Merge branch 'release/2.4.1'

UCLATALL · May 28, 2021 · f5d3b37 · f5d3b37
2 parents dce65c8 + 9264a35
commit f5d3b37
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diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
@@ -4,7 +4,6 @@ on:
   push:
     branches:
       - main
-      - develop
       - release/*
   pull_request:
     branches:
@@ -27,6 +26,7 @@ jobs:
           - {os: macOS-latest, r: 'release'}
           - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: '3.4', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -71,6 +71,12 @@ jobs:
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 
+      - name: Install dependencies not on RSPM
+        if: ${{ matrix.config.r == '3.4' }}
+        run: |
+          install.packages(c("lme4", "car"), repos = "https://mran.microsoft.com/snapshot/2018-04-01")
+        shell: Rscript {0}
+
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false

diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,4 @@
 # Personal R files
-**/*.Rproj
 .Rproj.user
 .Rhistory
 .RData

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: supernova
 Type: Package
 Title: Judd, McClelland, & Ryan Formatting for ANOVA Output
-Version: 2.4.0
-Date: 2021-05-03
+Version: 2.4.1
+Date: 2021-05-28
 Authors@R: c(
     person(
       "Adam", "Blake", 
@@ -29,7 +29,7 @@ Description: Produces ANOVA tables in the format used by Judd, McClelland, and R
     proportional reduction in error and formatting to improve ease the transition between the book 
     and R.
 License: GPL-3
-Depends: R (>= 3.5.0)
+Depends: R (>= 3.4.0)
 Suggests: 
     car,
     covr,
@@ -48,7 +48,8 @@ Imports:
     stringr,
     vctrs,
     pillar,
-    methods
+    methods,
+    backports
 RoxygenNote: 7.1.1
 URL: https://github.com/UCLATALL/supernova
 BugReports: https://github.com/UCLATALL/supernova/issues

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# supernova 2.4.1
+
+* Small tweaks to make the package work on R 3.4.0
+
+
 # supernova 2.4.0
 
 ## New features

diff --git a/R/generate_models.R b/R/generate_models.R
@@ -243,6 +243,7 @@ drop_term <- function(fit, term) {
     paste0(collapse = "") %>%
     stringr::str_squish()
   new_call_string <- sprintf("drop_term(%s, \"%s\")", call_string, term)
+  str2lang <- utils::getFromNamespace("str2lang", "backports")
   reduced_fit$call <- str2lang(new_call_string)
 
   oldClass(reduced_fit) <- "lm"

diff --git a/R/listwise_delete.R b/R/listwise_delete.R
@@ -50,6 +50,7 @@ listwise_delete.lm <- function(obj, vars = all.vars(formula(obj))) {
     class = "supernova_missing_values_message"
   )
 
+  str2lang <- utils::getFromNamespace("str2lang", "backports")
   rlang::with_handlers(
     eval(str2lang(call_string), envir = environment(as.formula(obj))),
     supernova_missing_values_message = rlang::calling(function(cnd) {

diff --git a/R/pairwise.R b/R/pairwise.R
@@ -123,7 +123,8 @@ pairwise_t <- function(fit, term = NULL, alpha = .05, correction = "none") {
         t = number(statistic),
         df = fit$df.residual,
         lower = number(diff - margin), upper = number(diff + margin),
-        p_val = number(p, 4, leading_zero = FALSE)
+        p_val = number(p, 4, leading_zero = FALSE),
+        stringsAsFactors = FALSE
       )
 
       if (correction == "bonferroni") {
@@ -185,7 +186,8 @@ pairwise_tukey <- function(fit, term = NULL, alpha = .05) {
         q = number(statistic),
         df = fit$df.residual,
         lower = number(diff - margin), upper = number(diff + margin),
-        p_adj = number(p, 4, leading_zero = FALSE)
+        p_adj = number(p, 4, leading_zero = FALSE),
+        stringsAsFactors = FALSE
       )
     })
 

