Re-build README.Rmd

README.md

@@ -52,26 +52,26 @@ mod1 <- lm(Sepal.Length ~ Sepal.Width + Species, data = iris)
 library(broom.helpers)
 ex1 <- mod1 %>% tidy_plus_plus()
 ex1
-#> # A tibble: 4 x 17
+#> # A tibble: 4 × 17
 #>   term              variable  var_label var_class var_type var_nlevels contrasts
 #>   <chr>             <chr>     <chr>     <chr>     <chr>          <int> <chr>    
-#> 1 Sepal.Width       Sepal.Wi~ Sepal.Wi~ numeric   continu~          NA <NA>     
-#> 2 Speciessetosa     Species   Species   factor    categor~           3 contr.tr~
-#> 3 Speciesversicolor Species   Species   factor    categor~           3 contr.tr~
-#> 4 Speciesvirginica  Species   Species   factor    categor~           3 contr.tr~
-#> # ... with 10 more variables: contrasts_type <chr>, reference_row <lgl>,
+#> 1 Sepal.Width       Sepal.Wi… Sepal.Wi… numeric   continu…          NA <NA>     
+#> 2 Speciessetosa     Species   Species   factor    categor…           3 contr.tr…
+#> 3 Speciesversicolor Species   Species   factor    categor…           3 contr.tr…
+#> 4 Speciesvirginica  Species   Species   factor    categor…           3 contr.tr…
+#> # … with 10 more variables: contrasts_type <chr>, reference_row <lgl>,
 #> #   label <chr>, n_obs <dbl>, estimate <dbl>, std.error <dbl>, statistic <dbl>,
 #> #   p.value <dbl>, conf.low <dbl>, conf.high <dbl>
 dplyr::glimpse(ex1)
 #> Rows: 4
 #> Columns: 17
-#> $ term           <chr> "Sepal.Width", "Speciessetosa", "Speciesversicolor", "S~
+#> $ term           <chr> "Sepal.Width", "Speciessetosa", "Speciesversicolor", "S…
 #> $ variable       <chr> "Sepal.Width", "Species", "Species", "Species"
 #> $ var_label      <chr> "Sepal.Width", "Species", "Species", "Species"
 #> $ var_class      <chr> "numeric", "factor", "factor", "factor"
-#> $ var_type       <chr> "continuous", "categorical", "categorical", "categorica~
+#> $ var_type       <chr> "continuous", "categorical", "categorical", "categorica…
 #> $ var_nlevels    <int> NA, 3, 3, 3
-#> $ contrasts      <chr> NA, "contr.treatment", "contr.treatment", "contr.treatm~
+#> $ contrasts      <chr> NA, "contr.treatment", "contr.treatment", "contr.treatm…
 #> $ contrasts_type <chr> NA, "treatment", "treatment", "treatment"
 #> $ reference_row  <lgl> NA, TRUE, FALSE, FALSE
 #> $ label          <chr> "Sepal.Width", "setosa", "versicolor", "virginica"
@@ -98,53 +98,53 @@ ex2 <- mod2 %>%
     add_header_rows = TRUE,
     show_single_row = "trt"
   )
-#> Le chargement a nécessité le package : emmeans
+#> Loading required namespace: emmeans
 ex2
-#> # A tibble: 17 x 19
+#> # A tibble: 17 × 19
 #>    term   variable var_label var_class var_type var_nlevels header_row contrasts
 #>    <chr>  <chr>    <chr>     <chr>     <chr>          <int> <lgl>      <chr>    
-#>  1 <NA>   age      Age (in ~ nmatrix.3 continu~          NA TRUE       <NA>     
-#>  2 poly(~ age      Age (in ~ nmatrix.3 continu~          NA FALSE      <NA>     
-#>  3 poly(~ age      Age (in ~ nmatrix.3 continu~          NA FALSE      <NA>     
