The cheese
package contains tools for working with data during statistical analysis–promoting flexible, intuitive, and reproducible workflows. There are functions designated for specific statistical tasks such as
univariate_table()
: To create a custom table of descriptive statistics for a datasetunivariate_associations()
: For computing pairwise association metrics for combinations of predictors
and responses
descriptives()
: To compute descriptive statistics on columns of a datasetThese are built on a collection of data manipulation tools designed for general use, many of which are motivated by the functional programming concept (i.e. purrr
) and use non-standard evaluation for column selection as in dplyr::select
. Here are a few:
depths()
: Find the depth(s) of elements in a list structure that satisfy a predicatedivide()
and fasten()
: Split/bind data frames to/from any list depthdish()
: Evaluate a function with pairwise combinations of columnsstratiply()
: Evaluate a function on subsets of a data frametyply()
: Evaluate a function on columns that inherit at least one (or none) of the specified classesinstall.packages("cheese")
devtools::install_github("zajichek/cheese")
#Load package
require(cheese)
#> Loading required package: cheese
#Make a descriptive table
heart_disease %>%
univariate_table(
format = "markdown" #Could also render as "html", "latex", "pandoc", or "none"
)
Variable | Level | Summary |
---|---|---|
Age | 56 (48, 61) | |
Sex | Female | 97 (32.01%) |
Male | 206 (67.99%) | |
ChestPain | Typical angina | 23 (7.59%) |
Atypical angina | 50 (16.5%) | |
Non-anginal pain | 86 (28.38%) | |
Asymptomatic | 144 (47.52%) | |
BP | 130 (120, 140) | |
Cholesterol | 241 (211, 275) | |
MaximumHR | 153 (133.5, 166) | |
ExerciseInducedAngina | No | 204 (67.33%) |
Yes | 99 (32.67%) | |
HeartDisease | No | 164 (54.13%) |
Yes | 139 (45.87%) |
#Run some models
heart_disease %>%
#Apply a function to subsets of the data
stratiply(
by = Sex,
f =
~.x %>%
#Apply a function to pairwise combinations of columns
dish(
left = c(ExerciseInducedAngina, HeartDisease),
f = function(y, x) glm(y ~ x, family = "binomial") %>% purrr::pluck("coefficients") %>% tibble::enframe()
)
) %>%
#Bind rows up to a specified depth
fasten(
into = c("Outcome", "Predictor"),
depth = 1
)
#> $Female
#> # A tibble: 28 x 4
#> Outcome Predictor name value
#> <chr> <chr> <chr> <dbl>
#> 1 ExerciseInducedAngina Age (Intercept) -1.46
#> 2 ExerciseInducedAngina Age x 0.00416
#> 3 ExerciseInducedAngina ChestPain (Intercept) -17.6
#> 4 ExerciseInducedAngina ChestPain xAtypical angina 15.5
#> 5 ExerciseInducedAngina ChestPain xNon-anginal pain 14.8
#> 6 ExerciseInducedAngina ChestPain xAsymptomatic 17.4
#> 7 ExerciseInducedAngina BP (Intercept) -6.47
#> 8 ExerciseInducedAngina BP x 0.0383
#> 9 ExerciseInducedAngina Cholesterol (Intercept) -2.06
#> 10 ExerciseInducedAngina Cholesterol x 0.00315
#> # … with 18 more rows
#>
#> $Male
#> # A tibble: 28 x 4
#> Outcome Predictor name value
#> <chr> <chr> <chr> <dbl>
#> 1 ExerciseInducedAngina Age (Intercept) -2.44
#> 2 ExerciseInducedAngina Age x 0.0356
#> 3 ExerciseInducedAngina ChestPain (Intercept) -1.32
#> 4 ExerciseInducedAngina ChestPain xAtypical angina -1.39
#> 5 ExerciseInducedAngina ChestPain xNon-anginal pain -0.219
#> 6 ExerciseInducedAngina ChestPain xAsymptomatic 1.71
#> 7 ExerciseInducedAngina BP (Intercept) 0.0385
#> 8 ExerciseInducedAngina BP x -0.00424
#> 9 ExerciseInducedAngina Cholesterol (Intercept) -1.70
#> 10 ExerciseInducedAngina Cholesterol x 0.00494
#> # … with 18 more rows
See the package vignettes and documentation for more thorough examples.