Implement package-level quiet option

R/models.R

@@ -4,7 +4,6 @@
 #'
 #' @param time Relative time of observation (typically seconds), numeric
 #' @param conc Greenhouse gas concentration, numeric
-#' @param quiet Be quiet? Logical
 #' @return A wide-form \code{\link{data.frame}} with fit statistics for linear,
 #' robust linear, and polynomial models. By default, extensive details are
 #' provided only for the linear fi; for robust linear and polynomial, only
@@ -25,11 +24,11 @@
 #' dat$SECONDS <- dat$SECONDS - min(dat$SECONDS) # normalize time to start at 0
 #' plot(dat$SECONDS, dat$CO2)
 #' wtf_fit_models(dat$SECONDS, dat$CO2)
-wtf_fit_models <- function(time, conc, quiet = FALSE) {
+wtf_fit_models <- function(time, conc) {
   # Basic linear model
   try(mod <- lm(conc ~ time))
   if(!exists("mod")) {
-    if(!quiet) warning("Could not fit linear model")
+    wtf_warning("Could not fit linear model")
     return(NULL)
   }
 
@@ -49,7 +48,7 @@ wtf_fit_models <- function(time, conc, quiet = FALSE) {
     coefficients(robust)[2]
   },
   error = function(e) {
-    if(!quiet) warning("Could not fit robust linear model")
+    wtf_warning("Could not fit robust linear model")
     NA_real_
   })
 
@@ -59,7 +58,7 @@ wtf_fit_models <- function(time, conc, quiet = FALSE) {
     summary(poly)$r.squared
   },
   error = function(e) {
-    if(!quiet) warning("Could not fit polynomial model")
+    wtf_warning("Could not fit polynomial model")
     NA_real_
   })
 

R/read_functions.R

@@ -4,13 +4,12 @@
 #'
 #' @param file Filename to read, character
 #' @param model Instrument model name, string
-#' @param quiet Be quiet? Logical
 #' @details The is an internal function used by \code{\link{wtf_read_LI7810}}
 #' and \code{\link{wtf_read_LI7820}}, and not normally called by users.
 #' @importFrom utils read.table
 #' @importFrom lubridate ymd_hms
 #' @return A \code{\link{data.frame}} with the parsed data.
-wtf_read_LI78x0 <- function(file, model, quiet) {
+wtf_read_LI78x0 <- function(file, model) {
 
   dat_raw <- readLines(file)
 
@@ -41,36 +40,34 @@ wtf_read_LI78x0 <- function(file, model, quiet) {
   dat$MODEL <- model
   dat$DATE <- dat$TIME <- NULL
 
-  if(!quiet) message(basename(file), ": read ", nrow(dat), " rows of ", sn, " data, ",
-                     min(dat$TIMESTAMP), " to ", max(dat$TIMESTAMP), " ", tz)
+  wtf_message(basename(file), ": read ", nrow(dat), " rows of ", sn, " data, ",
+              min(dat$TIMESTAMP), " to ", max(dat$TIMESTAMP), " ", tz)
 
   return(dat)
 }
 
 #' Read a LI-7810 data file
 #'
 #' @param file Filename to read, character
-#' @param quiet Be quiet? Logical
 #' @return A \code{\link{data.frame}} with the parsed data.
 #' @details Currently LI-7810 and LI-7820 files are handled identically.
 #' @export
 #' @examples
 #' f <- system.file("extdata/TG10-01087.data", package = "whattheflux")
 #' dat <- wtf_read_LI7810(f)
-wtf_read_LI7810 <- function(file, quiet = FALSE) {
-  wtf_read_LI78x0(file, "LI-7810", quiet)
+wtf_read_LI7810 <- function(file) {
+  wtf_read_LI78x0(file, "LI-7810")
 }
 
 #' Read a LI-7820 data file
 #'
 #' @param file Filename to read, character
-#' @param quiet Be quiet? Logical
 #' @return A \code{\link{data.frame}} with the parsed data.
 #' @details Currently LI-7810 and LI-7820 files are handled identically.
 #' @export
 #' @examples
 #' f <- system.file("extdata/TG20-01182.data", package = "whattheflux")
 #' dat <- wtf_read_LI7820(f)
-wtf_read_LI7820 <- function(file, quiet = FALSE) {
-  wtf_read_LI78x0(file, "LI-7820", quiet)
+wtf_read_LI7820 <- function(file) {
+  wtf_read_LI78x0(file, "LI-7820")
 }

R/zzz.R

@@ -0,0 +1,15 @@
+# zzz.R - miscellany
+
+wtf_message <- function(...) {
+  if (getOption("whattheflux.quiet", default = FALSE)) {
+    return()
+  }
+  message(...)
+}
+
+wtf_warning <- function(...) {
+  if (getOption("whattheflux.quiet", default = FALSE)) {
+    return()
+  }
+  warning(...)
+}

tests/testthat/test-read_functions.R

@@ -1,24 +1,24 @@
 test_that("wtf_read_LI7810 works", {
 
+  options(whattheflux.quiet = TRUE)
+
   # Good data
-  x <- wtf_read_LI7810("data/TG10-01087-good.data", quiet = TRUE)
+  x <- wtf_read_LI7810("data/TG10-01087-good.data")
   expect_s3_class(x, "data.frame")
   expect_true(is.na(x$CO2[1])) # parsed missing values
   expect_true("SN" %in% names(x)) # parsed serial number from header
 
-  suppressMessages({
-    expect_message(wtf_read_LI7810("data/TG10-01087-good.data", quiet = FALSE))
-  })
-
   # Bad data
-  expect_error(wtf_read_LI7810("data/TG10-01087-bad.data", quiet = TRUE),
+  expect_error(wtf_read_LI7810("data/TG10-01087-bad.data"),
                regexp = "does not appear")
 })
 
 test_that("wtf_read_LI7820 works", {
 
+  options(whattheflux.quiet = TRUE)
+
   # Good data
-  x <- wtf_read_LI7820("data/TG20-01182-good.data", quiet = TRUE)
+  x <- wtf_read_LI7820("data/TG20-01182-good.data")
   expect_s3_class(x, "data.frame")
   expect_true("SN" %in% names(x)) # parsed serial number from header
 

tests/testthat/test-zzz.R

@@ -0,0 +1,10 @@
+test_that("quiet functionality works", {
+  # Check that the wtf_message and wtf_warning functions respect quiet option
+  options(whattheflux.quiet = TRUE)
+  expect_no_message(wtf_message("hi"))
+  expect_no_warning(wtf_warning("hi"))
+
+  options(whattheflux.quiet = FALSE)
+  expect_message(wtf_message("hi"), regexp = "hi")
+  expect_warning(wtf_warning("hi"), regexp = "hi")
+})