[9] <- "procedure"
names(metacombohetero)[10] <- "GroupingTerm"
```
#### Meta-analysis of heterogeneity
```{r}
## *Perform meta-meta-analysis (3 for each of the 9 grouping terms: var.CVR, var.VR, var.RR)
metacombohetero_final <- metacombohetero %>%
group_by(GroupingTerm) %>%
nest()
# Final fixed effects meta-analyses within grouping terms, with SE of the estimate
# metacombohetero$var.CVR
heterog1 <- metacombohetero_final %>%
mutate(
model_heteroCVR = map(data, ~ metafor::rma.uni(
yi = .x$var.CVR, sei = sqrt(1 / 2 * (.x$N.CVR - 1)),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 10000, stepadj = 0.5), verbose = F
)),
model_heteroVR = map(data, ~ metafor::rma.uni(
yi = .x$var.VR, sei = sqrt(1 / 2 * (.x$N.VR - 1)),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 10000, stepadj = 0.5), verbose = F
)),
model_heteroRR = map(data, ~ metafor::rma.uni(
yi = .x$var.RR, sei = sqrt(1 / 2 * (.x$N.RR - 1)),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 10000, stepadj = 0.5), verbose = F
))
)
# **Re-structure data for each grouping term; extract heterogenenity/variance terms; delete un-used variables
Behaviour. <- heterog1 %>%
filter(., GroupingTerm == "Behaviour") %>%
select(., -data) %>%
mutate(
heteroCVR = .[[2]][[1]]$b, heteroCVR_lower = .[[2]][[1]]$ci.lb, heteroCVR_upper = .[[2]][[1]]$ci.ub, heteroCVR_se = .[[2]][[1]]$se,
heteroVR = .[[3]][[1]]$b, heteroVR_lower = .[[3]][[1]]$ci.lb, heteroVR_upper = .[[3]][[1]]$ci.ub, heteroVR_se = .[[3]][[1]]$se,
heteroRR = .[[4]][[1]]$b, heteroRR_lower = .[[4]][[1]]$ci.lb, heteroRR_upper = .[[4]][[1]]$ci.ub, heteroRR_se = .[[4]][[1]]$se
) %>%
select(., GroupingTerm, heteroCVR:heteroRR_se)
Immunology. <- heterog1 %>%
filter(., GroupingTerm == "Immunology") %>%
select(., -data) %>%
mutate(
heteroCVR = .[[2]][[1]]$b, heteroCVR_lower = .[[2]][[1]]$ci.lb, heteroCVR_upper = .[[2]][[1]]$ci.ub, heteroCVR_se = .[[2]][[1]]$se,
heteroVR = .[[3]][[1]]$b, heteroVR_lower = .[[3]][[1]]$ci.lb, heteroVR_upper = .[[3]][[1]]$ci.ub, heteroVR_se = .[[3]][[1]]$se,
heteroRR = .[[4]][[1]]$b, heteroRR_lower = .[[4]][[1]]$ci.lb, heteroRR_upper = .[[4]][[1]]$ci.ub, heteroRR_se = .[[4]][[1]]$se
) %>%
select(., GroupingTerm, heteroCVR:heteroRR_se)
Hematology. <- heterog1 %>%
filter(., GroupingTerm == "Hematology") %>%
select(., -data) %>%
mutate(
heteroCVR = .[[2]][[1]]$b, heteroCVR_lower = .[[2]][[1]]$ci.lb, heteroCVR_upper = .[[2]][[1]]$ci.ub, heteroCVR_se = .[[2]][[1]]$se,
heteroVR = .[[3]][[1]]$b, heteroVR_lower = .[[3]][[1]]$ci.lb, heteroVR_upper = .[[3]][[1]]$ci.ub, heteroVR_se = .[[3]][[1]]$se,
heteroRR = .[[4]][[1]]$b, heteroRR_lower = .[[4]][[1]]$ci.lb, heteroRR_upper = .[[4]][[1]]$ci.ub, heteroRR_se = .[[4]][[1]]$se
) %>%
select(., GroupingTerm, heteroCVR:heteroRR_se)
Hearing. <- heterog1 %>%
filter(., GroupingTerm == "Hearing") %>%
select(., -data) %>%
mutate(
heteroCVR = .[[2]][[1]]$b, heteroCVR_lower = .[[2]][[1]]$ci.lb, heteroCVR_upper = .[[2]][[1]]$ci.ub, heteroCVR_se = .[[2]][[1]]$se,
heteroVR = .[[3]][[1]]$b, heteroVR_lower = .[[3]][[1]]$ci.lb, heteroVR_upper = .[[3]][[1]]$ci.ub, heteroVR_se = .[[3]][[1]]$se,