-#>  4 poly(~ age      Age (in ~ nmatrix.3 continu~          NA FALSE      <NA>     
-#>  5 <NA>   stage    T Stage   factor    categor~           4 TRUE       contr.tr~
-#>  6 stage1 stage    T Stage   factor    categor~           4 FALSE      contr.tr~
-#>  7 stage2 stage    T Stage   factor    categor~           4 FALSE      contr.tr~
-#>  8 stage3 stage    T Stage   factor    categor~           4 FALSE      contr.tr~
-#>  9 stage4 stage    T Stage   factor    categor~           4 FALSE      contr.tr~
-#> 10 <NA>   grade    Grade     factor    categor~           3 TRUE       contr.sum
-#> 11 grade1 grade    Grade     factor    categor~           3 FALSE      contr.sum
-#> 12 grade2 grade    Grade     factor    categor~           3 FALSE      contr.sum
-#> 13 grade3 grade    Grade     factor    categor~           3 FALSE      contr.sum
-#> 14 trtDr~ trt      Chemothe~ character dichoto~           2 NA         contr.tr~
-#> 15 <NA>   grade:t~ Grade * ~ <NA>      interac~          NA TRUE       <NA>     
-#> 16 grade~ grade:t~ Grade * ~ <NA>      interac~          NA FALSE      <NA>     
-#> 17 grade~ grade:t~ Grade * ~ <NA>      interac~          NA FALSE      <NA>     
-#> # ... with 11 more variables: contrasts_type <chr>, reference_row <lgl>,
+#>  1 <NA>   age      Age (in … nmatrix.3 continu…          NA TRUE       <NA>     
+#>  2 poly(… age      Age (in … nmatrix.3 continu…          NA FALSE      <NA>     
+#>  3 poly(… age      Age (in … nmatrix.3 continu…          NA FALSE      <NA>     
+#>  4 poly(… age      Age (in … nmatrix.3 continu…          NA FALSE      <NA>     
+#>  5 <NA>   stage    T Stage   factor    categor…           4 TRUE       contr.tr…
+#>  6 stage1 stage    T Stage   factor    categor…           4 FALSE      contr.tr…
+#>  7 stage2 stage    T Stage   factor    categor…           4 FALSE      contr.tr…
+#>  8 stage3 stage    T Stage   factor    categor…           4 FALSE      contr.tr…
+#>  9 stage4 stage    T Stage   factor    categor…           4 FALSE      contr.tr…
+#> 10 <NA>   grade    Grade     factor    categor…           3 TRUE       contr.sum
+#> 11 grade1 grade    Grade     factor    categor…           3 FALSE      contr.sum
+#> 12 grade2 grade    Grade     factor    categor…           3 FALSE      contr.sum
+#> 13 grade3 grade    Grade     factor    categor…           3 FALSE      contr.sum
+#> 14 trtDr… trt      Chemothe… character dichoto…           2 NA         contr.tr…
+#> 15 <NA>   grade:t… Grade * … <NA>      interac…          NA TRUE       <NA>     
+#> 16 grade… grade:t… Grade * … <NA>      interac…          NA FALSE      <NA>     
+#> 17 grade… grade:t… Grade * … <NA>      interac…          NA FALSE      <NA>     
+#> # … with 11 more variables: contrasts_type <chr>, reference_row <lgl>,
 #> #   label <chr>, n_obs <dbl>, n_event <dbl>, estimate <dbl>, std.error <dbl>,
 #> #   statistic <dbl>, p.value <dbl>, conf.low <dbl>, conf.high <dbl>
 dplyr::glimpse(ex2)
 #> Rows: 17
 #> Columns: 19
-#> $ term           <chr> NA, "poly(age, 3)1", "poly(age, 3)2", "poly(age, 3)3", ~
