getRestingStateOK

#!/usr/bin/Rscript

# Load libraries required to download from REDCap and install custom packages.
# This loop installs missing pacakges.

for (package in c("REDCapR", "devtools"))
{
  if (!require(package, character.only = TRUE))
  {
    install.packages(package)
    library(package, character.only = TRUE)
  }
}

# Install the custom UdallR library. You may have to change the path, depending
## on where you downloaded UdallR to.
install("~/UdallR", quiet = TRUE)
library(UdallR, quietly = TRUE,  warn.conflicts = FALSE)

today <- gsub("[^0-9]", "", Sys.Date())
outfile <- paste0("closest-visits/closestVisits-", today, ".csv")

# It isn't secure to upload access tokens to GitHub, so store your access token
## in a file like this so R can read it.
rc.token <- readChar("~/UdallR/access-token.txt", nchars = 32)

# Read the data from the REDCap API. "stringsAsFactors" stops R from treating
## important strings as factors (which when written to file, are written as the
## underlying numeric representation.
dat <- as.data.frame(redcap_read(redcap_uri = "https://redcap.iths.org/api/",
                                 token = rc.token),
                     stringsAsFactors = FALSE)

# Test the UdallR cleaning function
# The visit variable doesn't do much right now.
cdat <- udallCleanREDCapDataWide(dat, visit = 1)

on.rest.ok <- as.logical(cdat$on_analyze_rest_fmri)
off.rest.ok <- as.logical(cdat$off_analyze_rest_fmri)

if (sum(is.na(on.rest.ok)) > 0)
    message(paste(sum(is.na(on.rest.ok)), "subjects have NA on rest status."))

if (sum(is.na(off.rest.ok)) > 0)
    message(paste(sum(is.na(on.rest.ok)), "subjects have NA off rest status."))

on.rest.subjs <- cdat$idnum[sapply(on.rest.ok, isTRUE)]
off.rest.subjs <- cdat$idnum[sapply(off.rest.ok, isTRUE)]

write.csv(file = "on-rest-OK.txt", on.rest.subjs, quote = FALSE,
            row.names = FALSE)
write.csv(file = "off-rest-OK.txt", off.rest.subjs, quote = FALSE,
            row.names = FALSE)