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Merge pull request #248 from larmarange/issue245
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Some cleaning
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@larmarange
larmarange authored Apr 5, 2024
2 parents 04fee03 + 651ecac commit 76bc422
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -12,7 +12,7 @@ Description: Provides suite of functions to work with regression model
regression model terms by variable, insert reference and header rows
for categorical variables, add variable labels, and more.
License: GPL (>= 3)
URL: https://larmarange.github.io/broom.helpers/
URL: https://larmarange.github.io/broom.helpers/, https://github.com/larmarange/broom.helpers
BugReports: https://github.com/larmarange/broom.helpers/issues
Depends:
R (>= 3.4)
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2 changes: 1 addition & 1 deletion R/select_helpers.R
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@@ -1,6 +1,6 @@
#' Select helper functions
#'
#' @description Set of functions to supplement the {tidyselect} set of
#' @description Set of functions to supplement the *tidyselect* set of
#' functions for selecting columns of data frames (and other items as well).
#' - `all_continuous()` selects continuous variables
#' - `all_categorical()` selects categorical (including `"dichotomous"`) variables
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139 changes: 67 additions & 72 deletions README.md
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Expand Up @@ -58,16 +58,15 @@ library(broom.helpers)
ex1 <- mod1 %>% tidy_plus_plus()
ex1
#> # A tibble: 4 × 17
#> term varia…¹ var_l…² var_c…³ var_t…⁴ var_n…⁵ contr…⁶ contr…⁷ refer…⁸ label
#> <chr> <chr> <chr> <chr> <chr> <int> <chr> <chr> <lgl> <chr>
#> 1 Sepal.W… Sepal.… Sepal.… numeric contin… NA <NA> <NA> NA Sepa…
#> 2 Species… Species Species factor catego… 3 contr.… treatm… TRUE seto…
#> 3 Species… Species Species factor catego… 3 contr.… treatm… FALSE vers…
#> 4 Species… Species Species factor catego… 3 contr.… treatm… FALSE virg…
#> # … with 7 more variables: n_obs <dbl>, estimate <dbl>, std.error <dbl>,
#> # statistic <dbl>, p.value <dbl>, conf.low <dbl>, conf.high <dbl>, and
#> # abbreviated variable names ¹​variable, ²​var_label, ³​var_class, ⁴​var_type,
#> # ⁵​var_nlevels, ⁶​contrasts, ⁷​contrasts_type, ⁸​reference_row
#> 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…
#> # ℹ 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
Expand Down Expand Up @@ -98,7 +97,7 @@ mod2 <- glm(
grade = contr.sum
)
)
ex2 <- mod2 %>%
ex2 <- mod2 %>%
tidy_plus_plus(
exponentiate = TRUE,
variable_labels = c(age = "Age (in years)"),
Expand All @@ -107,30 +106,28 @@ ex2 <- mod2 %>%
)
ex2
#> # A tibble: 17 × 19
#> term varia…¹ var_l…² var_c…³ var_t…⁴ var_n…⁵ heade…⁶ contr…⁷ contr…⁸ refer…⁹
#> <chr> <chr> <chr> <chr> <chr> <int> <lgl> <chr> <chr> <lgl>
#> 1 <NA> age Age (i… nmatri… contin… NA TRUE <NA> <NA> NA
#> 2 poly… age Age (i… nmatri… contin… NA FALSE <NA> <NA> NA
#> 3 poly… age Age (i… nmatri… contin… NA FALSE <NA> <NA> NA
#> 4 poly… age Age (i… nmatri… contin… NA FALSE <NA> <NA> NA
#> 5 <NA> stage T Stage factor catego… 4 TRUE contr.… treatm… NA
#> 6 stag… stage T Stage factor catego… 4 FALSE contr.… treatm… FALSE
#> 7 stag… stage T Stage factor catego… 4 FALSE contr.… treatm… FALSE
#> 8 stag… stage T Stage factor catego… 4 FALSE contr.… treatm… TRUE
#> 9 stag… stage T Stage factor catego… 4 FALSE contr.… treatm… FALSE
#> 10 <NA> grade Grade factor catego… 3 TRUE contr.… sum NA
#> 11 grad… grade Grade factor catego… 3 FALSE contr.… sum FALSE
#> 12 grad… grade Grade factor catego… 3 FALSE contr.… sum FALSE
#> 13 grad… grade Grade factor catego… 3 FALSE contr.… sum TRUE
#> 14 trtD… trt Chemot… charac… dichot… 2 NA contr.… treatm… FALSE
