From d7fe11563c03fddc62bde4015cb288c08bb4bc41 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Fri, 26 Feb 2021 17:52:58 +0000 Subject: [PATCH] Re-build README.Rmd --- README.md | 186 +++++++++++++++++++++++++++--------------------------- 1 file changed, 93 insertions(+), 93 deletions(-) diff --git a/README.md b/README.md index b52c93e4..1b78ef8f 100644 --- a/README.md +++ b/README.md @@ -53,25 +53,25 @@ library(broom.helpers) ex1 <- mod1 %>% tidy_plus_plus() ex1 #> # A tibble: 4 x 17 -#> term variable var_label var_class var_type var_nlevels contrasts -#> -#> 1 Sepa… Sepal.W… Sepal.Wi… numeric continu… NA -#> 2 Spec… Species Species factor categor… 3 contr.tr… -#> 3 Spec… Species Species factor categor… 3 contr.tr… -#> 4 Spec… Species Species factor categor… 3 contr.tr… +#> term variable var_label var_class var_type var_nlevels contrasts +#> +#> 1 Sepal.Width Sepal.Wid… Sepal.Wid… numeric continuo… NA +#> 2 Speciesset… Species Species factor categori… 3 contr.treat… +#> 3 Speciesver… Species Species factor categori… 3 contr.treat… +#> 4 Speciesvir… Species Species factor categori… 3 contr.treat… #> # … with 10 more variables: contrasts_type , reference_row , #> # label , n_obs , estimate , std.error , statistic , #> # p.value , conf.low , conf.high dplyr::glimpse(ex1) #> Rows: 4 #> Columns: 17 -#> $ term "Sepal.Width", "Speciessetosa", "Speciesversicolor", "… +#> $ term "Sepal.Width", "Speciessetosa", "Speciesversicolor", "S… #> $ variable "Sepal.Width", "Species", "Species", "Species" #> $ var_label "Sepal.Width", "Species", "Species", "Species" #> $ var_class "numeric", "factor", "factor", "factor" -#> $ var_type "continuous", "categorical", "categorical", "categoric… +#> $ var_type "continuous", "categorical", "categorical", "categorica… #> $ var_nlevels NA, 3, 3, 3 -#> $ contrasts NA, "contr.treatment", "contr.treatment", "contr.treat… +#> $ contrasts NA, "contr.treatment", "contr.treatment", "contr.treatm… #> $ contrasts_type NA, "treatment", "treatment", "treatment" #> $ reference_row NA, TRUE, FALSE, FALSE #> $ label "Sepal.Width", "setosa", "versicolor", "virginica" @@ -102,50 +102,50 @@ ex2 <- mod2 %>% #> Loading required namespace: emmeans ex2 #> # A tibble: 17 x 19 -#> term variable var_label var_class var_type var_nlevels header_row contrasts -#> -#> 1 age Age (in … nmatrix.3 continu… NA TRUE -#> 2 poly… age Age (in … nmatrix.3 continu… NA FALSE -#> 3 poly… age Age (in … nmatrix.3 continu… NA FALSE -#> 4 poly… age Age (in … nmatrix.3 continu… NA FALSE -#> 5 stage T Stage factor categor… 4 TRUE contr.tr… -#> 6 stag… stage T Stage factor categor… 4 FALSE contr.tr… -#> 7 stag… stage T Stage factor categor… 4 FALSE contr.tr… -#> 8 stag… stage T Stage factor categor… 4 FALSE contr.tr… -#> 9 stag… stage T Stage factor categor… 4 FALSE contr.tr… -#> 10 grade Grade factor categor… 3 TRUE contr.sum -#> 11 grad… grade Grade factor categor… 3 FALSE contr.sum -#> 12 grad… grade Grade factor categor… 3 FALSE contr.sum -#> 13 grad… grade Grade factor categor… 3 FALSE contr.sum -#> 14 trtD… trt Chemothe… character dichoto… 2 NA contr.tr… -#> 15 grade:t… Grade * … interac… NA TRUE -#> 16 grad… grade:t… Grade * … interac… NA