dpaudelR: Simple Tools For Data Wrangling

#' ANOVA LSD
#'
#' This function produces ANOVA table, LSD table, and barplot then copies table to clipboard
#'
#' 
#' @return A ggplot
#' @export
# anova_lsd(Petal.Length~Species, iris)
anova_lsd <- function (user_model, user_data){
  model1a <- as.formula(user_model)
user_treatment <- as.character(formula(user_model))[2]
user_group <- as.character(formula(user_model))[3]
user_factors <- sub("\\s","",unlist(strsplit(user_group,"[*+:]")))
library(agricolae)
library(ggplot2)
library(Rmisc)
library(dplyr)
aov1 <- aov(model1a, data=user_data)
print("ANOVA table")
print(summary(aov1))

# LSD test
lsd_aov1 <- LSD.test(aov1, user_factors[2], group=TRUE)

# Sort
order_aov1 <- lsd_aov1$groups[order(rownames(lsd_aov1$groups)),]

# Add species column
order_aov1 <- order_aov1 %>% mutate(Name=rownames(order_aov1))

# Get summary statistics from Rmisc package
data1a <- user_data
data_stats <- summarySE(data1a, measurevar= user_treatment , groupvars= user_factors[2], na.rm=TRUE)

# Merge LSD grouping and summary statistics

data_merged <- left_join(data_stats, order_aov1)
print("LSD ranking")
print(data_merged)
# Print
copy2clipboard(data_merged)
print("Use Ctrl+V to paste summary means into Excel worksheet")

# Create standard error bars
yerr_names1 <- colnames(data_merged)[c(3,5)]
yerrbar1 <- aes_string(ymin = paste(yerr_names1, collapse = '-'), 
                       ymax = paste(yerr_names1,collapse='+'))
nudge_amt <- 0
if (mean(data_merged$se) < 1){
  nudge_amt <- 5*mean(data_merged$se)
} else {
  nudge_amt <- 2*mean(data_merged$se)}
# Plot
plot1 <- ggplot(data_merged, aes_string(x=user_factors[2], y=user_treatment, fill=user_factors[2]))+
  geom_bar(position=position_dodge(.5), stat="identity", colour="black", width = 0.5)+
  geom_errorbar(mapping = yerrbar1, width=0.2)+
  geom_text(nudge_y=nudge_amt, label=data_merged$groups,  size=4) +
  ggtitle("LSD grouping")+
  theme_bw(base_size=12) %+replace% 
  theme(
    panel.background  = element_blank(),
    plot.background = element_rect(fill="white", colour=NA), 
    legend.background = element_rect(fill="transparent", colour=NA),
    legend.key        = element_rect(fill="transparent", colour=NA)
  )
#theme_uf() # from dpaudelR package
print(plot1)
}