joelnitta

#' Download all the files in a google drive folder.
#'
#' \code{dribble_data} should be obtained using \code{\link[googledrive]{drive_ls}}.
#'
#' @param dribble_data Data frame of class \code{dribble}.
#' @param folder Path to local folder to download data.
#' @param pattern Optional grep pattern; only file names matching this pattern
#' will be included.
#' @param negate Logical; should only file names that don't match the pattern
#' be included instead?

joelnitta

# List all functions and packages used by R scripts in a project.

library(NCmisc)
# IMPORTANT: Also load any libraries used by the project

# Make list of all functions by package
funcs <- 
  list.files(here::here(), pattern ="\\.R$", recursive = TRUE, full.names = TRUE) %>%
  map(list.functions.in.file) %>%
  flatten

joelnitta

# Convert ape::DNAbin format to Biostrings::DNAStringSet format,
# optionally removing gaps
DNAbin_to_DNAstringset <- function (seqs, remove_gaps = TRUE) {
  if(isTRUE(remove_gaps)) {
  seqs %>% as.list() %>% as.character %>% 
      lapply(.,paste0,collapse="") %>% 
      lapply( function (x) gsub("-", "", x)) %>% 
      unlist %>% Biostrings::DNAStringSet()
  } else {
    seqs %>% as.list() %>% as.character %>% 

joelnitta

#' Concatenate a list of aligned genes
#'
#' @param dna_list List of matrices of class DNAbin
#'
#' @return Matrix of class DNAbin
#'
#' @examples
#' data(woodmouse)
#' gene_1 <- woodmouse[,1:100]
#' gene_2 <- woodmouse[,101:200]

joelnitta

#' Run IQ-TREE
#' 
#' For details, see http://www.iqtree.org/doc/
#'
#' @param alignment DNA alignment to use for phylogenetic analysis. Must be matrix
#' (i.e., aligned sequences) of class DNAbin 
#' @param wd Path to working directory. The alignment and IQ-TREE intermediate files
#' and results will be written here.
#' @param bb Optional; number of ultrafast bootstrap replicates to run.
#' @param nt Optional; number of cores to use. Set to "AUTO" to determine automatically.

joelnitta

preview_pal <- function(colors) {
  
  labels <- if(is.null(names(colors))) {colors} else {names(colors)}
  
  pie(
    rep(1, length(colors)), 
    labels = labels,
    col = colors)
}

joelnitta

#' Compare the contents of two folders
#'
#' Comparison is done by checking file names and the MD5 hash of each
#' file. No recursion is used, so files in subfolders will not be checked.
#'
#' @param x The absolute path to the first folder.
#' @param y The absolut path the second folder.
#'
#' @return A confirmation if all files in the two folders are equal.
#' Otherwise, a list of two tibbles. Each tibble contains a column for

joelnitta

# Scale a color palette centered on zero

#' Get the lower, upper, or absolute maximum value
#' of a variable in a dataframe
#' 
#' For setting plotting limits manually
#'
#' @param data Dataframe
#' @param var Name of variable (column) in dataframe
#' @param digits Number of digits desired in output

joelnitta

library(hexSticker)
library(ggplot2)

# Make a blank plot because hexSticker::sticker() expects something.
p <- ggplot(mtcars, aes(wt, mpg)) + geom_blank() + theme_void() + theme_transparent()

sticker(p,
        package="generic",
        p_size=8, s_x=1, s_y=.8, s_width=1.2, s_height=1,
        h_color = "grey",

joelnitta

country
Afghanistan
Albania
Algeria
American Samoa
Andorra
Angola
Anguilla
Antarctica
Antigua and Barbuda