v1.1.2 - amended Life expectancy and proportion test scripts to resol…

…ve test execution in non-windows environments as requested by CRAN.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: PHEindicatormethods
 Type: Package
-Version: 1.1.1
+Version: 1.1.2
 Title: Common Public Health Statistics and their Confidence Intervals 
 Description: Functions to calculate commonly used public health statistics and 
     their confidence intervals using methods approved for use in the production  

NEWS.md

@@ -1,3 +1,8 @@
+## PHEindicatormethods v1.1.2
+
+Minor amendments to package testing scripts.  Updates will not affect end users.  
+
+
 ## PHEindicatormethods v1.1.1
 
 The following changes may affect backwards compatibility with earlier versions of the package:  

cran-comments.md

@@ -1,18 +1,14 @@
 
-## Resubmission of updated package version 1.1.1
-In this resubmission I have replaced spaces with %20s in a URL referenced in phe_life_expectancy.Rd 
+## Resubmission of updated package version 1.1.2
+Following recent release of package v1.1.1 to CRAN on 18/04/2019, I then received notification that 
+some tests were failing with nonsensical error messages on r-devel-linux-x86_64-fedora-clang and
+r-devel-linux-x86_64-debian-clang and r-oldrel-windows-ix86+x86_64. See <https://cran.r-project.org/web/checks/check_results_PHEindicatormethods.html>
 
+In this resubmission I have re-coded the affected tests in testProportions.R and testLifeExpectancy.R to resolve these issues although I have been unable to retest on the affected operating system environemnts.
 
-This package release v1.1.1 will replace the previous release v1.0.8 currently available on CRAN
+This package release v1.1.2 will replace the previous release v1.1.1 currently available on CRAN
 
-## Amendments in v1.1.1
-3 new functions have been added:  
-
-* phe_quantiles
-* phe_life_expectancy
-* phe_sii
-
-Also, minor amendments to existing functions.  These may result in backwards incompatibility - the circumstances when this may occur are clearly stated in the NEWS.md file and in the function documentation with solutions for how to make old code compatible with the later package version (eg logical 'percentage' argument replaced with numeric 'multiplier' argument - percentage = TRUE equivalent to multiplier = 100 etc).
+No changes have been made to the function code or documentation but I have incremented the version number and news file.
 
 ## Test Environments
 * local windows 10 install: R 3.5.1 and R 3.5.3 - Both OK

tests/testthat/testLifeExpectancy.R

@@ -251,17 +251,17 @@ test_that("LE - errors are generated when invalid arguments are used",{
   expect_error(phe_life_expectancy(df3, deaths, pops, startage),
                "the contents in the startage field do not match the contents of the age_contents vector")
   expect_error(phe_life_expectancy(df3, deaths, pops, startage,
-                                   age_contents = c("0", "1-4", "5-9",
-                                                    "20 – 24", "25 – 29",
-                                                    "10 – 14", "15 – 19",
-                                                    "30 – 34", "35 – 39",
-                                                    "40 – 44", "45 – 49",
-                                                    "50 – 54", "55 – 59",
-                                                    "60 – 64", "65 – 69",
-                                                    "70 – 74", "75 – 79",
-                                                    "80 – 84", "85 – 89",
-                                                    "90 +")),
-               "age_contents doesn't appear to be in ascending order; the following age bands appear out of position: 20 – 24, 25 – 29, 10 – 14, 15 – 19")
+                                   age_contents = c("0", "1 4", "5 9",
+                                                    "20 24", "25 29",
+                                                    "10 14", "15 19",
+                                                    "30 34", "35 39",
+                                                    "40 44", "45 49",
+                                                    "50 54", "55 59",
+                                                    "60 64", "65 69",
+                                                    "70 74", "75 79",
+                                                    "80 84", "85 89",
+                                                    "90+")),
+               "age_contents doesn't appear to be in ascending order; the following age bands appear out of position: 20 24, 25 29, 10 14, 15 19")
   expect_error(phe_life_expectancy(),
                "function life_expectancy requires at least 4 arguments: data, deaths, population, startage")
   expect_error(phe_life_expectancy(df1, deaths, pop, age,

tests/testthat/testProportions.R

@@ -28,8 +28,8 @@ test_that("proportions and CIs calculate correctly",{
   expect_equal(phe_proportion(slice(test_Prop,1:8)[1:3], Numerator, Denominator, type="upper"),
                select(slice(test_Prop,1:8),1:3,6),check.attributes=FALSE, check.names=FALSE, info="test upper")
 
-  expect_equal(phe_proportion(slice(test_Prop,33:35)[1:3], Numerator, Denominator, type="full"),
-               select(slice(test_Prop,33:35),1:9),check.attributes=FALSE, check.names=FALSE, info="test NAs")
+  expect_equal(phe_proportion(filter(test_Prop,Area %in% c("Area9","Area10","Area11"))[1:3], Numerator, Denominator, type="full"),
+               select(filter(test_Prop,Area %in% c("Area9","Area10","Area11")),1:9),check.attributes=FALSE, check.names=FALSE, info="test NAs")
 
   expect_equal(data.frame(phe_proportion(slice(test_Prop_g,1:8)[1:3], Numerator, Denominator, type="standard")),
                arrange(data.frame(test_Prop_g_results[1:6]),Area),check.attributes=FALSE, check.names=FALSE, info="test grouped")