Skip to content

R and R studio

ggplot2

Xpose4

VPC

Personal use

Packages

Binom

  • Uses eight different methods to obtain a confidence interval on the binomial probability.
  • Example: 5 successes out of 100 independent trials with 95% of confidence in the binomial experiment
  • Input 
library(binom)
binom.confint(5, 100, conf.level = 0.95, Method = "all")
  • Output
Method Description Successes Trials Mean Lower Upper
Agresti-Coull Agresti-Coull method 5 100 0.05000000 0.018676359 0.11461779
Asymptotic Using the Central Limit Theorem 5 100 0.05000000 0.007283575 0.09271642
Bayes Using Bayesian inference 5 100 0.05445545 0.015338169 0.09900926
Cloglog Using the complementary log parameterization 5 100 0.05000000 0.018604802 0.10514408
Exact Pearson-Klopper method 5 100 0.05000000 0.016431879 0.11283491
Logit Using the logistic parameterization 5 100 0.05000000 0.020964608 0.11454379
Probit Using the probit parameterization 5 100 0.05000000 0.019745646 0.10922194
Profile Using the profile likelihood 5 100 0.05000000 0.018242887 0.10439789
LRT 5 100 0.05000000 0.018250112 0.10439673
Prop.test 5 100 0.05000000 0.018552564 0.11829946
Wilson Wilson method 5 100 0.05000000 0.021543679 0.11175047

Functions

leave()

  • Remove all objects except:
    • functions
    • objects that contain specified string within their name
  • I just find it easier than writing every object in rm()
 leave <- function(exclude_strings) {
  # Get all objects in the global environment
  all_objects <- ls(envir = .GlobalEnv)

  # Identify functions and objects containing specified strings in their names
  functions <- all_objects[sapply(all_objects, function(x) is.function(get(x)))]
  exclude_objects <- all_objects[sapply(all_objects, function(x) any(sapply(exclude_strings, function(s) grepl(s, x))))]

  # Remove all objects except functions and objects containing specified strings in their names
  objects_to_remove <- setdiff(all_objects, c(functions, exclude_objects))
  rm(list = objects_to_remove, envir = .GlobalEnv)
}

plotsave()

  • save all objects that are named as str+i (e.g. plot1, plot_1 or p1) in path (path specified folder)
    • the folder will be created if it doesn't exist
plotsave <- function(path, str) {
  for (i in 1:30) {
    tryCatch({
      plot_object <- get(paste0(str, i))
    if (!is.null(plot_object)) {
      plot_name <- paste0(path, "plot", i, ".png")
      ggsave(plot_name, plot = plot_object, width = 6, height = 4.5, units = "in", dpi = 300, create.dir = TRUE)
    }}, error = function(e) {})
  }
}

theme_custom()

  • Custom ggplot2 theme that can be re-used
    • if there are additional changes it can be added in ...
theme_custom <- function(...) {
  theme_bw()+
  theme(
          legend.text  = element_text(size = 6),
          axis.text.x  = element_text(size = 6, angle = 0, vjust = 0, hjust=0.5),
          axis.text.y  = element_text(size = 6),
          plot.caption = element_text(size = 6, hjust = 0),
          legend.title = element_text(size = 8, face="bold"),
          axis.title.y = element_text(size = 8, face="bold"),
          axis.title.x = element_text(size = 8, face="bold"),
          strip.text.x = element_text(size = 8, face="bold"),
          title = element_text(size = 10, face="bold")
        ) +
    theme(...)
}