FALSE -#> 17 grad… grade:t… Grade * … interac… NA FALSE +#> term variable var_label var_class var_type var_nlevels header_row contrasts +#> +#> 1 age Age (in … nmatrix.3 continu… NA TRUE +#> 2 poly(… age Age (in … nmatrix.3 continu… NA FALSE +#> 3 poly(… age Age (in … nmatrix.3 continu… NA FALSE +#> 4 poly(… age Age (in … nmatrix.3 continu… NA FALSE +#> 5 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 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 grade:t… Grade * … interac… NA TRUE +#> 16 grade… grade:t… Grade * … interac… NA FALSE +#> 17 grade… grade:t… Grade * … interac… NA FALSE #> # … with 11 more variables: contrasts_type , reference_row , #> # label , n_obs , n_event , estimate , std.error , #> # statistic , p.value , conf.low , conf.high dplyr::glimpse(ex2) #> Rows: 17 #> Columns: 19 -#> $ term NA, "poly(age, 3)1", "poly(age, 3)2", "poly(age, 3)3",… -#> $ variable "age", "age", "age", "age", "stage", "stage", "stage",… -#> $ var_label "Age (in years)", "Age (in years)", "Age (in years)", … -#> $ var_class "nmatrix.3", "nmatrix.3", "nmatrix.3", "nmatrix.3", "f… -#> $ var_type "continuous", "continuous", "continuous", "continuous"… -#> $ var_nlevels NA, NA, NA, NA, 4, 4, 4, 4, 4, 3, 3, 3, 3, 2, NA, NA, … -#> $ header_row TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, … -#> $ contrasts NA, NA, NA, NA, "contr.treatment(base=3)", "contr.trea… -#> $ contrasts_type NA, NA, NA, NA, "treatment", "treatment", "treatment",… -#> $ reference_row NA, NA, NA, NA, NA, FALSE, FALSE, TRUE, FALSE, NA, FAL… -#> $ label "Age (in years)", "Age (in years)", "Age (in years)²",… -#> $ n_obs NA, 92, 56, 80, NA, 46, 50, 35, 42, NA, 63, 53, 57, 90… -#> $ n_event NA, 31, 17, 22, NA, 17, 12, 13, 12, NA, 20, 16, 18, 30… -#> $ estimate NA, 20.2416394, 1.2337899, 0.4931553, NA, 1.0047885, 0… -#> $ std.error NA, 2.3254455, 2.3512842, 2.3936657, NA, 0.4959893, 0.… -#> $ statistic NA, 1.29340459, 0.08935144, -0.29533409, NA, 0.0096313… -#> $ p.value NA, 0.1958712, 0.9288026, 0.7677387, NA, 0.9923154, 0.… -#> $ conf.low NA, 0.225454425, 0.007493208, 0.004745694, NA, 0.37977… -#> $ conf.high NA, 2315.587655, 100.318341, 74.226179, NA, 2.683385, … +#> $ term NA, "poly(age, 3)1", "poly(age, 3)2", "poly(age, 3)3", … +#> $ variable "age", "age", "age", "age", "stage", "stage", "stage", … +#> $ var_label "Age (in years)", "Age (in years)", "Age (in years)", "… +#> $ var_class "nmatrix.3", "nmatrix.3", "nmatrix.3", "nmatrix.3", "fa… +#> $ var_type "continuous", "continuous", "continuous", "continuous",… +#> $ var_nlevels NA, NA, NA, NA, 4, 4, 4, 4, 4, 3, 3, 3, 3, 2, NA, NA, NA +#> $ header_row TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, F… +#> $ contrasts NA, NA, NA, NA, "contr.treatment(base=3)", "contr.treat… +#> $ contrasts_type NA, NA, NA, NA, "treatment", "treatment", "treatment", … +#> $ reference_row NA, NA, NA, NA, NA, FALSE, FALSE, TRUE, FALSE, NA, FALS… +#> $ label "Age (in years)", "Age (in years)", "Age (in years)²", … +#> $ n_obs NA, 92, 56, 80, NA, 46, 50, 35, 42, NA, 63, 53, 57, 90,… +#> $ n_event NA, 31, 17, 22, NA, 17, 12, 13, 12, NA, 20, 16, 18, 30,… +#> $ estimate NA, 20.2416394, 1.2337899, 0.4931553, NA, 1.0047885, 0.