knitr::opts_chunk$set(echo = TRUE) knitr::opts_chunk$set(message = FALSE) knitr::opts_chunk$set(warning = FALSE) library(ProvidenciaChemo)
library(tidyverse) library(patchwork) library(tidybayes) library(modelr) library(emmeans) library(magrittr) library(emmeans) library(kableExtra) theme_set(theme_my) filepath <- here::here("extdata/Figure_Ext1e_lidAvoidance.csv") lid_data <- read_csv(filepath) %>% format_AvoidData(day.correct = "treatment") %>% mutate(plate = factor(seq(1:nrow(.))), treatment = factor(treatment, levels = c("none", "lid")), data_type = "raw") %>% mutate(group.id = interaction(strain, treatment)) %>% droplevels() #convergence errors with date random effect, left out of this model glmm <- lme4::glmer(data = lid_data, formula = cbind(nCue,nControl) ~ strain * treatment + (1|plate), family = binomial, control= lme4::glmerControl(optimizer="bobyqa")) stan_glmm <- rstanarm::stan_glmer(data = lid_data, formula = cbind(nCue,nControl) ~ strain * treatment + (1|plate), chains = 4, cores = 4, seed = 2000,iter=6000, family = binomial, control = list(adapt_delta=0.99)) fitted <- recenter_fittedValues(lid_data, stan_glmm, day.correct = "treatment", BayesFit = "fitted_draws") plot1 <- lid_data %>% plot_plasticityIndex(xvar = data_type, width = 0.2, BayesFit = TRUE, bar = TRUE, alpha = 0.75) + scale_color_plot(palette = "grey-blue", drop = TRUE) + scale_fill_plot(palette = "grey-blue", drop = TRUE) + guides(color = FALSE) + facet_grid(~treatment+strain) + coord_cartesian(ylim = c(-2,3)) #glm.contrasts <- emmeans::emmeans(glmm, pairwise ~ strain | treatment) emmeans::ref_grid(glmm) %>% emmeans::contrast(., method = "pairwise") %>% broom::tidy() %>% kable() %>% kable_styling() # plot1 + # geom_text(data = glm.contrasts.1, # aes(label = paste0("P~",round(p.value, 3)), # y = max(1.3*lid_data$rel.Logit))) plot1
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