heteroRR = .[[4]][[1]]$b, heteroRR_lower = .[[4]][[1]]$ci.lb, heteroRR_upper = .[[4]][[1]]$ci.ub, heteroRR_se = .[[4]][[1]]$se
) %>%
select(., GroupingTerm, heteroCVR:heteroRR_se)
Physiology. <- heterog1 %>%
filter(., GroupingTerm == "Physiology") %>%
select(., -data) %>%
mutate(
heteroCVR = .[[2]][[1]]$b, heteroCVR_lower = .[[2]][[1]]$ci.lb, heteroCVR_upper = .[[2]][[1]]$ci.ub, heteroCVR_se = .[[2]][[1]]$se,
heteroVR = .[[3]][[1]]$b, heteroVR_lower = .[[3]][[1]]$ci.lb, heteroVR_upper = .[[3]][[1]]$ci.ub, heteroVR_se = .[[3]][[1]]$se,
heteroRR = .[[4]][[1]]$b, heteroRR_lower = .[[4]][[1]]$ci.lb, heteroRR_upper = .[[4]][[1]]$ci.ub, heteroRR_se = .[[4]][[1]]$se
) %>%
select(., GroupingTerm, heteroCVR:heteroRR_se)
Metabolism. <- heterog1 %>%
filter(., GroupingTerm == "Metabolism") %>%
select(., -data) %>%
mutate(
heteroCVR = .[[2]][[1]]$b, heteroCVR_lower = .[[2]][[1]]$ci.lb, heteroCVR_upper = .[[2]][[1]]$ci.ub, heteroCVR_se = .[[2]][[1]]$se,
heteroVR = .[[3]][[1]]$b, heteroVR_lower = .[[3]][[1]]$ci.lb, heteroVR_upper = .[[3]][[1]]$ci.ub, heteroVR_se = .[[3]][[1]]$se,
heteroRR = .[[4]][[1]]$b, heteroRR_lower = .[[4]][[1]]$ci.lb, heteroRR_upper = .[[4]][[1]]$ci.ub, heteroRR_se = .[[4]][[1]]$se
) %>%
select(., GroupingTerm, heteroCVR:heteroRR_se)
Morphology. <- heterog1 %>%
filter(., GroupingTerm == "Morphology") %>%
select(., -data) %>%
mutate(
heteroCVR = .[[2]][[1]]$b, heteroCVR_lower = .[[2]][[1]]$ci.lb, heteroCVR_upper = .[[2]][[1]]$ci.ub, heteroCVR_se = .[[2]][[1]]$se,
heteroVR = .[[3]][[1]]$b, heteroVR_lower = .[[3]][[1]]$ci.lb, heteroVR_upper = .[[3]][[1]]$ci.ub, heteroVR_se = .[[3]][[1]]$se,
heteroRR = .[[4]][[1]]$b, heteroRR_lower = .[[4]][[1]]$ci.lb, heteroRR_upper = .[[4]][[1]]$ci.ub, heteroRR_se = .[[4]][[1]]$se
) %>%
select(., GroupingTerm, heteroCVR:heteroRR_se)
Heart. <- heterog1 %>%
filter(., GroupingTerm == "Heart") %>%
select(., -data) %>%
mutate(
heteroCVR = .[[2]][[1]]$b, heteroCVR_lower = .[[2]][[1]]$ci.lb, heteroCVR_upper = .[[2]][[1]]$ci.ub, heteroCVR_se = .[[2]][[1]]$se,
heteroVR = .[[3]][[1]]$b, heteroVR_lower = .[[3]][[1]]$ci.lb, heteroVR_upper = .[[3]][[1]]$ci.ub, heteroVR_se = .[[3]][[1]]$se,
heteroRR = .[[4]][[1]]$b, heteroRR_lower = .[[4]][[1]]$ci.lb, heteroRR_upper = .[[4]][[1]]$ci.ub, heteroRR_se = .[[4]][[1]]$se
) %>%
select(., GroupingTerm, heteroCVR:heteroRR_se)
Eye. <- heterog1 %>%
filter(., GroupingTerm == "Eye") %>%
select(., -data) %>%
mutate(
heteroCVR = .[[2]][[1]]$b, heteroCVR_lower = .[[2]][[1]]$ci.lb, heteroCVR_upper = .[[2]][[1]]$ci.ub, heteroCVR_se = .[[2]][[1]]$se,
heteroVR = .[[3]][[1]]$b, heteroVR_lower = .[[3]][[1]]$ci.lb, heteroVR_upper = .[[3]][[1]]$ci.ub, heteroVR_se = .[[3]][[1]]$se,
heteroRR = .[[4]][[1]]$b, heteroRR_lower = .[[4]][[1]]$ci.lb, heteroRR_upper = .[[4]][[1]]$ci.ub, heteroRR_se = .[[4]][[1]]$se
) %>%
select(., GroupingTerm, heteroCVR:heteroRR_se)
heterog2 <- bind_rows(Behaviour., Morphology., Metabolism., Physiology., Immunology., Hematology., Heart., Hearing., Eye.)
# str(heterog2)
```
#### Heterogeneity PLOT
Restructure data for plotting
```{r}
