diff --git a/DESCRIPTION b/DESCRIPTION
index e275d03..fe607fa 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -54,7 +54,7 @@ License: GPL (>=3)
Copyright: This package contains codes copyrighted by third parites. See file COPYRIGHTS for details.
LazyLoad: true
Encoding: UTF-8
-URL: https://imbi-heidelberg.github.io/DescrTab2, https://imbi-heidelberg.github.io/DescrTab2/
+URL: https://imbi-heidelberg.github.io/DescrTab2/
BugReports: https://github.com/imbi-heidelberg/DescrTab2/issues
Config/testthat/edition: 3
RoxygenNote: 7.1.2
diff --git a/README.md b/README.md
index 07abf3d..aaba5a1 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
[![R-CMD-check](https://github.com/imbi-heidelberg/DescrTab2/workflows/R-CMD-check/badge.svg)](https://github.com/imbi-heidelberg/DescrTab2/actions)
-[![codecov](https://codecov.io/gh/imbi-heidelberg/DescrTab2/branch/master/graph/badge.svg)](https://codecov.io/gh/imbi-heidelberg/DescrTab2)
+[![codecov](https://codecov.io/gh/imbi-heidelberg/DescrTab2/branch/master/graph/badge.svg)](https://app.codecov.io/gh/imbi-heidelberg/DescrTab2)
[![Github version](https://img.shields.io/github/r-package/v/imbi-heidelberg/DescrTab2/master?label=Github%20version%20%40master)](https://github.com/imbi-heidelberg/DescrTab2/tree/master)
[![CRAN Version](https://www.r-pkg.org/badges/version/DescrTab2)](https://www.r-pkg.org/badges/version/DescrTab2)
[![Downloads CRAN](https://cranlogs.r-pkg.org/badges/grand-total/DescrTab2)](https://cranlogs.r-pkg.org/badges/grand-total/DescrTab2)
diff --git a/docs/404.html b/docs/404.html
index 0986a22..6da8254 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -73,7 +73,7 @@
DescrTab2
- 2.1.3
+ 2.1.7
diff --git a/docs/articles/index.html b/docs/articles/index.html
index b1e018f..13748b3 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -73,7 +73,7 @@
DescrTab2
- 2.1.3
+ 2.1.7
diff --git a/docs/authors.html b/docs/authors.html
index f1c8cf1..065bd68 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -73,7 +73,7 @@
DescrTab2
- 2.1.3
+ 2.1.7
diff --git a/docs/index.html b/docs/index.html
index a13196d..8d63e6d 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -38,7 +38,7 @@
DescrTab2
- 2.1.3
+ 2.1.7
@@ -159,7 +159,8 @@
Developers
Dev status
-
+
+
diff --git a/docs/news/index.html b/docs/news/index.html
index c928721..70e3780 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -73,7 +73,7 @@
DescrTab2
- 2.1.3
+ 2.1.7
@@ -140,6 +140,32 @@ Changelog
Source: NEWS.md
+
+
+
+- Fixed a bug where indices could not be specified inside var_options
+- fixed bug with printing CI abbreviations in tex mode
+
+
+
+
+
+- Add hline between footnotes and table in tex mode
+- make pagebreak alogrithm less aggressive
+
+
+
+
+
+- Fix bug with group_labels that lead to group N numbers not being dispalyed.
