Merge pull request #182 from iNZightVIT/release/1.12.1

Release 1.12.1

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: iNZightTools
 Type: Package
 Title: Tools for 'iNZight'
-Version: 1.12.0
+Version: 1.12.1
 Depends: R (>= 4.0)
 Imports:
     chron,

NEWS.Md

@@ -1,3 +1,8 @@
+## iNZightTools 1.12.1
+
+- fix bug in `smart_read()` where parsing column types (numerc -> categorical) failed if `NA`s in column
+- fix test failing in new version of survey (2.4)
+
 # iNZightTools 1.12.0
 
 - add new support for metadata formats:

R/import_data.R

@@ -374,7 +374,10 @@ validate_type_changes <- function(x, column_types) {
             "c" = {
                 ## Convert numeric to factor
                 ncol <- suppressWarnings(as.numeric(as.character(col)))
-                if (any(is.na(ncol)) || !all(ncol == col))
+                # skip if ONE missing (not both)
+                colm <- ncol == col | (is.na(col) + is.na(ncol)) == 2L
+                colm <- ifelse(is.na(colm), FALSE, colm)
+                if (!all(colm))
                     return("")
                 lvls <- sort(unique(ncol))
                 if (is.factor(col)) {

tests/testthat/cas500-missing.csv

@@ -0,0 +1,24 @@
+cellsource,rightfoot,travel,getlunch,height,gender,age,year,armspan,cellcost
+pocket,20,walk,home,152,2,12,7,150,30
+parent,25,other,friend,153,1,11,6,152,50
+parent,21,motor,home,137,2,10,6,132,55
+pocket,20,walk,home,115,2,9,5,130,60
+pocket,23,other,home,165,1,14,10,160,20
+parent,19,motor,home,137,,11,7,50,50
+parent,23,motor,home,164,1,12,8,164,10
+pocket,35,motor,tuckshop,150,1,15,11,100,20
+parent,22,motor,home,150,,12,8,152,10
+other,30,walk,tuckshop,123,2,14,9,23,0
+parent,30,motor,tuckshop,185,2,14,9,180,60
+parent,23,other,home,162,1,13,9,157,20
+job,13,bus,home,180,1,14,9,165,20
+parent,22,bus,home,164,1,15,10,127,26
+job,24,train,home,153,,10,6,158,55
+parent,28,motor,home,176,2,14,9,178,20
+parent,11,bike,home,129,2,10,5,165,0
+other,23,motor,home,145,2,10,6,144,25
+parent,40,motor,tuckshop,160,2,14,9,160,60
+pocket,25,bus,home,155,,13,8,150,10
+parent,28,motor,home,155,2,12,8,155,0
+parent,19,motor,home,146,1,9,4,140,25
+job,29,walk,none,165,,13,9,164,50

tests/testthat/test_aggregateData.R

@@ -89,11 +89,11 @@ test_that("Aggregating survey data is valid", {
         skip("Old version of srvyr")
     }
 
-    qf <- survey::svyquantile
+    skip_if(packageVersion("survey") < package_version('4.2'))
     expect_equal(
         svy_agg$api99_q25,
         svyby(~api99, ~stype, svy, survey::svyquantile,
-            quantiles = 0.25, keep.var = FALSE)[1, c(2, 6, 10)] %>% as.double()
+            quantiles = 0.25, keep.var = FALSE, ci = FALSE)$statistic
     )
     expect_equal(eval(parse(text = code(svy_agg))), svy_agg, ignore_attr = TRUE)
 })

tests/testthat/test_smart_read.R

@@ -71,6 +71,15 @@ test_that("Column type overrides are respected", {
 
     # null should also work
     expect_s3_class(smart_read("cas500.csv", column_types = NULL), "data.frame")
+
+    # NA values in num to cat conversion is OK
+    cas_missing <- smart_read("cas500-missing.csv", column_types = c(gender = "c"))
+    expect_s3_class(cas_missing$gender, "factor")
+    expect_equal(
+        eval(parse(text = paste(code(cas_missing), collapse = "\n"))),
+        cas_missing,
+        ignore_attr = TRUE
+    )
 })
 
 test_that("SAS Import num to cat works", {