-#> $ variable       <chr> "age", "age", "age", "age", "stage", "stage", "stage", ~
-#> $ var_label      <chr> "Age (in years)", "Age (in years)", "Age (in years)", "~
-#> $ var_class      <chr> "nmatrix.3", "nmatrix.3", "nmatrix.3", "nmatrix.3", "fa~
-#> $ var_type       <chr> "continuous", "continuous", "continuous", "continuous",~
+#> $ term           <chr> NA, "poly(age, 3)1", "poly(age, 3)2", "poly(age, 3)3", …
+#> $ variable       <chr> "age", "age", "age", "age", "stage", "stage", "stage", …
+#> $ var_label      <chr> "Age (in years)", "Age (in years)", "Age (in years)", "…
+#> $ var_class      <chr> "nmatrix.3", "nmatrix.3", "nmatrix.3", "nmatrix.3", "fa…
+#> $ var_type       <chr> "continuous", "continuous", "continuous", "continuous",…
 #> $ var_nlevels    <int> NA, NA, NA, NA, 4, 4, 4, 4, 4, 3, 3, 3, 3, 2, NA, NA, NA
-#> $ header_row     <lgl> TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, F~
-#> $ contrasts      <chr> NA, NA, NA, NA, "contr.treatment(base=3)", "contr.treat~
-#> $ contrasts_type <chr> NA, NA, NA, NA, "treatment", "treatment", "treatment", ~
-#> $ reference_row  <lgl> NA, NA, NA, NA, NA, FALSE, FALSE, TRUE, FALSE, NA, FALS~
-#> $ label          <chr> "Age (in years)", "Age (in years)", "Age (in years)²", ~
-#> $ n_obs          <dbl> NA, 92, 56, 80, NA, 46, 50, 35, 42, NA, 63, 53, 57, 90,~
-#> $ n_event        <dbl> NA, 31, 17, 22, NA, 17, 12, 13, 12, NA, 20, 16, 18, 30,~
-#> $ estimate       <dbl> NA, 20.2416394, 1.2337899, 0.4931553, NA, 1.0047885, 0.~
-#> $ std.error      <dbl> NA, 2.3254455, 2.3512842, 2.3936657, NA, 0.4959893, 0.5~
-#> $ statistic      <dbl> NA, 1.29340459, 0.08935144, -0.29533409, NA, 0.00963137~
-#> $ p.value        <dbl> NA, 0.1958712, 0.9288026, 0.7677387, NA, 0.9923154, 0.1~
-#> $ conf.low       <dbl> NA, 0.225454425, 0.007493208, 0.004745694, NA, 0.379776~
-#> $ conf.high      <dbl> NA, 2315.587655, 100.318341, 74.226179, NA, 2.683385, 1~
+#> $ header_row     <lgl> TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, F…
+#> $ contrasts      <chr> NA, NA, NA, NA, "contr.treatment(base=3)", "contr.treat…
+#> $ contrasts_type <chr> NA, NA, NA, NA, "treatment", "treatment", "treatment", …
+#> $ reference_row  <lgl> NA, NA, NA, NA, NA, FALSE, FALSE, TRUE, FALSE, NA, FALS…
+#> $ label          <chr> "Age (in years)", "Age (in years)", "Age (in years)²", …
+#> $ n_obs          <dbl> NA, 92, 56, 80, NA, 46, 50, 35, 42, NA, 63, 53, 57, 90,…
+#> $ n_event        <dbl> NA, 31, 17, 22, NA, 17, 12, 13, 12, NA, 20, 16, 18, 30,…
+#> $ estimate       <dbl> NA, 20.2416394, 1.2337899, 0.4931553, NA, 1.0047885, 0.…
+#> $ std.error      <dbl> NA, 2.3254455, 2.3512842, 2.3936657, NA, 0.4959893, 0.5…
+#> $ statistic      <dbl> NA, 1.29340459, 0.08935144, -0.29533409, NA, 0.00963137…
+#> $ p.value        <dbl> NA, 0.1958712, 0.9288026, 0.7677387, NA, 0.9923154, 0.1…
+#> $ conf.low       <dbl> NA, 0.225454425, 0.007493208, 0.004745694, NA, 0.379776…
+#> $ conf.high      <dbl> NA, 2315.587655, 100.318341, 74.226179, NA, 2.683385, 1…
 ```
 
 ### fine control
@@ -160,26 +160,26 @@ ex3 <- mod1 %>%