heterog3 <- gather(heterog2, parameter, value, c(heteroCVR, heteroVR, heteroRR), factor_key = TRUE)
heteroCVR.ci <- heterog3 %>%
filter(parameter == "heteroCVR") %>%
mutate(ci.low = heteroCVR_lower, ci.high = heteroCVR_upper)
heteroVR.ci <- heterog3 %>%
filter(parameter == "heteroVR") %>%
mutate(ci.low = heteroVR_lower, ci.high = heteroVR_upper)
heteroRR.ci <- heterog3 %>%
filter(parameter == "heteroRR") %>%
mutate(ci.low = heteroRR_lower, ci.high = heteroRR_upper)
heterog4 <- bind_rows(heteroCVR.ci, heteroVR.ci, heteroRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high)
# **Re-order grouping terms
heterog4$GroupingTerm <- factor(heterog4$GroupingTerm, levels = c("Behaviour", "Morphology", "Metabolism", "Physiology", "Immunology", "Hematology", "Heart", "Hearing", "Eye"))
heterog4$GroupingTerm <- factor(heterog4$GroupingTerm, rev(levels(heterog4$GroupingTerm)))
heterog4$label <- "All traits"
# write.csv(heterog4, "heterog4.csv")
```
### Plot FIGURE 4 - C(Second-order meta analysis on heterogeneity)
Plot Fig4 all traits
```{r}
heterog5 <- heterog4
heterog5$mean <- as.numeric(exp(heterog5$value))
heterog5$ci.l <- as.numeric(exp(heterog5$ci.low))
heterog5$ci.h <- as.numeric(exp(heterog5$ci.high))
heterog6 <- heterog5
Hetero4c <-
heterog6 %>%
filter(
parameter == "heteroCVR" | parameter == "heteroRR"
) %>%
ggplot(aes(y = GroupingTerm, x = mean)) +
geom_errorbarh(aes(
xmin = ci.l,
xmax = ci.h
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(shape = parameter),
fill = "black",
color = "black", size = 2.2,
show.legend = FALSE
) +
scale_x_continuous(
limits = c(-0.1, 1.4),
# breaks = c(0, 0.1, 0.2),
name = "sigma^2"
) +
# geom_vline(xintercept=0,
# color='black',
# linetype='dashed')+
facet_grid(
cols = vars(parameter), rows = vars(label),
labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_text(hjust = 0.5, size = 14),
axis.title.y = element_blank()
)
# Hetero4c
# ggsave("Fig4.pdf", plot = Metameta_Fig4_alltraits, width = 7, height = 6)
```
#### Combined Figure 4: overall (Count data, Meta anlysis results, Heterogeneity)
```{r}
Fig4 <- ggarrange(malebias_Fig2_alltraits, Metameta_Fig3_alltraits, Hetero4c, nrow = 3, align = "v", heights = c(1, 1, 1), labels = c("A", "B", "C"))
Fig4
# ggsave("Fig4_OverallResults.pdf", plot = Fig4, width = 6, height = 5)
```
## Supplemental Figures
```{r}
## Heterogneity, S1 C
HeteroS1 <- heterog5 %>%
ggplot(aes(y = GroupingTerm, x = mean)) +
geom_errorbarh(aes(
xmin = ci.l,
xmax = ci.h
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(shape = parameter),
fill = "black",
color = "black", size = 2.2,
show.legend = FALSE
) +
scale_x_continuous(
limits = c(-0.1, 1.4),
# breaks = c(0, 0.1, 0.2),
name = "Effect size"
) +
# geom_vline(xintercept=0,
# color='black',
# linetype='dashed')+
facet_grid(
cols = vars(parameter), rows = vars(label),
labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank()
)
# HeteroS1
# ggsave("Fig4.pdf", plot = Metameta_Fig4_alltraits, width = 7, height = 6)
```
## Count data, including lnVR (Fig S1 A)
```{r}
# *Prepare data for all traits
meta.plot2.all <- meta_clean %>%
select(lnCVR, lnVR, lnRR, GroupingTerm) %>%
