R/chmi.dirs.R

In mvazquezs/chmitools: Package to manage & obtain results of the CHMI Study

#-------------------
# load directories
#-------------------

#' @export
chmi.phendir <- function()
{
  nodename <- Sys.info()[["nodename"]]

  switch(nodename,
			'crp1028.csc.es' = '/Users/migvazquez/datasets/chmiddbb',
      'CRP1028.local' = '/Users/migvazquez/datasets/chmiddbb',
      'annamiquel-H110M-S2H' = '/home/annamiquel/datasets/chmiddbb',
      'LAPTOP-UJDSJL8E' = '~/datasets/chmiddbb',
      'mbp-de-csc.csc.es' = '~/Documents/datasets/chmiddbb',
      'LAPTOP-V8QUEKTJ' = '~/Documents/datasets/chmiddbb',

    stop(paste0("`nodemname` (", nodename, ") is unknown")))
}



#---------------
# load packages
#---------------

chmi.required_packages <- function()
{
	### repositories
	local({r <- getOption('repos')
       r['CRAN'] <- 'https://cloud.r-project.org/'
       options(repos = r)})

	### funtion to auto_load
	auto_load <- function(a.package){
		 			 			suppressWarnings(suppressPackageStartupMessages(
   		 					library(a.package, character.only = T)))
	}

	### list of packages
	pacman::p_load(
    tidyverse, lubridate, data.table, testthat, assertthat,
		plyr, Hmisc, reshape, viridis, RColorBrewer, scales, magrittr, gtools,
    gridExtra, rmarkdown, knitr, prettydoc, DT, forcats,
    nlme, readxl, openxlsx, tidyr, stringr, lmerTest,
    janitor, broom, tidymodels, extrafont,
    install = TRUE)

if(R.Version()$os == 'linux-gnu') {
	### option screen 'width'
 	options(width = 150)
  }

	### rm funtions `R.profile`
	rm(list = ls(all = T))
}


#------------------
# load theme_set()
#------------------

chmi.theme_ggplot_setup <- function()
{
# setup 'ggplot'
  theme_set(theme_light() +
    theme(
    	legend.position = 'bottom',
    	text = element_text(family = 'Arial'),
      plot.title = element_text(size = 12, hjust = .5, face = 'bold'),
      axis.text.x = element_text(size = 9, angle = 45, hjust = .95, vjust = .9),
      axis.title = element_text(size = 12, face = 'bold')))
}