   # remove intercept
   tidy_remove_intercept
 ex3
-#> # A tibble: 4 x 16
+#> # A tibble: 4 × 16
 #>   term              variable  var_label var_class var_type var_nlevels contrasts
 #>   <chr>             <chr>     <chr>     <chr>     <chr>          <int> <chr>    
-#> 1 Sepal.Width       Sepal.Wi~ Sepal.Wi~ numeric   continu~          NA <NA>     
-#> 2 Speciessetosa     Species   Species   factor    categor~           3 contr.tr~
-#> 3 Speciesversicolor Species   Species   factor    categor~           3 contr.tr~
-#> 4 Speciesvirginica  Species   Species   factor    categor~           3 contr.tr~
-#> # ... with 9 more variables: contrasts_type <chr>, reference_row <lgl>,
+#> 1 Sepal.Width       Sepal.Wi… Sepal.Wi… numeric   continu…          NA <NA>     
+#> 2 Speciessetosa     Species   Species   factor    categor…           3 contr.tr…
+#> 3 Speciesversicolor Species   Species   factor    categor…           3 contr.tr…
+#> 4 Speciesvirginica  Species   Species   factor    categor…           3 contr.tr…
+#> # … with 9 more variables: contrasts_type <chr>, reference_row <lgl>,
 #> #   label <chr>, estimate <dbl>, std.error <dbl>, statistic <dbl>,
 #> #   p.value <dbl>, conf.low <dbl>, conf.high <dbl>
 dplyr::glimpse(ex3)
 #> Rows: 4
 #> Columns: 16
-#> $ term           <chr> "Sepal.Width", "Speciessetosa", "Speciesversicolor", "S~
+#> $ term           <chr> "Sepal.Width", "Speciessetosa", "Speciesversicolor", "S…
 #> $ variable       <chr> "Sepal.Width", "Species", "Species", "Species"
 #> $ var_label      <chr> "Sepal.Width", "Species", "Species", "Species"
 #> $ var_class      <chr> "numeric", "factor", "factor", "factor"
-#> $ var_type       <chr> "continuous", "categorical", "categorical", "categorica~
+#> $ var_type       <chr> "continuous", "categorical", "categorical", "categorica…
 #> $ var_nlevels    <int> NA, 3, 3, 3
-#> $ contrasts      <chr> NA, "contr.treatment", "contr.treatment", "contr.treatm~
+#> $ contrasts      <chr> NA, "contr.treatment", "contr.treatment", "contr.treatm…
 #> $ contrasts_type <chr> NA, "treatment", "treatment", "treatment"
 #> $ reference_row  <lgl> NA, TRUE, FALSE, FALSE
 #> $ label          <chr> "Sepal.Width", "setosa", "versicolor", "virginica"
@@ -201,50 +201,50 @@ ex4 <- mod2 %>%
   # add header rows for categorical variables
   tidy_add_header_rows()
 ex4
-#> # A tibble: 20 x 17
+#> # A tibble: 20 × 17
 #>    term   variable var_label var_class var_type var_nlevels header_row contrasts
 #>    <chr>  <chr>    <chr>     <chr>     <chr>          <int> <lgl>      <chr>    
-#>  1 (Inte~ (Interc~ (Interce~ <NA>      interce~          NA NA         <NA>     
-#>  2 <NA>   age      Age in y~ nmatrix.3 continu~          NA TRUE       <NA>     
-#>  3 poly(~ age      Age in y~ nmatrix.3 continu~          NA FALSE      <NA>     
-#>  4 poly(~ age      Age in y~ nmatrix.3 continu~          NA FALSE      <NA>     
-#>  5 poly(~ age      Age in y~ nmatrix.3 continu~          NA FALSE      <NA>     
-#>  6 <NA>   stage    T Stage   factor    categor~           4 TRUE       contr.tr~