arrange(GroupingTerm)
meta.plot2.all.bS1 <- gather(meta.plot2.all, trait, value, c(lnCVR, lnVR, lnRR))
meta.plot2.all.bS1$trait <- factor(meta.plot2.all.bS1$trait, levels = c("lnCVR", "lnVR", "lnRR"))
meta.plot2.all.cS1 <- meta.plot2.all.bS1 %>%
group_by_at(vars(trait, GroupingTerm)) %>%
summarise(
malebias = sum(value > 0), femalebias = sum(value <= 0), total = malebias + femalebias,
malepercent = malebias * 100 / total, femalepercent = femalebias * 100 / total
)
meta.plot2.all.cS1$label <- "All traits"
# restructure to create stacked bar plots
meta.plot2.all.dS1 <- as.data.frame(meta.plot2.all.cS1)
meta.plot2.all.eS1 <- gather(meta.plot2.all.dS1, key = sex, value = percent, malepercent:femalepercent, factor_key = TRUE)
# create new sample size variable
meta.plot2.all.eS1$samplesize <- with(meta.plot2.all.eS1, ifelse(sex == "malepercent", malebias, femalebias))
malebias_FigS1_alltraits <-
ggplot(meta.plot2.all.eS1) +
aes(x = GroupingTerm, y = percent, fill = sex) +
geom_col() +
geom_hline(yintercept = 50, linetype = "dashed", color = "gray40") +
geom_text(
data = subset(meta.plot2.all.eS1, samplesize != 0), aes(label = samplesize), position = position_stack(vjust = .5),
color = "white", size = 3.5
) +
facet_grid(
cols = vars(trait), rows = vars(label), labeller = label_wrap_gen(width = 18),
scales = "free", space = "free"
) +
scale_fill_brewer(palette = "Set2") +
theme_bw(base_size = 18) +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.position = "none",
axis.title.x = element_blank(),
axis.title.y = element_blank()
) +
coord_flip()
# malebias_FigS1_alltraits #(panel A in Figure S1)
```
### Overall results of second order meta analysis (Figure 4: overall, Figure 5: sex-bias), INCLUDING VR
#### Restructure data for plotting
Restructure MALE data for plotting
```{r}
overall3.male.sigS <- gather(overall.male.plot3, parameter, value, c(lnCVR, lnVR, lnRR), factor_key = TRUE)
lnCVR.ci <- overall3.male.sigS %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
lnVR.ci <- overall3.male.sigS %>%
filter(parameter == "lnVR") %>%
mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3.male.sigS %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4.male.sigS <- bind_rows(lnCVR.ci, lnVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high)
overall4.male.sigS$label <- "CI not overlapping zero"
```
Data are restructured, and grouping terms are being re-ordered
```{r}
overall3S <- gather(overall2, parameter, value, c(lnCVR, lnVR, lnRR), factor_key = TRUE)
lnCVR.ci <- overall3S %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
lnVR.ci <- overall3S %>%
filter(parameter == "lnVR") %>%
mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3S %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4S <- bind_rows(lnCVR.ci, lnVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high)
# re-order Grouping Terms
overall4S$GroupingTerm <- factor(overall4S$GroupingTerm, levels = c("Behaviour", "Morphology", "Metabolism", "Physiology", "Immunology", "Hematology", "Heart", "Hearing", "Eye", "All"))
overall4S$GroupingTerm <- factor(overall4S$GroupingTerm, rev(levels(overall4S$GroupingTerm)))