diff --git a/README.md b/README.md
@@ -612,9 +612,8 @@ pairwise(lm(Thumb ~ Sex, data = supernova::Fingers))
 #> 
 #> ── Tukey's Honestly Significant Differences ────────────────────────────────────
 #> Model: Thumb ~ Sex
-#> 
-#> ── Sex
-#> 1 comparison of 2 levels
+#> Sex
+#> Levels: 2
 #> Family-wise error-rate: 0.05
 #> 
 #>   group_1 group_2  diff pooled_se     q    df lower upper p_adj
@@ -635,26 +634,24 @@ pairwise(lm(Thumb ~ Sex, data = supernova::Fingers), correction = "none")
 #> 
 #> ── Pairwise t-tests ────────────────────────────────────────────────────────────
 #> Model: Thumb ~ Sex
-#> 
-#> ── Sex
-#> 1 comparison of 2 levels
+#> Sex
+#> Levels: 2
 #> Family-wise error-rate: 0.05
 #> 
 #>   group_1 group_2  diff pooled_se     t    df lower upper p_val
 #>   <chr>   <chr>   <dbl>     <dbl> <dbl> <int> <dbl> <dbl> <dbl>
-#> 1 male    female  6.447     1.456 4.428   155 4.038 8.856 .0000
+#> 1 male    female  6.447     1.029 6.262   155 4.743 8.150 .0000
 pairwise(lm(Thumb ~ Sex, data = supernova::Fingers), correction = "Bonferroni")
 #> 
 #> ── Pairwise t-tests with Bonferroni correction ─────────────────────────────────
 #> Model: Thumb ~ Sex
-#> 
-#> ── Sex
-#> 1 comparison of 2 levels
+#> Sex
+#> Levels: 2
 #> Family-wise error-rate: 0.05
 #> 
 #>   group_1 group_2  diff pooled_se     t    df lower upper p_adj
 #>   <chr>   <chr>   <dbl>     <dbl> <dbl> <int> <dbl> <dbl> <dbl>
-#> 1 male    female  6.447     1.456 4.428   155 4.038 8.856 .0000
+#> 1 male    female  6.447     1.029 6.262   155 4.743 8.150 .0000
 ```
 
 In these data the `Sex` variable did not have any other values than male
@@ -671,9 +668,8 @@ pairwise(lm(Thumb ~ Sex + Height, data = supernova::Fingers))
 #> 
 #> ── Tukey's Honestly Significant Differences ────────────────────────────────────
 #> Model: Thumb ~ Sex + Height
-#> 
-#> ── Sex
-#> 1 comparison of 2 levels
+#> Sex
+#> Levels: 2
 #> Family-wise error-rate: 0.05
 #> 
 #>   group_1 group_2  diff pooled_se     q    df lower upper p_adj

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,18 +1,17 @@
 ## Release summary
 
-This release adds a simple interface for running pairwise t and Tukey tests on a linear model.
+Small tweaks to make the package work on R 3.4
 
 
 ## Test environments
 
 - Local install on macOS Big Sur 11.3; R 4.0.4
 - Win Builder via `devtools::check_win_devel()`
-- R-Hub via `devtools::check_rhub()` 
-  * (only note was about the Date field which is now updated)
+- R-Hub via `devtools::check_rhub()`
 - GitHub Actions
   * Mac OS X, 10.15.7; R 4.0.5
   * Microsoft Windows Server 2019, 10.0.17763; R 4.0.5
-  * Ubuntu, 20.04; R-devel, R 4.0.5
+  * Ubuntu, 20.04; R-devel, R 4.0.5, 3.4.4
 
 
 ## R CMD check results

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -1,5 +1,6 @@
 Bonferroni
 Codecov
+HSD
 McClelland
 PRE
 README

diff --git a/supernova.Rproj b/supernova.Rproj
@@ -0,0 +1,21 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace
diff --git a/tests/testthat/_snaps/pairwise.md b/tests/testthat/_snaps/pairwise.md
@@ -2,90 +2,3 @@
 
     `correction` must be one of "none", "Bonferroni", or "Tukey".
 
-# catch all other data here
-
-    Code
-      pairwise_t(fit)
-    Message <cliMessage>
-      
-      -- Pairwise t-tests ------------------------------------------------------------
-      Model: Thumb ~ RaceEthnic
-    Output
-      
-    Message <cliMessage>
-      RaceEthnic
-      Levels: 5
-      Family-wise error-rate: 0.401
-    Output
-      
-         group_1       group_2         diff pooled_se      t    df  lower  upper p_val
-         <chr>         <chr>          <dbl>     <dbl>  <dbl> <int>  <dbl>  <dbl> <dbl>
-       1 African Amer~ White          2.985     2.023  1.476   152 -0.363  6.333 .1421
-       2 Asian         White         -0.964     1.182 -0.816   152 -2.920  0.992 .4160
-       3 Latino        White         -1.796     1.434 -1.253   152 -4.169  0.577 .2122
-       4 Other         White          5.929     1.953  3.037   152  2.698  9.161 .0028
-       5 Asian         African Amer~ -3.949     2.003 -1.971   152 -7.265 -0.634 .0505
-       6 Latino        African Amer~ -4.782     2.162 -2.212   152 -8.359 -1.204 .0285
-       7 Other         African Amer~  2.944     2.536  1.161   152 -1.252  7.140 .2474
-       8 Latino        Asian         -0.832     1.406 -0.592   152 -3.159  1.495 .5548
-       9 Other         Asian          6.894     1.932  3.567   152  3.696 10.092 .0005
-      10 Other         Latino         7.726     2.096  3.686   152  4.257 11.194 .0003
-
----
-
-    Code
-      pairwise_bonferroni(fit)
-    Message <cliMessage>
-      
-      -- Pairwise t-tests with Bonferroni correction ---------------------------------
-      Model: Thumb ~ RaceEthnic
-    Output
-      
-    Message <cliMessage>
-      RaceEthnic
