In hbc/hbcABC: Rmarkdown templates for bioinformatic analysis

R scripts at rmarkdown/Rscripts

library(tidyverse)
setwd(here::here())
fns = list.files("inst/rmarkdown/Rscripts", recursive = TRUE)
lapply(fns, function(fn){
    desc = readr::read_lines(file.path("inst/rmarkdown/Rscripts", fn), n_max = 1)
    if (!grepl("# ", desc)){
        desc = "Not given."
    }
    data.frame(fn = basename(fn),
               category = dirname(fn),
               description = gsub("#", "", desc),
               stringsAsFactors = FALSE)
}) %>% bind_rows() %>% distinct() %>%  knitr::kable()

You can get any of this doing:

source = file.path(system.file("rmarkdown", package="hbcABC"),
          "Rscripts",
          category,
          fn)

file.copy(source, final_R)

R markdown files rmarkdown/templates

library(tidyverse)
setwd(here::here())
fns = list.files("inst/rmarkdown/templates", pattern = "yaml", recursive = TRUE)
lapply(fns, function(fn){
    yaml::read_yaml(file.path("inst/rmarkdown/templates", fn)) %>% 
        as.data.frame() %>% 
        select(name, description) %>% 
        mutate(fn = dirname(fn))
}) %>% bind_rows() %>% knitr::kable()

You can get any of this doing:

source = file.path(system.file("rmarkdown", package="hbcABC"),
          "templates",
          fn,
          "skeleton",
          "skeleton.Rmd")

file.copy(source, final_Rmd)

hbc/hbcABC documentation built on Sept. 5, 2019, 9:51 p.m.