overall4S$label <- "All traits"
```
#### Preparation for Plots FIGURE S1B & S2B, S2D (Second-order meta analysis results, INCL lnVR)
Preparation: Sub-Plot for Figure S1: all traits (S1 B)
```{r}
Metameta_FigS1_alltraits <- overall4S %>%
ggplot(aes(y = GroupingTerm, x = value)) +
geom_errorbarh(aes(
xmin = ci.low,
xmax = ci.high
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(shape = parameter),
fill = "black",
color = "black", size = 2.2,
show.legend = FALSE
) +
scale_x_continuous(
limits = c(-0.24, 0.25),
breaks = c(-0.2, -0.1, 0, 0.1, 0.2),
name = "Effect size"
) +
geom_vline(
xintercept = 0,
color = "black",
linetype = "dashed"
) +
facet_grid(
cols = vars(parameter), rows = vars(label),
labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_text(hjust = 0.5, size = 14),
axis.title.y = element_blank()
)
# Metameta_FigS1_alltraits
```
#### Combined Figure S1: overall Count data, Meta anlysis results, Heterogeneity)
```{r}
FigS1 <- ggarrange(malebias_FigS1_alltraits + xlab("percentage sex bias"), Metameta_FigS1_alltraits, HeteroS1, nrow = 3, align = "v", heights = c(1, 1, 1), labels = c("A", "B", "C"))
FigS1
# ggsave("FigS1_OverallResults.pdf", plot = Fig4, width = 6, height = 5)
```
## Figure S2: sex-bias, including VR
Plot FigS2 all significant results (CI not overlapping zero) for males
```{r}
meta.plot2.sig.bS <- meta.plot2.sig[, c("lnCVR", "lnVR", "lnRR", "lnCVRsig", "lnVRsig", "lnRRsig", "GroupingTerm")]
meta.plot2.sig.cS <- gather(meta.plot2.sig.bS, trait, value, lnCVR:lnRR)
meta.plot2.sig.cS$sig <- "placeholder"
meta.plot2.sig.cS$trait <- factor(meta.plot2.sig.cS$trait, levels = c("lnCVR", "lnVR", "lnRR"))
meta.plot2.sig.cS$sig <- ifelse(meta.plot2.sig.cS$trait == "lnCVR", meta.plot2.sig.cS$lnCVRsig,
ifelse(meta.plot2.sig.cS$trait == "lnVR", meta.plot2.sig.cS$lnVRsig, meta.plot2.sig.cS$lnRRsig)
)
# choosing sex biased ln-ratios significantly larger than 0
meta.plotS2.sig.malebias <- meta.plot2.sig.cS %>%
group_by_at(vars(trait, GroupingTerm)) %>%
filter(sig == 1) %>%
summarise(male_sig = sum(value > 0), female_sig = sum(value < 0), total = male_sig + female_sig)
meta.plotS2.sig.malebias <- ungroup(meta.plotS2.sig.malebias) %>%
add_row(trait = "lnCVR", GroupingTerm = "Hearing", male_sig = 0, female_sig = 0, .before = 4) %>% # add "Hearing" for lnCVR (not filtered as only zeros)
mutate(malepercent = male_sig * 100 / total, femalepercent = female_sig * 100 / total)
meta.plotS2.sig.malebias$label <- "CI not overlapping zero"
# restructure to create stacked bar plots
meta.plotS2.sig.bothsexes <- as.data.frame(meta.plotS2.sig.malebias)
meta.plotS2.sig.bothsexes.b <- gather(meta.plotS2.sig.bothsexes, key = sex, value = percent, malepercent:femalepercent, factor_key = TRUE)
# create new sample size variable
meta.plotS2.sig.bothsexes.b$samplesize <- with(meta.plotS2.sig.bothsexes.b, ifelse(sex == "malepercent", male_sig, female_sig))
# *Plot Fig2 all significant results (CI not overlapping zero):
# no sig. lnCVR for 'Hearing' in either sex; no sig. male-biased lnCVR for 'Immunology' and 'Eye, and no sig. male-biased lnVR for 'Eye'
malebias_FigS2_sigtraits <-