+
+
diff --git a/docs/reference/descr.html b/docs/reference/descr.html
index d443515..9c8f3a5 100644
--- a/docs/reference/descr.html
+++ b/docs/reference/descr.html
@@ -79,7 +79,7 @@
DescrTab2
- 2.1.3
+ 2.1.7
@@ -186,7 +186,7 @@ Calculate descriptive statistics
"missing_as_separate_category"), caption = NULL, replace_empty_string_with_NA = TRUE,
categories_first_summary_stats_second = FALSE),
test_options = list(paired = FALSE, nonparametric = FALSE, exact = FALSE, indices =
- c(), guess_id = TRUE, include_group_missings_in_test = FALSE,
+ c(), guess_id = FALSE, include_group_missings_in_test = FALSE,
include_categorical_missings_in_test = FALSE, test_override = NULL,
additional_test_args = list(), boschloo_max_n = 200),
reshape_rows = list(`Q1 - Q3` = list(args = c("Q1", "Q3"), fun = function(Q1, Q3) {
diff --git a/docs/reference/dot-onLoad.html b/docs/reference/dot-onLoad.html
index 129ae0a..4b4e1e2 100644
--- a/docs/reference/dot-onLoad.html
+++ b/docs/reference/dot-onLoad.html
@@ -74,7 +74,7 @@
DescrTab2
- 2.1.3
+ 2.1.7
diff --git a/docs/reference/farrington.manning.html b/docs/reference/farrington.manning.html
index 3a7448d..91eb4ef 100644
--- a/docs/reference/farrington.manning.html
+++ b/docs/reference/farrington.manning.html
@@ -77,7 +77,7 @@
DescrTab2
- 2.1.3
+ 2.1.7
diff --git a/docs/reference/format_freqs.html b/docs/reference/format_freqs.html
index 8a3a84b..1d453b0 100644
--- a/docs/reference/format_freqs.html
+++ b/docs/reference/format_freqs.html
@@ -74,7 +74,7 @@
DescrTab2
- 2.1.3
+ 2.1.7
diff --git a/docs/reference/ignore_unused_args.html b/docs/reference/ignore_unused_args.html
index 4d1f08e..518981a 100644
--- a/docs/reference/ignore_unused_args.html
+++ b/docs/reference/ignore_unused_args.html
@@ -74,7 +74,7 @@
DescrTab2
- 2.1.3
+ 2.1.7
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 69f0613..5562187 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -73,7 +73,7 @@
DescrTab2
- 2.1.3
+ 2.1.7
diff --git a/docs/reference/print.DescrList.html b/docs/reference/print.DescrList.html
index cea5ee1..50b698b 100644
--- a/docs/reference/print.DescrList.html
+++ b/docs/reference/print.DescrList.html
@@ -75,7 +75,7 @@
DescrTab2
- 2.1.3
+ 2.1.7
@@ -236,7 +236,7 @@ Examp
#> \endhead
#>
#> \endfoot
-#> \bottomrule
+#>
#> \endlastfoot
#> \addlinespace[0.5cm]
#> \multicolumn{3}{l}{\textbf{\begin{minipage}[t]{7em}\raggedright Sepal.Length\end{minipage}}}\\*
@@ -269,12 +269,13 @@ Examp
#> \hspace{1em}\begin{minipage}[t]{6em}\raggedright sd\end{minipage} & 0.76 & \\*
#> \hspace{1em}\begin{minipage}[t]{6em}\raggedright median\end{minipage} & 1.3 & \\*
#> \hspace{1em}\begin{minipage}[t]{6em}\raggedright Q1 - Q3\end{minipage} & 0.3 -- 1.8 & \\*
-#> \hspace{1em}\begin{minipage}[t]{6em}\raggedright min - max\end{minipage} & 0.1 -- 2.5 & \\ \noalign{\vskip 0pt plus 12pt} \noalign{\penalty-5000}