… +#> $ std.error NA, 2.3254455, 2.3512842, 2.3936657, NA, 0.4959893, 0.5… +#> $ statistic NA, 1.29340459, 0.08935144, -0.29533409, NA, 0.00963137… +#> $ p.value NA, 0.1958712, 0.9288026, 0.7677387, NA, 0.9923154, 0.1… +#> $ conf.low NA, 0.225454425, 0.007493208, 0.004745694, NA, 0.379776… +#> $ conf.high NA, 2315.587655, 100.318341, 74.226179, NA, 2.683385, 1… ``` ### fine control @@ -162,25 +162,25 @@ ex3 <- mod1 %>% tidy_remove_intercept ex3 #> # A tibble: 4 x 14 -#> term variable var_label var_class var_type var_nlevels contrasts -#> -#> 1 Sepa… Sepal.W… Sepal.Wi… numeric continu… NA -#> 2 Spec… Species Species factor categor… 3 contr.tr… -#> 3 Spec… Species Species factor categor… 3 contr.tr… -#> 4 Spec… Species Species factor categor… 3 contr.tr… +#> term variable var_label var_class var_type var_nlevels contrasts +#> +#> 1 Sepal.Width Sepal.Wid… Sepal.Wid… numeric continuo… NA +#> 2 Speciesset… Species Species factor categori… 3 contr.treat… +#> 3 Speciesver… Species Species factor categori… 3 contr.treat… +#> 4 Speciesvir… Species Species factor categori… 3 contr.treat… #> # … with 7 more variables: contrasts_type , reference_row , #> # label , estimate , std.error , statistic , #> # p.value dplyr::glimpse(ex3) #> Rows: 4 #> Columns: 14 -#> $ term "Sepal.Width", "Speciessetosa", "Speciesversicolor", "… +#> $ term "Sepal.Width", "Speciessetosa", "Speciesversicolor", "S… #> $ variable "Sepal.Width", "Species", "Species", "Species" #> $ var_label "Sepal.Width", "Species", "Species", "Species" #> $ var_class "numeric", "factor", "factor", "factor" -#> $ var_type "continuous", "categorical", "categorical", "categoric… +#> $ var_type "continuous", "categorical", "categorical", "categorica… #> $ var_nlevels NA, 3, 3, 3 -#> $ contrasts NA, "contr.treatment", "contr.treatment", "contr.treat… +#> $ contrasts NA, "contr.treatment", "contr.treatment", "contr.treatm… #> $ contrasts_type NA, "treatment", "treatment", "treatment" #> $ reference_row NA, TRUE, FALSE, FALSE #> $ label "Sepal.Width", "setosa", "versicolor", "virginica" @@ -202,47 +202,47 @@ ex4 <- mod2 %>% tidy_add_header_rows() ex4 #> # A tibble: 20 x 15 -#> term variable var_label var_class var_type var_nlevels header_row contrasts -#> -#> 1 (Int… (Interc… (Interce… interce… NA NA -#> 2 age Age in y… nmatrix.3 continu… NA TRUE -#> 3 poly… age Age in y… nmatrix.3 continu… NA FALSE -#> 4 poly… age Age in y… nmatrix.3 continu… NA FALSE -#> 5 poly… age Age in y… nmatrix.3 continu… NA FALSE -#> 6 stage T Stage factor categor… 4 TRUE contr.tr… -#> 7 stag… stage T Stage factor categor… 4 FALSE contr.tr… -#> 8 stag… stage T Stage factor categor… 4 FALSE contr.tr… -#> 9 stag… stage T Stage factor categor… 4 FALSE contr.tr… -#> 10 stag… stage T Stage factor categor… 4 FALSE contr.tr… -#> 11 grade Grade factor categor… 3 TRUE contr.sum -#> 12 grad… grade Grade factor categor… 3 FALSE contr.sum -#> 13 grad… grade Grade factor categor… 3 FALSE contr.sum -#> 14 grad… grade Grade factor categor… 3 FALSE contr.sum -#> 15 trt Chemothe… character dichoto… 2 TRUE contr.tr… -#> 16 trtD… trt Chemothe… character dichoto… 2 FALSE contr.tr… -#> 17 trtD… trt Chemothe… character