ggplot(meta.plotS2.sig.bothsexes.b) +
aes(x = GroupingTerm, y = percent, fill = sex) +
geom_col() +
geom_hline(yintercept = 50, linetype = "dashed", color = "gray40") +
geom_text(
data = subset(meta.plotS2.sig.bothsexes.b, samplesize != 0), aes(label = samplesize), position = position_stack(vjust = .5),
color = "white", size = 3.5
) +
facet_grid(
cols = vars(trait), rows = vars(label), labeller = label_wrap_gen(width = 18),
scales = "free", space = "free"
) +
scale_fill_brewer(palette = "Set2") +
theme_bw(base_size = 18) +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.position = "none",
axis.title.x = element_blank(),
axis.title.y = element_blank()
) +
coord_flip()
# malebias_FigS2_sigtraits # this is Figure S2 A
```
Prepare data for traits with effect size ratios > 10% larger in males
```{r}
meta.plotS2.over10 <- meta_clean %>%
select(lnCVR, lnVR, lnRR, GroupingTerm) %>%
arrange(GroupingTerm)
meta.plotS2.over10.b <- gather(meta.plotS2.over10, trait, value, c(lnCVR, lnVR, lnRR))
meta.plotS2.over10.b$trait <- factor(meta.plotS2.over10.b$trait, levels = c("lnCVR", "lnVR", "lnRR"))
meta.plotS2.over10.c <- meta.plotS2.over10.b %>%
group_by_at(vars(trait, GroupingTerm)) %>%
summarise(
malebias = sum(value > log(11 / 10)), femalebias = sum(value < log(9 / 10)), total = malebias + femalebias,
malepercent = malebias * 100 / total, femalepercent = femalebias * 100 / total
)
meta.plotS2.over10.c$label <- "Sex difference in m/f ratios > 10%"
# restructure to create stacked bar plots
meta.plotS2.over10.c <- as.data.frame(meta.plotS2.over10.c)
meta.plotS2.over10.d <- gather(meta.plotS2.over10.c, key = sex, value = percent, malepercent:femalepercent, factor_key = TRUE)
# create new sample size variable
meta.plotS2.over10.d$samplesize <- with(meta.plotS2.over10.d, ifelse(sex == "malepercent", malebias, femalebias))
# *Plot FigS2 Sex difference in m/f ratio > 10%
malebias_FigS2_over10 <-
ggplot(meta.plotS2.over10.d) +
aes(x = GroupingTerm, y = percent, fill = sex) +
geom_col() +
geom_hline(yintercept = 50, linetype = "dashed", color = "gray40") +
geom_text(
data = subset(meta.plot2.over10.d, samplesize != 0), aes(label = samplesize), position = position_stack(vjust = .5),
color = "white", size = 3.5
) +
facet_grid(
cols = vars(trait), rows = vars(label), labeller = label_wrap_gen(width = 18),
scales = "free", space = "free"
) +
scale_fill_brewer(palette = "Set2") +
theme_bw(base_size = 18) +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_blank(),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.position = "none",
axis.title.x = element_blank(),
axis.title.y = element_blank()
) +
coord_flip()
# malebias_FigS2_over10 #(Panel B in Fig S2 in ms)
```
#### Female Figure, significant traits
Female FigS2 B sig
Prepare data for traits with CI not overlapping 0
create column with 1= different from zero, 0= zero included in CI
Restructure data for plotting
```{r}
overall3.female.sigS <- gather(overall.female.plot3, parameter, value, c(lnCVR, lnVR, lnRR), factor_key = TRUE)