+#> \hspace{1em}\begin{minipage}[t]{6em}\raggedright min - max\end{minipage} & 0.1 -- 2.5 & \\ \noalign{\vskip 0pt plus 12pt} \pagebreak[3]
#> \addlinespace[0.5cm]
#> \multicolumn{3}{l}{\textbf{\begin{minipage}[t]{7em}\raggedright Species\end{minipage}}}\\*
#> \hspace{1em}\begin{minipage}[t]{6em}\raggedright setosa\end{minipage} & 50 (33\%) & \textgreater0.999\textsuperscript{chi1}\\*
#> \hspace{1em}\begin{minipage}[t]{6em}\raggedright versicolor\end{minipage} & 50 (33\%) & \\*
#> \hspace{1em}\begin{minipage}[t]{6em}\raggedright virginica\end{minipage} & 50 (33\%) & \\*
+#> \bottomrule
#> \multicolumn{3}{l}{\rule{0pt}{1em}\textsuperscript{tt1} Student's one-sample t-test}\\*
#> \multicolumn{3}{l}{\rule{0pt}{1em}\textsuperscript{chi1} Chi-squared goodness-of-fit test}\\*
#> \end{longtable}
#> # A tibble: 44 x 3
-#> Variable Total Test
-#> <chr> <dbl> <chr>
-#> 1 Sepal.Length Student's one-sample t-test
-#> 2 N 150
-#> 3 Nmiss 0
-#> 4 mean 5.84
-#> 5 sd 0.828
-#> 6 median 5.8
-#> 7 Q1 5.1
-#> 8 Q3 6.4
-#> 9 min 4.3
-#> 10 max 7.9
-#> 11 Sepal.Width Student's one-sample t-test
-#> 12 N 150
-#> 13 Nmiss 0
-#> 14 mean 3.06
-#> 15 sd 0.436
-#> 16 median 3
-#> 17 Q1 2.8
-#> 18 Q3 3.3
-#> 19 min 2
-#> 20 max 4.4
-#> 21 Petal.Length Student's one-sample t-test
-#> 22 N 150
-#> 23 Nmiss 0
-#> 24 mean 3.76
-#> 25 sd 1.77
-#> 26 median 4.35
-#> 27 Q1 1.6
-#> 28 Q3 5.1
-#> 29 min 1
-#> 30 max 6.9
-#> 31 Petal.Width Student's one-sample t-test
-#> 32 N 150
-#> 33 Nmiss 0
-#> 34 mean 1.20
-#> 35 sd 0.762
-#> 36 median 1.3
-#> 37 Q1 0.3
-#> 38 Q3 1.8
-#> 39 min 0.1
-#> 40 max 2.5
-#> 41 Species Chi-squared goodness-of-fit test
-#> 42 setosa 50
-#> 43 versicolor 50
-#> 44 virginica 50
#> # A tibble: 44 x 4
+#> Variable Total p Test
+#> <chr> <dbl> <dbl> <chr>
+#> 1 Sepal.Length 3.33e-129 Student's one-sample t-test
+#> 2 N 150
+#> 3 Nmiss 0
+#> 4 mean 5.84
+#> 5 sd 0.828
+#> 6 median 5.8
+#> 7 Q1 5.1
+#> 8 Q3 6.4
+#> 9 min 4.3
+#> 10 max 7.9
+#> 11 Sepal.Width 8.00e-129 Student's one-sample t-test
+#> 12 N 150
+#> 13 Nmiss 0
+#> 14 mean 3.06
+#> 15 sd 0.436
+#> 16 median 3
+#> 17 Q1 2.8
+#> 18 Q3 3.3
+#> 19 min 2
+#> 20 max 4.4
+#> 21 Petal.Length 2.17e- 57 Student's one-sample t-test
+#> 22 N 150
+#> 23 Nmiss 0
+#> 24 mean 3.76
+#> 25 sd 1.77
+#> 26 median 4.35
+#> 27 Q1 1.6
+#> 28 Q3 5.1
+#> 29 min 1
+#> 30 max 6.9
+#> 31 Petal.Width 2.66e- 42 Student's one-sample t-test
+#> 32 N 150
+#> 33 Nmiss 0
+#> 34 mean 1.20
+#> 35 sd 0.762
+#> 36 median 1.3
+#> 37 Q1 0.3
+#> 38 Q3 1.8
+#> 39 min 0.1
+#> 40 max 2.5
+#> 41 Species 1 e+ 0 Chi-squared goodness-of-fit test
+#> 42 setosa 50
+#> 43 versicolor 50
+#> 44 virginica 50
#> \needspace{2cm}
#>
@@ -505,7 +506,7 @@
Examp
#> \endhead
#>
#> \endfoot
-#> \bottomrule
+#>
#> \endlastfoot
#> \addlinespace[0.5cm]