#> 15 <NA> grade:… Grade … <NA> intera… NA TRUE <NA> <NA> NA
#> 16 grad… grade:… Grade … <NA> intera… NA FALSE <NA> <NA> NA
#> 17 grad… grade:… Grade … <NA> intera… NA FALSE <NA> <NA> NA
#> # … with 9 more variables: label <chr>, n_obs <dbl>, n_event <dbl>,
#> # estimate <dbl>, std.error <dbl>, statistic <dbl>, p.value <dbl>,
#> # conf.low <dbl>, conf.high <dbl>, and abbreviated variable names ¹​variable,
#> # ²​var_label, ³​var_class, ⁴​var_type, ⁵​var_nlevels, ⁶​header_row, ⁷​contrasts,
#> # ⁸​contrasts_type, ⁹​reference_row
#> 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>
#> # ℹ 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
Expand Down Expand Up @@ -166,19 +163,18 @@ ex3 <- mod1 %>%
# add term labels
tidy_add_term_labels() %>%
# remove intercept
tidy_remove_intercept
tidy_remove_intercept()
ex3
#> # A tibble: 4 × 16
#> term varia…¹ var_l…² var_c…³ var_t…⁴ var_n…⁵ contr…⁶ contr…⁷ refer…⁸ label
#> <chr> <chr> <chr> <chr> <chr> <int> <chr> <chr> <lgl> <chr>
#> 1 Sepal.W… Sepal.… Sepal.… numeric contin… NA <NA> <NA> NA Sepa…
#> 2 Species… Species Species factor catego… 3 contr.… treatm… TRUE seto…
#> 3 Species… Species Species factor catego… 3 contr.… treatm… FALSE vers…
#> 4 Species… Species Species factor catego… 3 contr.… treatm… FALSE virg…
#> # … with 6 more variables: estimate <dbl>, std.error <dbl>, statistic <dbl>,
#> # p.value <dbl>, conf.low <dbl>, conf.high <dbl>, and abbreviated variable
#> # names ¹​variable, ²​var_label, ³​var_class, ⁴​var_type, ⁵​var_nlevels,
#> # ⁶​contrasts, ⁷​contrasts_type, ⁸​reference_row
#> 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…
#> # ℹ 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
Expand Down Expand Up @@ -212,32 +208,31 @@ ex4 <- mod2 %>%
tidy_add_header_rows()
ex4
#> # A tibble: 20 × 17
#> term varia…¹ var_l…² var_c…³ var_t…⁴ var_n…⁵ heade…⁶ contr…⁷ contr…⁸ refer…⁹
#> <chr> <chr> <chr> <chr> <chr> <int> <lgl> <chr> <chr> <lgl>
#> 1 (Int… (Inter… (Inter… <NA> interc… NA NA <NA> <NA> NA
#> 2 <NA> age Age in… nmatri… contin… NA TRUE <NA> <NA> NA
#> 3 poly… age Age in… nmatri… contin… NA FALSE <NA> <NA> NA
#> 4 poly… age Age in… nmatri… contin… NA FALSE <NA> <NA> NA
#> 5 poly… age Age in… nmatri… contin… NA FALSE <NA> <NA> NA
#> 6 <NA> stage T Stage factor catego… 4 TRUE contr.… treatm… NA
#> 7 stag… stage T Stage factor catego… 4 FALSE contr.… treatm… FALSE
#> 8 stag… stage T Stage factor catego… 4 FALSE contr.… treatm… FALSE
#> 9 stag… stage T Stage factor catego… 4 FALSE contr.… treatm… TRUE
#> 10 stag… stage T Stage factor catego… 4 FALSE contr.… treatm… FALSE
#> 11 <NA> grade Grade factor catego… 3 TRUE contr.… sum NA
#> 12 grad… grade Grade factor catego… 3 FALSE contr.… sum FALSE
#> 13 grad… grade Grade factor catego… 3 FALSE contr.… sum FALSE
#> 14 grad… grade Grade factor catego… 3 FALSE contr.… sum TRUE
#> 15 <NA> trt Chemot… charac… dichot… 2 TRUE contr.… treatm… NA
#> 16 trtD… trt Chemot… charac… dichot… 2 FALSE contr.… treatm… TRUE
#> 17 trtD… trt Chemot… charac… dichot… 2 FALSE contr.… treatm… FALSE
#> 18 <NA> grade:… Grade … <NA> intera… NA TRUE <NA> <NA> NA
#> 19 grad… grade:… Grade … <NA> intera… NA FALSE <NA> <NA> NA
#> 20 grad… grade:… Grade … <NA> intera… NA FALSE <NA> <NA> NA
#> # … with 7 more variables: label <chr>, estimate <dbl>, std.error <dbl>,
#> # statistic <dbl>, p.value <dbl>, conf.low <dbl>, conf.high <dbl>, and
#> # abbreviated variable names ¹​variable, ²​var_label, ³​var_class, ⁴​var_type,
#> # ⁵​var_nlevels, ⁶​header_row, ⁷​contrasts, ⁸​contrasts_type, ⁹​reference_row
#> 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>
#> # ℹ 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
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2 changes: 1 addition & 1 deletion man/select_helpers.Rd
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