lnCVR.ci <- overall3.female.sigS %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
lnVR.ci <- overall3.female.sigS %>%
filter(parameter == "lnVR") %>%
mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3.female.sigS %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4.female.sigS <- bind_rows(lnCVR.ci, lnVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high)
overall4.female.sigS$label <- "CI not overlapping zero"
##
Metameta_FigS2_female.sig <- overall4.female.sigS %>%
ggplot(aes(y = GroupingTerm, x = value)) +
geom_errorbarh(aes(
xmin = ci.low,
xmax = ci.high
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(shape = parameter),
fill = "salmon1", color = "salmon1", size = 2.2,
show.legend = FALSE
) +
scale_x_continuous(
limits = c(-0.4, 0),
breaks = c(-0.3, 0),
name = "Effect size"
) +
geom_vline(
xintercept = 0,
color = "black",
linetype = "dashed"
) +
facet_grid(
cols = vars(parameter), # rows = vars(label),
# labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank()
)
# Metameta_FigS2_female.sig
```
#Metameta_FigS2_male.sig (Figure 5B right panel)
Restructure MALE data for plotting
```{r}
overall3.male.sigS <- gather(overall.male.plot3, parameter, value, c(lnCVR, lnVR, lnRR), factor_key = TRUE)
lnCVR.ci <- overall3.male.sigS %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
lnVR.ci <- overall3.male.sigS %>%
filter(parameter == "lnVR") %>%
mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3.male.sigS %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4.male.sigS <- bind_rows(lnCVR.ci, lnVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high)
overall4.male.sigS$label <- "CI not overlapping zero"
```
Plot FigS2 all significant results (CI not overlapping zero, male )
```{r}
Metameta_FigS2_male.sig <- overall4.male.sigS %>%
ggplot(aes(y = GroupingTerm, x = value)) +
geom_errorbarh(aes(
xmin = ci.low,
xmax = ci.high
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(shape = parameter),
fill = "mediumaquamarine", color = "mediumaquamarine", size = 2.2,
show.legend = FALSE
) +
scale_x_continuous(
limits = c(0, 0.4),
breaks = c(0, 0.3),
name = "Effect size"
) +
geom_vline(
xintercept = 0,
color = "black",
linetype = "dashed"
) +
facet_grid(
cols = vars(parameter), rows = vars(label),
labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank()
)
# Metameta_FigS2_male.sig
```
### 10 % Perc sex difference, male bias
Restructure data for plotting : Male biased, 10% difference
```{r}
overall3S.perc <- gather(overall.male.plot3.perc, parameter, value, c(lnCVR, lnVR, lnRR), factor_key = TRUE) # lnVR,
lnCVR.ci <- overall3S.perc %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
lnVR.ci <- overall3S.perc %>%
filter(parameter == "lnVR") %>%
mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3S.perc %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4S.male.perc <- bind_rows(lnCVR.ci, lnVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high) # lnVR.ci,
overall4S.male.perc$label <- "Sex difference in m/f ratios > 10%"
overall4S.male.perc$value <- as.numeric(overall4S.male.perc$value)
overall4S.male.perc$ci.low <- as.numeric(overall4S.male.perc$ci.low)
