R/biocDownloadStats.R

In Liubuntu/BiocPkgTools: Collection of simple tools for learning about Bioc Packages

#' get bioconductor download stats
#'
#' @details Note that bioconductor package download
#' stats are not version-specific.
#'
#' @importFrom dplyr mutate
#' @importFrom magrittr %>%
#' @importFrom utils read.table
#' @importFrom tibble as_tibble
#' 
#' @return a \code{data.frame} of download stats for
#' all bioconductor packages, in tidy format
#'
#' @examples
#' biocDownloadStats()
#'
#' @export
biocDownloadStats = function() {
  tmp = read.table('http://bioconductor.org/packages/stats/bioc/bioc_pkg_stats.tab',
                   sep="\t", header = TRUE, stringsAsFactors = FALSE)
  tmp$repo = 'Software'
  tmp2 = read.table('http://bioconductor.org/packages/stats/data-annotation/annotation_pkg_stats.tab',
                    sep="\t", header = TRUE, stringsAsFactors = FALSE)
  tmp2$repo = 'AnnotationData'
  tmp3 = read.table('http://bioconductor.org/packages/stats/data-experiment/experiment_pkg_stats.tab',
                    sep="\t", header = TRUE, stringsAsFactors = FALSE)
  tmp3$repo = 'ExperimentData'
  tmp = rbind(tmp,tmp2,tmp3)
  tmp = as_tibble(tmp) %>% 
    mutate(Date = as.Date(paste(Year, Month, '01'), '%Y %b %d'))
  class(tmp) = c('bioc_downloads', class(tmp))
  tmp
}

#' When did a package enter Bioconductor?
#' 
#' This function uses the biocDownloadStats
#' data to *approximate* when a package entered
#' Bioconductor. Note that the download stats
#' go back only to 2009.
#' 
#' @importFrom dplyr filter group_by top_n collect
#' 
#' @param download_stats a data.frame from \code{\link{biocDownloadStats}}
#' 
#' @example 
#' dls = biocDownloadStats()
#' tail(firstInBioc(dls))
#' @export
firstInBioc = function(download_stats) {
  download_stats %>% 
    filter(Month!='all') %>%
    group_by(Package) %>%
    # thanks: https://stackoverflow.com/questions/43832434/arrange-within-a-group-with-dplyr
    top_n(1, desc(Date)) %>%
    collect()
}