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Re-build README.Rmd
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@actions-user
actions-user committed Feb 26, 2021
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186 changes: 93 additions & 93 deletions README.md
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Expand Up @@ -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
#> <chr> <chr> <chr> <chr> <chr> <int> <chr>
#> 1 Sepa… Sepal.W… Sepal.Wi… numeric continu… NA <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
#> <chr> <chr> <chr> <chr> <chr> <int> <chr>
#> 1 Sepal.Width Sepal.Wid… Sepal.Wid… numeric continuo… NA <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 <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", "…
#> $ 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", "categoric…
#> $ var_type <chr> "continuous", "categorical", "categorical", "categorica…
#> $ var_nlevels <int> NA, 3, 3, 3
#> $ contrasts <chr> NA, "contr.treatment", "contr.treatment", "contr.treat…
#> $ 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"
Expand Down Expand Up @@ -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
#> <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 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 <NA> 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 <NA> grade:t… Grade * … <NA> interac… NA TRUE <NA>
#> 16 grad… grade:t… Grade * … <NA> interac… NA FALSE <NA>
#> 17 grad… grade:t… Grade * … <NA> interac… NA FALSE <NA>
#> 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>,
#> # 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", "f…
#> $ 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, …
#> $ header_row <lgl> TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, …
#> $ contrasts <chr> NA, NA, NA, NA, "contr.treatment(base=3)", "contr.trea…
#> $ contrasts_type <chr> NA, NA, NA, NA, "treatment", "treatment", "treatment",…
#> $ reference_row <lgl> NA, NA, NA, NA, NA, FALSE, FALSE, TRUE, FALSE, NA, FAL…
#> $ 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.…
#> $ statistic <dbl> NA, 1.29340459, 0.08935144, -0.29533409, NA, 0.0096313…
#> $ p.value <dbl> NA, 0.1958712, 0.9288026, 0.7677387, NA, 0.9923154, 0.…
#> $ conf.low <dbl> NA, 0.225454425, 0.007493208, 0.004745694, NA, 0.37977…
#> $ conf.high <dbl> NA, 2315.587655, 100.318341, 74.226179, NA, 2.683385, …
#> $ 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…
```

### fine control
Expand All @@ -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
#> <chr> <chr> <chr> <chr> <chr> <int> <chr>
#> 1 Sepa… Sepal.W… Sepal.Wi… numeric continu… NA <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
#> <chr> <chr> <chr> <chr> <chr> <int> <chr>
#> 1 Sepal.Width Sepal.Wid… Sepal.Wid… numeric continuo… NA <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 <chr>, reference_row <lgl>,
#> # label <chr>, estimate <dbl>, std.error <dbl>, statistic <dbl>,
#> # p.value <dbl>
dplyr::glimpse(ex3)
#> Rows: 4
#> Columns: 14
#> $ term <chr> "Sepal.Width", "Speciessetosa", "Speciesversicolor", "…
#> $ 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", "categoric…
#> $ var_type <chr> "continuous", "categorical", "categorical", "categorica…
#> $ var_nlevels <int> NA, 3, 3, 3
#> $ contrasts <chr> NA, "contr.treatment", "contr.treatment", "contr.treat…
#> $ 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"
Expand All @@ -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
#> <chr> <chr> <chr> <chr> <chr> <int> <lgl> <chr>
#> 1 (Int… (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 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 <NA> 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 <NA> 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 <NA> grade:t… Grade * … <NA> interac… NA TRUE <NA>
#> 19 grad… grade:t… Grade * … <NA> interac… NA FALSE <NA>
#> 20 grad… grade:t… Grade * … <NA> interac… NA FALSE <NA>
#> 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 7 more variables: contrasts_type <chr>, reference_row <lgl>,
#> # label <chr>, estimate <dbl>, std.error <dbl>, statistic <dbl>,
#> # p.value <dbl>
dplyr::glimpse(ex4)
#> Rows: 20
#> Columns: 15
#> $ term <chr> "(Intercept)", NA, "poly(age, 3)1", "poly(age, 3)2", "…
#> $ variable <chr> "(Intercept)", "age", "age", "age", "age", "stage", "s…
#> $ 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, FAL…
#> $ contrasts <chr> NA, NA, NA, NA, NA, "contr.treatment(base=3)", "contr.…
#> $ contrasts_type <chr> NA, NA, NA, NA, NA, "treatment", "treatment", "treatme…
#> $ 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.…
#> $ statistic <dbl> -1.55229592, NA, 1.29340459, 0.08935144, -0.29533409, …
#> $ p.value <dbl> 0.1205914, NA, 0.1958712, 0.9288026, 0.7677387, NA, 0.…
#> $ 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…
```

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