statcheck command line interface

statcheck-cli

# License is GPLv2+
#!/usr/bin/env Rscript

library(statcheck)
library(stringr)
args <- commandArgs(trailingOnly=TRUE)

if (length(args)==0) {
    stop("Usage: statcheck-cli filename.txt", call.=FALSE)
} else if (length(args)==1) {
    ## default output file
    filename <- args[1]
}

buffer <- readLines(filename)

res <- statcheck(buffer,stat = c("t", "F", "cor", "chisq", "Z", "Q"),
          OneTailedTests = FALSE, alpha = 0.05, pEqualAlphaSig = TRUE,
          pZeroError = TRUE, OneTailedTxt = FALSE, AllPValues = FALSE)

if (length(res) == 0) {
    print("No report found")
    q()
}

lines <- list()
for(i in 1:nrow(res)) {
    stat <- as.character(res$Raw[i])
    lines <- grep(stat, buffer, fixed = TRUE)
    for (line in lines) {
        found <- str_locate_all(buffer[line], fixed(stat))
        for (point in 1:length(found)) {
            lp <- found[[point]]
            lineend <- lp[2]
            exp <- format(round(res$Computed[i], 3))
            if (res$Error[i]) {
                message <- paste("The expected value is ",
                                 exp, " (", res$Computed[i], ")", sep = "")
                mtype <- "error: "
            } else {
                message <- stat
                mtype <- "info: "
            }
            cat(filename, ":", line, ":", lp[1], ": ", mtype,
                message, "\n",
                sep = "")
        }
    }
}

statcheck.el

;; add this to your emacs config. `statcheck-cli` must be in your PATH
(flycheck-define-checker statscheck
  "A linter for statistics."
  :command ("statscheck-cli" source)
  :error-patterns
  ((error line-start (file-name) ":" line ":" column ": error: "
	    (message) line-end)
   (info line-start (file-name) ":" line ":" column ": info: "
	    (message) line-end))
  :modes (text-mode markdown-mode org-mode))

(add-to-list 'flycheck-checkers 'statscheck)