I'd like to add the significance letters to a plot using ggeffects
and ggplot2
packages. In my case:
# Packages
library(ggeffects)
library(dplyr)
library(glmmTMB)
library(multcomp)
library(lsmeans)
library(ggplot2)
# My data set
ds <- read.csv("https://raw.githubusercontent.com/Leprechault/trash/main/temp_ger_ds.csv")
str(ds)
#'data.frame': 140 obs. of 4 variables:
# $ temp : chr "constante" "constante" "constante" "constante" ...
# $ generation : chr "G0" "G0" "G0" "G0" ...
# $ development: int 22 24 22 27 27 24 25 26 27 18 ...
#General model:
mTCFd <- glmmTMB(development ~ temp * generation, data = ds,
family = ziGamma(link = "log"))
#3 combinations plot:
#1) Plot for temp
lsm.mTCFd.temp <- lsmeans(mTCFd, c("temp"))
lt<-cld(lsm.mTCFd.temp, Letters=letters, decreasing = TRUE)
ds <- ds %>% mutate(x_1= 1+(readr::parse_number(generation)-2)*0.05,
group = generation)
df_gg <-ggpredict(mTCFd, terms = c("temp"))%>%
mutate(x_1= 1+(readr::parse_number(as.character(group))-2)*0.05)
df_gg %>% plot(add.data = TRUE) +
geom_text(aes(x = x_1, label = lt[,7]), vjust = -0.5, show.legend = FALSE)
#2) Plot for generation
lsm.mTCFd.gera <- lsmeans(mTCFd, c("generation"))
lt<-cld(lsm.mTCFd.gera, Letters=letters, decreasing = TRUE)
ds <- ds %>% mutate(x_1= 1+(readr::parse_number(generation)-2)*0.05,
group = generation)
df_gg <-ggpredict(mTCFd, terms = c("generation"))%>%
mutate(x_1= 1+(readr::parse_number(as.character(group))-2)*0.05)
df_gg %>% plot(add.data = TRUE) +
geom_text(aes(x = x_1, label = lt[,7]), vjust = -0.5, show.legend = FALSE)
#3) Plot for temp and generation interaction
lsm.mTCFd.temp.gera <- lsmeans(mTCFd, c("temp","generation"))
lt<-cld(lsm.mTCFd.temp.gera , Letters=letters, decreasing = TRUE)
ds <- ds %>% mutate(x_1= 1+(readr::parse_number(generation)-2)*0.05,
group = generation)
df_gg <-ggpredict(mTCFd, terms = c("temp","generation"))%>%
mutate(x_1= 1+(readr::parse_number(as.character(group))-2)*0.05)
df_gg %>% plot(add.data = TRUE) +
geom_text(aes(x = x_1, label = lt[,8]), vjust = -0.5, show.legend = FALSE)
But I always as output:
Raw data not available.
Error in if (attr(x, "logistic", exact = TRUE) == "1" && attr(x, "is.trial", :
missing value where TRUE/FALSE needed
Please, any help with it?