allow suppressing messages to console

R/dcc.R

@@ -137,6 +137,8 @@
 ##' @param sb \code{logical} flag indicating whether textual status
 ##'   bar for moving case should be suppressed. Suppression is
 ##'   recommended for e.g.  Sweave files.
+##' @param verbose \code{logical} flag indicating if informative messages should
+##'   be written to the console (default is `TRUE`).
 ##' @return 'dcc' returns an 'object' of class '"tc_dcc"'.
 ##'   
 ##'   The functions 'summary' and 'plot' are used to obtain and print
@@ -193,9 +195,7 @@
 ##'   selection for the dependent bootstrap, Econometric Reviews
 ##'   23(1), 53-70.
 ##' @examples
-##' \dontrun{
 ##' dc_resp <- dcc(muc_spruce, muc_clim)
-##' }
 ##' @author Christian Zang; the original MATLAB code for exact
 ##'   bootstrapping was written by Dave Meko
 ##' @import Rcpp
@@ -216,7 +216,8 @@ dcc <- function(chrono,
                var_names = NULL,
                ci = 0.05,
                boot = "stationary",
-               sb = TRUE
+               sb = TRUE,
+               verbose = TRUE
                )
 {
 
@@ -253,7 +254,8 @@ dcc <- function(chrono,
   ## time span
   truncated_input <- truncate_input(chrono, climate,
                                    timespan = timespan, minmonth,
-                                   .dynamic)
+                                   .dynamic,
+                                   silent = !verbose)
 
   if (dynamic != "static" & truncated_input$missing) {
     stop("Missing data in proxy series, moving or evolving functions are not computed.\n")

R/dlm.R

@@ -98,7 +98,8 @@ dlm <- function(chrono,
                 var_names = NULL,
                 param_names = NULL,
                 intercept = TRUE,
-                scale = FALSE) {
+                scale = FALSE,
+                verbose = TRUE) {
 
   climate <- apply_var_names(as_tcclimate(climate), var_names)
   selection <- unify_selection(selection)
@@ -115,7 +116,8 @@ dlm <- function(chrono,
   ## time span
   truncated_input <- truncate_input(chrono, climate,
                                     timespan = timespan, minmonth,
-                                    dynamic = "static")
+                                    dynamic = "static",
+                                    silent = !verbose)
 
   climate_pmat <- make_pmat(truncated_input$climate, truncated_input$pad)
 

R/gershunov.R

@@ -27,6 +27,10 @@
 ##' @param boot \code{logical} shall the individual correlations be
 ##'     bootstrapped?  (see details)
 ##' @param sb \code{logical} shall a status bar be drawn?
+##' @param check_duration \code{logical} should the duration be checked before 
+##'     running with individually boostrapped correlations? The default is `TRUE`, 
+##'     set to `FALSE` to suppress interactive selections and messages to the
+##'     console.
 ##' @return a \code{data.frame} with p values for the testing the null
 ##'     hypothesis that the low-frequency modulation of the
 ##'     correlations of the variables with tree-growth can be
@@ -36,13 +40,13 @@
 ##'     Monsoon rainfall relationship: Signal or noise? Journal of
 ##'     Climate 14:2486-2492.
 ##' @examples
-##' \dontrun{
+##' \donttest{
 ##' dc_cor <- dcc(muc_spruce, muc_clim, 3:9, method = "cor", moving = TRUE)
 ##' g_test(dc_cor)
 ##' }
 ##' @keywords test
 ##' @export
-g_test <- function(x, boot = FALSE, sb = TRUE) {
+g_test <- function(x, boot = FALSE, sb = TRUE, check_duration = TRUE) {
   if (!any(class(x) != "tc_dcc"))
     stop("Please provide output of function `dcc`.")
 
@@ -80,26 +84,28 @@ g_test <- function(x, boot = FALSE, sb = TRUE) {
 
   ## if boot is TRUE, warn because of long calculation, and give the
   ## option to cancel
-  if (boot) {
-    cat("Checking duration...\n")
-    dur <- system.time({
-      tc_mfunc(x$truncated$tree, x$design,
-               method = "correlation",
-               start_last = .start_last,
-               win_size = .win_size,
-               win_offset = .win_offset,
-               boot = .boot,
-               sb = FALSE,
-               ci = 0.05)
-    })
-    dur1000 <- ceiling(dur[3] * niter / 60)
-    cat("Running this test with bootstrapping on the individual correlations enabled will take around", dur1000, "minutes.\n")
-    ans <- readline("Do you really want to run this? [Y/n]\n")
-    if (ans != "Y")
-      stop("Execution interrupted by user.")
-    cat("Ok then. Maybe time to grab a sandwich?\n")
-  } else {
-    cat("Performing test without bootstrapping individual correlations.\n")
+  if (check_duration) {
+    if (boot) {
+      cat("Checking duration...\n")
+      dur <- system.time({
+        tc_mfunc(x$truncated$tree, x$design,
+                 method = "correlation",
+                 start_last = .start_last,
+                 win_size = .win_size,
+                 win_offset = .win_offset,
+                 boot = .boot,
+                 sb = FALSE,
+                 ci = 0.05)
+      })
+      dur1000 <- ceiling(dur[3] * niter / 60)
+      cat("Running this test with bootstrapping on the individual correlations enabled will take around", dur1000, "minutes.\n")
+      ans <- readline("Do you really want to run this? [Y/n]\n")
+      if (ans != "Y")
+        stop("Execution interrupted by user.")
+      cat("Ok then. Maybe time to grab a sandwich?\n")
+    } else {
+      cat("Performing test without bootstrapping individual correlations.\n")
+    }
   }
 
   ## test tree-ring data and the columns of the design matrix for normality

R/seascorr.R

@@ -67,6 +67,9 @@
 ##' 
 ##' @param secondary position \code{numeric} or name \code{character}
 ##'   of secondary climate variable
+##'   
+##' @param verbose \code{logical} flag indicating if informative messages should
+##'   be written to the console (default is `TRUE`).
 ##' 
 ##' @return 'seascorr' returns an 'object' of class '"tc_seascorr"'.
 ##'
@@ -106,7 +109,7 @@
 ##' @export
 seascorr <- function(chrono, climate, var_names = NULL, timespan =
                      NULL, complete = 9, season_lengths = c(1, 3, 6),
-                     primary = 1, secondary = 2, ci = 0.05) {
+                     primary = 1, secondary = 2, ci = 0.05, verbose = TRUE) {
 
   ## check input
   if (!any(1:12 == complete))
@@ -189,7 +192,8 @@ seascorr <- function(chrono, climate, var_names = NULL, timespan =
   truncated_input <- truncate_input(chrono, climate,
                                     timespan = timespan,
                                     minmonth = minmonth,
-                                    dynamic = "static")
+                                    dynamic = "static",
+                                    silent = !verbose)
 
   m <- length(truncated_input$chrono)