-#>  7 stage1 stage    T Stage   factor    categor~           4 FALSE      contr.tr~
-#>  8 stage2 stage    T Stage   factor    categor~           4 FALSE      contr.tr~
-#>  9 stage3 stage    T Stage   factor    categor~           4 FALSE      contr.tr~
-#> 10 stage4 stage    T Stage   factor    categor~           4 FALSE      contr.tr~
-#> 11 <NA>   grade    Grade     factor    categor~           3 TRUE       contr.sum
-#> 12 grade1 grade    Grade     factor    categor~           3 FALSE      contr.sum
-#> 13 grade2 grade    Grade     factor    categor~           3 FALSE      contr.sum
-#> 14 grade3 grade    Grade     factor    categor~           3 FALSE      contr.sum
-#> 15 <NA>   trt      Chemothe~ character dichoto~           2 TRUE       contr.tr~
-#> 16 trtDr~ trt      Chemothe~ character dichoto~           2 FALSE      contr.tr~
-#> 17 trtDr~ trt      Chemothe~ character dichoto~           2 FALSE      contr.tr~
-#> 18 <NA>   grade:t~ Grade * ~ <NA>      interac~          NA TRUE       <NA>     
-#> 19 grade~ grade:t~ Grade * ~ <NA>      interac~          NA FALSE      <NA>     
-#> 20 grade~ grade:t~ Grade * ~ <NA>      interac~          NA FALSE      <NA>     
-#> # ... with 9 more variables: contrasts_type <chr>, reference_row <lgl>,
+#>  1 (Inte… (Interc… (Interce… <NA>      interce…          NA NA         <NA>     
+#>  2 <NA>   age      Age in y… nmatrix.3 continu…          NA TRUE       <NA>     
+#>  3 poly(… age      Age in y… nmatrix.3 continu…          NA FALSE      <NA>     
+#>  4 poly(… age      Age in y… nmatrix.3 continu…          NA FALSE      <NA>     
+#>  5 poly(… age      Age in y… nmatrix.3 continu…          NA FALSE      <NA>     
+#>  6 <NA>   stage    T Stage   factor    categor…           4 TRUE       contr.tr…
+#>  7 stage1 stage    T Stage   factor    categor…           4 FALSE      contr.tr…
+#>  8 stage2 stage    T Stage   factor    categor…           4 FALSE      contr.tr…
+#>  9 stage3 stage    T Stage   factor    categor…           4 FALSE      contr.tr…
+#> 10 stage4 stage    T Stage   factor    categor…           4 FALSE      contr.tr…
+#> 11 <NA>   grade    Grade     factor    categor…           3 TRUE       contr.sum
+#> 12 grade1 grade    Grade     factor    categor…           3 FALSE      contr.sum
+#> 13 grade2 grade    Grade     factor    categor…           3 FALSE      contr.sum
+#> 14 grade3 grade    Grade     factor    categor…           3 FALSE      contr.sum
+#> 15 <NA>   trt      Chemothe… character dichoto…           2 TRUE       contr.tr…
+#> 16 trtDr… trt      Chemothe… character dichoto…           2 FALSE      contr.tr…
+#> 17 trtDr… trt      Chemothe… character dichoto…           2 FALSE      contr.tr…
+#> 18 <NA>   grade:t… Grade * … <NA>      interac…          NA TRUE       <NA>     
+#> 19 grade… grade:t… Grade * … <NA>      interac…          NA FALSE      <NA>     
+#> 20 grade… grade:t… Grade * … <NA>      interac…          NA FALSE      <NA>     
+#> # … with 9 more variables: contrasts_type <chr>, reference_row <lgl>,