dichoto… 2 FALSE contr.tr… -#> 18 grade:t… Grade * … interac… NA TRUE -#> 19 grad… grade:t… Grade * … interac… NA FALSE -#> 20 grad… grade:t… Grade * … interac… NA FALSE +#> term variable var_label var_class var_type var_nlevels header_row contrasts +#> +#> 1 (Inte… (Interc… (Interce… interce… NA NA +#> 2 age Age in y… nmatrix.3 continu… NA TRUE +#> 3 poly(… age Age in y… nmatrix.3 continu… NA FALSE +#> 4 poly(… age Age in y… nmatrix.3 continu… NA FALSE +#> 5 poly(… age Age in y… nmatrix.3 continu… NA FALSE +#> 6 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 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 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 grade:t… Grade * … interac… NA TRUE +#> 19 grade… grade:t… Grade * … interac… NA FALSE +#> 20 grade… grade:t… Grade * … interac… NA FALSE #> # … with 7 more variables: contrasts_type , reference_row , #> # label , estimate , std.error , statistic , #> # p.value dplyr::glimpse(ex4) #> Rows: 20 #> Columns: 15 -#> $ term "(Intercept)", NA, "poly(age, 3)1", "poly(age, 3)2", "… -#> $ variable "(Intercept)", "age", "age", "age", "age", "stage", "s… -#> $ var_label "(Intercept)", "Age in years", "Age in years", "Age in… -#> $ var_class NA, "nmatrix.3", "nmatrix.3", "nmatrix.3", "nmatrix.3"… -#> $ var_type "intercept", "continuous", "continuous", "continuous",… -#> $ var_nlevels NA, NA, NA, NA, NA, 4, 4, 4, 4, 4, 3, 3, 3, 3, 2, 2, 2… -#> $ header_row NA, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FAL… -#> $ contrasts NA, NA, NA, NA, NA, "contr.treatment(base=3)", "contr.… -#> $ contrasts_type NA, NA, NA, NA, NA, "treatment", "treatment", "treatme… -#> $ reference_row NA, NA, NA, NA, NA, NA, FALSE, FALSE, TRUE, FALSE, NA,… -#> $ label "(Intercept)", "Age in years", "Age in years", "Age in… -#> $ estimate 0.5266376, NA, 20.2416394, 1.2337899, 0.4931553, NA, 1… -#> $ std.error 0.4130930, NA, 2.3254455, 2.3512842, 2.3936657, NA, 0.… -#> $ statistic -1.55229592, NA, 1.29340459, 0.08935144, -0.29533409, … -#> $ p.value 0.1205914, NA, 0.1958712, 0.9288026, 0.7677387, NA, 0.… +#> $ term "(Intercept)", NA, "poly(age, 3)1", "poly(age, 3)2", "p… +#> $ variable "(Intercept)", "age", "age", "age", "age", "stage", "st… +#> $ var_label "(Intercept)", "Age in years", "Age in years", "Age in … +#> $ var_class NA, "nmatrix.3", "nmatrix.3", "nmatrix.3", "nmatrix.3",… +#> $ var_type "intercept", "continuous", "continuous", "continuous", … +#> $ var_nlevels NA, NA, NA, NA, NA, 4, 4, 4, 4, 4, 3, 3, 3, 3, 2, 2, 2,… +#> $ header_row NA, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALS… +#> $ contrasts NA, NA, NA, NA, NA, "contr.treatment(base=3)", "contr.t… +#> $ contrasts_type NA, NA, NA, NA, NA, "treatment", "treatment", "treatmen… +#> $ reference_row NA, NA, NA, NA, NA, NA, FALSE, FALSE, TRUE, FALSE, NA, … +#> $ label "(Intercept)", "Age in years", "Age in years", "Age in … +#> $ estimate 0.5266376, NA, 20.2416394, 1.2337899, 0.4931553, NA, 1.… +#> $ std.error 0.4130930, NA, 2.3254455, 2.3512842, 2.3936657, NA, 0.4… +#> $ statistic -1.55229592, NA, 1.29340459, 0.08935144, -0.29533409, N… +#> $ p.value 0.1205914, NA, 0.1958712, 0.9288026, 0.7677387, NA, 0.9… ```