-      Levels: 5
-      Family-wise error-rate: 0.049
-    Output
-      
-         group_1      group_2        diff pooled_se      t    df   lower  upper  p_adj
-         <chr>        <chr>         <dbl>     <dbl>  <dbl> <int>   <dbl>  <dbl>  <dbl>
-       1 African Ame~ White         2.985     2.023  1.476   152  -2.292  8.263 1.0000
-       2 Asian        White        -0.964     1.182 -0.816   152  -4.047  2.119 1.0000
-       3 Latino       White        -1.796     1.434 -1.253   152  -5.536  1.944 1.0000
-       4 Other        White         5.929     1.953  3.037   152   0.836 11.023  .0282
-       5 Asian        African Ame~ -3.949     2.003 -1.971   152  -9.175  1.276  .5049
-       6 Latino       African Ame~ -4.782     2.162 -2.212   152 -10.420  0.857  .2845
-       7 Other        African Ame~  2.944     2.536  1.161   152  -3.670  9.559 1.0000
-       8 Latino       Asian        -0.832     1.406 -0.592   152  -4.500  2.835 1.0000
-       9 Other        Asian         6.894     1.932  3.567   152   1.853 11.934  .0048
-      10 Other        Latino        7.726     2.096  3.686   152   2.258 13.193  .0032
-
----
-
-    Code
-      pairwise_tukey(fit)
-    Message <cliMessage>
-      
-      -- Tukey's Honestly Significant Differences ------------------------------------
-      Model: Thumb ~ RaceEthnic
-    Output
-      
-    Message <cliMessage>
-      RaceEthnic
-      Levels: 5
-      Family-wise error-rate: 0.05
-    Output
-      
-         group_1       group_2        diff pooled_se      q    df   lower  upper p_adj
-         <chr>         <chr>         <dbl>     <dbl>  <dbl> <int>   <dbl>  <dbl> <dbl>
-       1 African Amer~ White         2.985     2.023  1.476   152  -4.913 10.884 .8347
-       2 Asian         White        -0.964     1.182 -0.816   152  -5.579  3.651 .9783
-       3 Latino        White        -1.796     1.434 -1.253   152  -7.394  3.802 .9018
-       4 Other         White         5.929     1.953  3.037   152  -1.695 13.554 .2058
-       5 Asian         African Ame~ -3.949     2.003 -1.971   152 -11.771  3.872 .6325
-       6 Latino        African Ame~ -4.782     2.162 -2.212   152 -13.221  3.658 .5227
-       7 Other         African Ame~  2.944     2.536  1.161   152  -6.956 12.844 .9238
-       8 Latino        Asian        -0.832     1.406 -0.592   152  -6.322  4.657 .9935
-       9 Other         Asian         6.894     1.932  3.567   152  -0.651 14.438 .0910
-      10 Other         Latino        7.726     2.096  3.686   152  -0.458 15.909 .0742
-
diff --git a/tests/testthat/test-pairwise.R b/tests/testthat/test-pairwise.R
@@ -85,16 +85,6 @@ test_that("pairwise_t family-wise error-rate is larger than alpha when more than
 })
 
 
-# Catch all -----------------------------------------------------------------------------------
-
-test_that("catch all other data here", {
-  fit <- lm(Thumb ~ RaceEthnic, supernova::Fingers)
-  expect_snapshot(pairwise_t(fit))
-  expect_snapshot(pairwise_bonferroni(fit))
-  expect_snapshot(pairwise_tukey(fit))
-})
-
-
 # Plots ---------------------------------------------------------------------------------------
 
 test_that("each type of comparisons object plots well", {

diff --git a/tests/testthat/test-print.supernova.R b/tests/testthat/test-print.supernova.R
@@ -120,6 +120,11 @@ test_that("nested repeated measures tables are beautifully formatted", {
 })
 
 test_that("crossed repeated measures tables are beautifully formatted", {
+  skip_if(
+    package_version(R.version) < 3.5,
+    "The MSE between will be off negligibly on older R versions (~.001)."
+  )
+
   model <- fit_lmer(
     rating ~ sex * yearsmarried * children + (1 | couple),
     data = get_data("jmr_ex11.22")

diff --git a/tests/testthat/test-supernova.lmerMod.R b/tests/testthat/test-supernova.lmerMod.R
@@ -75,7 +75,8 @@ test_that("supernova object has table, fit, and models", {
     MS = double(),
     `F` = double(),
     PRE = double(),
-    p = double()
+    p = double(),
+    stringsAsFactors = FALSE
   ))
 })
 
@@ -89,6 +90,11 @@ test_that("magrittr can pipe lmer() to supernova", {
 })
 
 test_that("magrittr can pipe data to lm() to supernova", {
+  skip_if(
+    package_version(R.version) < 3.5,
+    "This is only skipped to make this package compatible with DataCamp Light."
+  )
+
   # Believe it or not, this might not work. Do not remove or refactor test.
   # When stats::update() tries to get the call, the data object is just "."
   # supernova has to middle-man with supernova::update() to get this to work

diff --git a/tests/testthat/test-supernova.r b/tests/testthat/test-supernova.r
@@ -193,7 +193,8 @@ test_that("supernova table structure is well-formed", {
     MS = double(),
     `F` = double(),
     PRE = double(),
-    p = double()
+    p = double(),
+    stringsAsFactors = FALSE
   ))
 })