overall4S.male.perc$ci.high <- as.numeric(overall4S.male.perc$ci.high)
```
Plot FigS2 all >10% difference (male bias)
```{r}
Metameta_FigS2_male.perc <- overall4S.male.perc %>% # filter(., GroupingTerm != "Hearing") %>%
ggplot(aes(y = GroupingTerm, x = value)) +
geom_errorbarh(aes(
xmin = ci.low,
xmax = ci.high
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(
shape = parameter,
fill = parameter
),
color = "mediumaquamarine", size = 2.2,
show.legend = FALSE
) +
scale_x_continuous(
limits = c(-0.2, 0.62),
breaks = c(0, 0.3),
name = "Effect size"
) +
geom_vline(
xintercept = 0,
color = "black",
linetype = "dashed"
) +
facet_grid(
cols = vars(parameter), rows = vars(label),
labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_blank(),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_text(hjust = 0.5, size = 14),
axis.title.y = element_blank()
)
# Metameta_FigS2_male.perc (Figure 5D right panel)
```
Restructure data for plotting:
Female bias, 10 percent difference, including VR
```{r}
overall3S.perc <- gather(overall.plot3.perc, parameter, value, c(lnCVR, lnVR, lnRR), factor_key = TRUE) # lnVR,
lnCVR.ci <- overall3S.perc %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
lnVR.ci <- overall3S.perc %>%
filter(parameter == "lnVR") %>%
mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3S.perc %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4S.perc <- bind_rows(lnCVR.ci, lnVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high)
overall4S.perc$label <- "Sex difference in m/f ratios > 10%"
overall4S.perc$value <- as.numeric(overall4S.perc$value)
overall4S.perc$ci.low <- as.numeric(overall4S.perc$ci.low)
overall4S.perc$ci.high <- as.numeric(overall4S.perc$ci.high)
```
Plot Fig5D all >10% difference (female)
```{r}
Metameta_Fig3S_female.perc <- overall4S.perc %>%
ggplot(aes(y = GroupingTerm, x = value)) +
geom_errorbarh(aes(
xmin = ci.low,
xmax = ci.high
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(shape = parameter),
fill = "salmon1", color = "salmon1", size = 2.2,
show.legend = FALSE
) +
# scale_shape_manual(values =
scale_x_continuous(
limits = c(-0.53, 0.2),
breaks = c(-0.3, 0),
name = "Effect size"
) +
geom_vline(
xintercept = 0,
color = "black",
linetype = "dashed"
) +
facet_grid(
cols = vars(parameter), # rows = vars(label),
# labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_blank(),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_text(hjust = 0.5, size = 14),
axis.title.y = element_blank()
)
# Metameta_Fig3S_female.perc (Figure 5D left panel)
```
Figure S2
```{r}
FigS2c <- ggarrange(Metameta_FigS2_female.sig, Metameta_FigS2_male.sig,
ncol = 2, nrow = 1, widths = c(1, 1.20), heights = c(1, 1)
)
FigS2d <- ggarrange(Metameta_Fig3S_female.perc, Metameta_FigS2_male.perc,
ncol = 2, nrow = 1, widths = c(1, 1.20), heights = c(1, 1)
)
# end combination Figure 5
FigS2 <- ggarrange(malebias_FigS2_sigtraits, malebias_FigS2_over10, FigS2c, FigS2d, ncol = 1, nrow = 4, heights = c(2.2, 2, 2.2, 2), labels = c("A", " ", "B", " "))
FigS2
```
## Acknowledgements
tbd
## R Session Information
```{r}
sessionInfo()
```