#> \multicolumn{3}{l}{\textbf{\begin{minipage}[t]{7em}\raggedright Sepal.Length\end{minipage}}}\\*
@@ -538,12 +539,13 @@ Examp
#> \hspace{1em}\begin{minipage}[t]{6em}\raggedright sd\end{minipage} & 0.76 & \\*
#> \hspace{1em}\begin{minipage}[t]{6em}\raggedright median\end{minipage} & 1.3 & \\*
#> \hspace{1em}\begin{minipage}[t]{6em}\raggedright Q1 - Q3\end{minipage} & 0.3 -- 1.8 & \\*
-#> \hspace{1em}\begin{minipage}[t]{6em}\raggedright min - max\end{minipage} & 0.1 -- 2.5 & \\ \noalign{\vskip 0pt plus 12pt} \noalign{\penalty-5000}
+#> \hspace{1em}\begin{minipage}[t]{6em}\raggedright min - max\end{minipage} & 0.1 -- 2.5 & \\ \noalign{\vskip 0pt plus 12pt} \pagebreak[3]
#> \addlinespace[0.5cm]
#> \multicolumn{3}{l}{\textbf{\begin{minipage}[t]{7em}\raggedright Species\end{minipage}}}\\*
#> \hspace{1em}\begin{minipage}[t]{6em}\raggedright setosa\end{minipage} & 50 (33\%) & \textgreater0.999\textsuperscript{chi1}\\*
#> \hspace{1em}\begin{minipage}[t]{6em}\raggedright versicolor\end{minipage} & 50 (33\%) & \\*
#> \hspace{1em}\begin{minipage}[t]{6em}\raggedright virginica\end{minipage} & 50 (33\%) & \\*
+#> \bottomrule
#> \multicolumn{3}{l}{\rule{0pt}{1em}\textsuperscript{tt1} Student's one-sample t-test}\\*
#> \multicolumn{3}{l}{\rule{0pt}{1em}\textsuperscript{chi1} Chi-squared goodness-of-fit test}\\*
#> \end{longtable}
@@ -573,63 +573,63 @@ Examp
#> function (x)
#> pvalue(x, accuracy = accuracy, decimal.mark = decimal.mark, prefix = prefix,
#> add_p = add_p)
-#> <bytecode: 0x00000000165f50d8>
-#> <environment: 0x00000000502c5058>
+#> <bytecode: 0x0000000041cbbac0>
+#> <environment: 0x00000000549f3168>
#>
#> $format$summary_stats
#> $format$summary_stats$N
#> function(x) {
#> format(x, digits = 2, scientific = 3)
#> }
-#> <environment: 0x000000004ffeecd8>
+#> <environment: 0x000000005472ad78>
#>
#> $format$summary_stats$mean
#> function(x) {
#> format(x, digits = 2, scientific = 3)
#> }
-#> <environment: 0x000000004ffeecd8>
+#> <environment: 0x000000005472ad78>
#>
#> $format$summary_stats$sd
#> function(x) {
#> format(x, digits = 2, scientific = 3)
#> }
-#> <environment: 0x000000004ffeecd8>
+#> <environment: 0x000000005472ad78>
#>
#> $format$summary_stats$median
#> function(x) {
#> format(x, digits = 2, scientific = 3)
#> }
-#> <environment: 0x000000004ffeecd8>
+#> <environment: 0x000000005472ad78>
#>
#> $format$summary_stats$Q1
#> function(x) {
#> format(x, digits = 2, scientific = 3)
#> }
-#> <environment: 0x000000004ffeecd8>
+#> <environment: 0x000000005472ad78>
#>
#> $format$summary_stats$Q3
#> function(x) {
#> format(x, digits = 2, scientific = 3)
#> }
-#> <environment: 0x000000004ffeecd8>
+#> <environment: 0x000000005472ad78>
#>
#> $format$summary_stats$min
#> function(x) {
#> format(x, digits = 2, scientific = 3)
#> }
-#> <environment: 0x000000004ffeecd8>
