R/renderRmdFiles.R

In sbalci/AutoJournalWatch: Auto Journal Watch.

if (file.exists("~/JournalWatchPBPath/.RData")) {
    
load("~/JournalWatchPBPath/.RData")
    
}


PubMedString <- "PubMed: https://www.ncbi.nlm.nih.gov/pubmed/?term="

doiString <- "doi: https://doi.org/"


# source_rmd <- function(rmd_file){
#     knitr::knit(rmd_file,
#                 output = tempfile(),
#                 envir = globalenv(),
#                 quiet = TRUE,
#                 encoding = "UTF-8")
# }

# list_of_Rmd <- list.files(path = "~/JournalWatchPBPath", pattern = "*Recent.Rmd", full.names = TRUE)

# purrr::map(.x = list_of_Rmd, .f = source_rmd)


# mypandoc <- Sys.getenv("RSTUDIO_PANDOC")
# Sys.setenv(RSTUDIO_PANDOC=mypandoc)
Sys.setenv(RSTUDIO_PANDOC= "/Applications/RStudio.app/Contents/MacOS/pandoc"); rmarkdown::render(input = "~/JournalWatchPBPath/RecentPBPathJW.Rmd",
                  output_format = "html_notebook",
                  output_dir = "~/JournalWatchPBPath/",
                  output_file = "RecentPBPathJW.nb.html",
                  quiet = TRUE,
                  encoding = "UTF-8"
)

save.image("~/JournalWatchPBPath/.RData")