 #> #   label <chr>, estimate <dbl>, std.error <dbl>, statistic <dbl>,
 #> #   p.value <dbl>, conf.low <dbl>, conf.high <dbl>
 dplyr::glimpse(ex4)
 #> Rows: 20
 #> Columns: 17
-#> $ term           <chr> "(Intercept)", NA, "poly(age, 3)1", "poly(age, 3)2", "p~
-#> $ variable       <chr> "(Intercept)", "age", "age", "age", "age", "stage", "st~
-#> $ var_label      <chr> "(Intercept)", "Age in years", "Age in years", "Age in ~
-#> $ var_class      <chr> NA, "nmatrix.3", "nmatrix.3", "nmatrix.3", "nmatrix.3",~
-#> $ var_type       <chr> "intercept", "continuous", "continuous", "continuous", ~
-#> $ var_nlevels    <int> NA, NA, NA, NA, NA, 4, 4, 4, 4, 4, 3, 3, 3, 3, 2, 2, 2,~
-#> $ header_row     <lgl> NA, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALS~
-#> $ contrasts      <chr> NA, NA, NA, NA, NA, "contr.treatment(base=3)", "contr.t~
-#> $ contrasts_type <chr> NA, NA, NA, NA, NA, "treatment", "treatment", "treatmen~
-#> $ reference_row  <lgl> NA, NA, NA, NA, NA, NA, FALSE, FALSE, TRUE, FALSE, NA, ~
-#> $ label          <chr> "(Intercept)", "Age in years", "Age in years", "Age in ~
-#> $ estimate       <dbl> 0.5266376, NA, 20.2416394, 1.2337899, 0.4931553, NA, 1.~
-#> $ std.error      <dbl> 0.4130930, NA, 2.3254455, 2.3512842, 2.3936657, NA, 0.4~
-#> $ statistic      <dbl> -1.55229592, NA, 1.29340459, 0.08935144, -0.29533409, N~
-#> $ p.value        <dbl> 0.1205914, NA, 0.1958712, 0.9288026, 0.7677387, NA, 0.9~
-#> $ conf.low       <dbl> 0.227717775, NA, 0.225454425, 0.007493208, 0.004745694,~
-#> $ conf.high      <dbl> 1.164600, NA, 2315.587655, 100.318341, 74.226179, NA, 2~
+#> $ term           <chr> "(Intercept)", NA, "poly(age, 3)1", "poly(age, 3)2", "p…
+#> $ variable       <chr> "(Intercept)", "age", "age", "age", "age", "stage", "st…
+#> $ var_label      <chr> "(Intercept)", "Age in years", "Age in years", "Age in …
+#> $ var_class      <chr> NA, "nmatrix.3", "nmatrix.3", "nmatrix.3", "nmatrix.3",…
+#> $ var_type       <chr> "intercept", "continuous", "continuous", "continuous", …
+#> $ var_nlevels    <int> NA, NA, NA, NA, NA, 4, 4, 4, 4, 4, 3, 3, 3, 3, 2, 2, 2,…
+#> $ header_row     <lgl> NA, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALS…
+#> $ contrasts      <chr> NA, NA, NA, NA, NA, "contr.treatment(base=3)", "contr.t…
+#> $ contrasts_type <chr> NA, NA, NA, NA, NA, "treatment", "treatment", "treatmen…
+#> $ reference_row  <lgl> NA, NA, NA, NA, NA, NA, FALSE, FALSE, TRUE, FALSE, NA, …
+#> $ label          <chr> "(Intercept)", "Age in years", "Age in years", "Age in …
+#> $ estimate       <dbl> 0.5266376, NA, 20.2416394, 1.2337899, 0.4931553, NA, 1.…
+#> $ std.error      <dbl> 0.4130930, NA, 2.3254455, 2.3512842, 2.3936657, NA, 0.4…
+#> $ statistic      <dbl> -1.55229592, NA, 1.29340459, 0.08935144, -0.29533409, N…
+#> $ p.value        <dbl> 0.1205914, NA, 0.1958712, 0.9288026, 0.7677387, NA, 0.9…
+#> $ conf.low       <dbl> 0.227717775, NA, 0.225454425, 0.007493208, 0.004745694,…
+#> $ conf.high      <dbl> 1.164600, NA, 2315.587655, 100.318341, 74.226179, NA, 2…
 ```