+#> <environment: 0x000000005472ad78>
#>
#> $format$summary_stats$max
#> function(x) {
#> format(x, digits = 2, scientific = 3)
#> }
-#> <environment: 0x000000004ffeecd8>
+#> <environment: 0x000000005472ad78>
#>
#> $format$summary_stats$CI
#> function(x) {
#> format(x, digits = 2, scientific = 3)
#> }
-#> <environment: 0x000000004ffeecd8>
+#> <environment: 0x000000005472ad78>
#>
#>
#> $format$options
@@ -698,7 +698,7 @@ Examp
#> function(Q1, Q3) {
#> paste0(Q1, " -- ", Q3)
#> }
-#> <environment: 0x000000004ffeecd8>
+#> <environment: 0x000000005472ad78>
#>
#>
#> $format$reshape_rows$`min - max`
@@ -709,7 +709,7 @@ Examp
#> function(min, max) {
#> paste0(min, " -- ", max)
#> }
-#> <environment: 0x000000004ffeecd8>
+#> <environment: 0x000000005472ad78>
#>
#>
#>
diff --git a/docs/reference/print_test_names.html b/docs/reference/print_test_names.html
index 55d1a5c..e64879f 100644
--- a/docs/reference/print_test_names.html
+++ b/docs/reference/print_test_names.html
@@ -74,7 +74,7 @@
DescrTab2
- 2.1.3
+ 2.1.7
@@ -161,20 +161,21 @@ Examp
#> [4] "Pearson's chi-squared test"
#> [5] "Exact McNemar's test"
#> [6] "Boschloo's test"
-#> [7] "Fisher's exact test"
-#> [8] "Exact binomal test"
-#> [9] "Friedman test"
-#> [10] "Wilcoxon two-sample signed-rank test"
-#> [11] "Wilcoxon's one-sample signed-rank test"
-#> [12] "Mann-Whitney's U test"
-#> [13] "Kruskal-Wallis's one-way ANOVA"
-#> [14] "Student's paired t-test"
-#> [15] "Mixed model ANOVA"
-#> [16] "Student's one-sample t-test"
-#> [17] "Welch's two-sample t-test"
-#> [18] "Cochran-Armitage's test"
-#> [19] "Jonckheere-Terpstra's test"
-#> [20] "F-test (ANOVA)"
+#> [7] "Exact binomial test"
+#> [8] "Fisher's exact test"
+#> [9] "Exact binomal test"
+#> [10] "Friedman test"
+#> [11] "Wilcoxon two-sample signed-rank test"
+#> [12] "Wilcoxon's one-sample signed-rank test"
+#> [13] "Mann-Whitney's U test"
+#> [14] "Kruskal-Wallis's one-way ANOVA"
+#> [15] "Student's paired t-test"
+#> [16] "Mixed model ANOVA"
+#> [17] "Student's one-sample t-test"
+#> [18] "Welch's two-sample t-test"
+#> [19] "Cochran-Armitage's test"
+#> [20] "Jonckheere-Terpstra's test"
+#> [21] "F-test (ANOVA)"
diff --git a/tests/testthat/test_tests.R b/tests/testthat/test_tests.R
index 1fa3ca4..2808779 100644
--- a/tests/testthat/test_tests.R
+++ b/tests/testthat/test_tests.R
@@ -338,7 +338,14 @@ test_that("mcnemar.test works with var_options and a character string as indices
{
expect_warning(descr(
dat, "group", var_options = list( var = list(test_options = list(paired = TRUE, indices = "id"))
- )))})
+ )))
+
+ expect_warning(descr(
+ dat, "group", test_options = list(indices = "id"),
+ var_options = list( var = list(test_options = list(paired = TRUE, indices = "id"))
+ )))
+
+ })
test_that("mcnemar.test doesn't work if data is not properly paired",
{