- let nonconvergence warnings be caught despite future

- turn off OS X on travis for now

Author: rubenarslan

.travis.yml

@@ -54,12 +54,12 @@ matrix:
         - pander
         - minpack.lm
         - StanHeaders
-    - os: osx
-      osx_image: xcode9.2
-    - os: osx
-      osx_image: xcode7.3
-      r_build_args: '--no-build-vignettes'
-      r_check_args: '--ignore-vignettes --no-examples'
+#    - os: osx
+#      osx_image: xcode9.2
+#    - os: osx
+#      osx_image: xcode7.3
+#      r_build_args: '--no-build-vignettes'
+#      r_check_args: '--ignore-vignettes --no-examples'
 
 addons:
   apt:
@@ -74,4 +74,3 @@ after_success:
 
 repos:
   CRAN: https://cloud.r-project.org
-  ropensci: http://packages.ropensci.org

R/misc.R

@@ -34,9 +34,9 @@ md.pattern <- function(x, plot = FALSE)
     mpat <- sortR[!duplicated(sortR), ]
   }
   if (all(!is.na(x))) {
-    cat(" /\\     /\\\n{  `---'  }\n{  O   O  }\n==>  V <==")
-    cat("  No need for mice. This data set is completely observed.\n")
-    cat(" \\  \\|/  /\n  `-----'\n\n")
+    message(" /\\     /\\\n{  `---'  }\n{  O   O  }\n==>  V <==")
+    message("  No need for mice. This data set is completely observed.\n")
+    message(" \\  \\|/  /\n  `-----'\n\n")
     mpat <- t(as.matrix(mpat, byrow = TRUE))
     rownames(mpat) <- table(pat)
   }
@@ -73,7 +73,7 @@ md_pattern <- function(data, omit_complete = TRUE, min_freq = 0.01) {
       # mice::md.pattern coerces character/factor to NA
       data[[i]] <- as.numeric(as.factor(data[[i]]))
     }
-    md_pattern <- md.pattern(data, plot = FALSE)
+    md_pattern <- suppressMessages(md.pattern(data, plot = FALSE))
     n_miss <- rownames(md_pattern)
     if (is.null(n_miss)) {
       n_miss <- rep(0, nrow(md_pattern))
@@ -84,7 +84,7 @@ md_pattern <- function(data, omit_complete = TRUE, min_freq = 0.01) {
       missing_by_var <- md_pattern[nrow(md_pattern), ]
       md_pattern <- md_pattern[, missing_by_var > 0]
     }
-    md_pattern <- tibble::as.tibble(md_pattern)
+    md_pattern <- tibble::as_tibble(md_pattern)
     stopifnot(!exists("n_miss", md_pattern))
     md_pattern$n_miss <- as.numeric(n_miss)
     md_pattern$n_miss[nrow(md_pattern)] <-

R/reliability.R

@@ -42,11 +42,14 @@ compute_reliabilities <- function(results, survey_repetition = "single") {
                                           survey_repetition, ci = TRUE)
         }, error = function(e) {
           tryCatch({
+            warning("Reliability CIs could not be computed for ", var)
+            warning(conditionMessage(e))
             compute_appropriate_reliability(var, scale_info,
                                           items,
                                           survey_repetition, ci = FALSE)
           }, error = function(e) {
-            warning(e)
+            warning("Reliability could not be computed for ", var)
+            warning(conditionMessage(e))
             NULL
           })
 

tests/testthat/test_misc.R

@@ -31,11 +31,17 @@ test_that("Missing values are computed properly", {
   expect_silent(mdp <- md_pattern(nhanes))
   expect_equal(mdp$n_miss[1], 27)
   expect_equal(nrow(mdp), 6)
+})
+
+test_that("Missing values are computed properly, omit complete", {
   expect_silent(mdp <- md_pattern(nhanes,
                         omit_complete = FALSE, min_freq = 0.2))
   expect_equal(mdp$n_miss[1], 27)
   expect_equal(mdp$n_miss[4], 5)
   expect_equal(nrow(mdp), 4)
+})
+
+test_that("Missing values are computed properly, degenerate cases", {
   expect_message(mdp <- md_pattern(data.frame()), "No missing")
   expect_message(mdp <- md_pattern(data.frame(x = 1, y = 1)), "No missing")
   expect_null(mdp)

tests/testthat/test_reliability.R

@@ -6,7 +6,7 @@ test_that("Internal consistencies can be computed", {
   library(dplyr)
   bfi <- bfi %>% select(-starts_with("BFIK_extra"),
                         -starts_with("BFIK_neuro"),
-                        -starts_with("BFIK_consc"))
+                        -starts_with("BFIK_open"))
   expect_silent(rels <- compute_reliabilities(bfi))
   expect_equal(length(rels), 2)
   expect_equal(length(rels$BFIK_agree), 1)
@@ -84,3 +84,11 @@ test_that("Multilevel reliabilities can be computed", {
 
   expect_equal(round(rels$BFIK_agree$multilevel_reliability$Rcn,3), 0)
 })
+
+test_that("Nonconvergence warnings are caught", {
+  data("bfi", package = "codebook")
+  library(dplyr)
+  bfi <- bfi %>% select(starts_with("BFIK_open"))
+  expect_warning(compute_reliabilities(bfi),
+                 "Reliability CIs could not be computed for BFIK_open")
+})