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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,39 +1,40 @@ | ||
| Package: nsqipr | ||
| Title: Interact with NSQIP data via R | ||
| Version: 0.0.0.9000 | ||
| Authors@R: | ||
| person(given = "Dylan", | ||
| family = "Russell", | ||
| role = c("aut", "cre"), | ||
| email = "[email protected]", | ||
| comment = c(ORCID = "0000-0002-9543-9897")) | ||
| Description: Streamlines reading and writing clean NSQIP data. | ||
| License: CC0 | ||
| Encoding: UTF-8 | ||
| LazyData: true | ||
| Roxygen: list(markdown = TRUE) | ||
| RoxygenNote: 7.1.0 | ||
| Suggests: | ||
| knitr, | ||
| rmarkdown, | ||
| testthat, | ||
| spelling | ||
| VignetteBuilder: knitr | ||
| URL: https://github.com/dylanrussellmd/nsqipr | ||
| BugReports: https://github.com/dylanrussellmd/nsqipr/issues | ||
| Language: en-US | ||
| Imports: | ||
| stringr, | ||
| readr, | ||
| magrittr, | ||
| usethis, | ||
| dplyr, | ||
| tibble, | ||
| lubridate, | ||
| purrr, | ||
| tools, | ||
| utils, | ||
| filesstrings, | ||
| progress | ||
| Depends: | ||
| R (>= 3.5.0) | ||
| Package: nsqipr | ||
| Title: Interact with NSQIP data via R | ||
| Version: 0.0.0.9000 | ||
| Authors@R: | ||
| person(given = "Dylan", | ||
| family = "Russell", | ||
| role = c("aut", "cre"), | ||
| email = "[email protected]", | ||
| comment = c(ORCID = "0000-0002-9543-9897")) | ||
| Description: Streamlines reading and writing clean NSQIP data. | ||
| License: CC0 | ||
| Encoding: UTF-8 | ||
| LazyData: true | ||
| Roxygen: list(markdown = TRUE) | ||
| RoxygenNote: 7.1.1 | ||
| Suggests: | ||
| knitr, | ||
| rmarkdown, | ||
| testthat, | ||
| spelling | ||
| VignetteBuilder: knitr | ||
| URL: https://github.com/dylanrussellmd/nsqipr | ||
| BugReports: https://github.com/dylanrussellmd/nsqipr/issues | ||
| Language: en-US | ||
| Imports: | ||
| stringr, | ||
| readr, | ||
| magrittr, | ||
| usethis, | ||
| dplyr, | ||
| tibble, | ||
| lubridate, | ||
| purrr, | ||
| tools, | ||
| utils, | ||
| filesstrings, | ||
| progress, | ||
| furniture | ||
| Depends: | ||
| R (>= 3.5.0) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,82 @@ | ||
| #' Check if a boolean is TRUE and not NA | ||
| #' | ||
| #' This represent a key assumption about the Dindo classification sorting. If a complication is missing (NA), it is considered FALSE | ||
| #' for the purposes of the Dindo classification. | ||
| #' | ||
| #' @param bool a logical vector | ||
| #' | ||
| #' @return a logical vector | ||
| #' | ||
| #' @keywords internal | ||
| #' | ||
| checkTrue <- function(bool) { | ||
| (bool %in% TRUE) & !is.na(bool) | ||
| } | ||
|
|
||
| #' Check if any trues exist row-wise in a logical matrix. | ||
| #' | ||
| #' @param ... a list of logical vectors or a data frame | ||
| #' | ||
| #' @return a logical vector. TRUE if any trues, FALSE if no trues. | ||
| #' | ||
| #' @keywords internal | ||
| #' | ||
| checkAnyTrue <- function(...) { | ||
| apply(cbind(...), 2, checkTrue) %>% | ||
| apply(., 1, any) | ||
| } | ||
|
|
||
| #' Check if a patient has died within 30 days of the index procedure. Assumes that if a patient died, a date would be | ||
| #' recorded in `yrdeath`. | ||
| #' | ||
| #' @param col a vector of any type | ||
| #' | ||
| #' @return a logical vector. TRUE if not NA, FALSE if NA. | ||
| #' | ||
| #' @keywords internal | ||
| #' | ||
| isDead <- function(col) { | ||
| !is.na(col) | ||
| } | ||
|
|
||
| #' Check if any trues exist row-wise in a logical matrix. | ||
| #' | ||
| #' @param ... a list of vectors of any type or a data frame | ||
| #' | ||
| #' @return a logical vector. TRUE if any NA values in row, FALSE if no NA values in row. | ||
| #' | ||
| #' @keywords internal | ||
| #' | ||
| checkAnyDead <- function(...) { | ||
| apply(cbind(...), 2, isDead) %>% | ||
| apply(., 1, any) | ||
| } | ||
|
|
||
|
|
||
| #' Classifies a patient according to the Dindo-Clavien surgical complication grading scale. | ||
| #' | ||
| #' @param df a dataframe including relevant columns containing information on specific post-operative complications. | ||
| #' | ||
| #' @return a numeric vector representing the Dindo-Clavien classification. | ||
| #' | ||
| #' @export | ||
| #' | ||
| dindo <- function(df) { | ||
| e <- new.env() | ||
| dindo_list <- list(dindo_1, dindo_2, dindo_3, dindo_4, dindo_5) | ||
| dindo <- rep(0, nrow(df)) | ||
|
|
||
| dindo_cat <- function(x, y, df) { | ||
| dindo_cols <- colnames(df)[which(colnames(df) %in% x)] | ||
| if(length(dindo_cols) > 0) { | ||
| if(y == 5) { | ||
| dindo[which(checkAnyDead(df[dindo_cols]))] <<- y | ||
| } else { | ||
| dindo[which(checkAnyTrue(df[dindo_cols]))] <<- y | ||
| } | ||
| } | ||
| } | ||
|
|
||
| purrr::imap(dindo_list, ~dindo_cat(.x, .y, df)) | ||
| return(dindo) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| testthat::test_that("checkTrue assigns TRUE correctly", { | ||
| testthat::expect_true(checkTrue(TRUE)) | ||
| testthat::expect_false(checkTrue(NA)) | ||
| testthat::expect_false(checkTrue(FALSE)) | ||
| }) | ||
|
|
||
| testthat::test_that("checkAnyTrue assigns TRUE correctly", { | ||
| testthat::expect_equal(checkAnyTrue(c(TRUE, FALSE, TRUE, FALSE), c(FALSE, FALSE, NA, NA )), c(TRUE, FALSE, TRUE, FALSE)) | ||
| }) | ||
|
|
||
| testthat::test_that("checkTrue and checkAnyTrue are equal if given a single vector", { | ||
| testthat::expect_equal(checkTrue(c(TRUE, TRUE, TRUE, FALSE)), checkAnyTrue(c(TRUE, TRUE, TRUE, FALSE))) | ||
| }) | ||
|
|
||
| testthat::test_that("isDead assigns TRUE correctly", { | ||
| testthat::expect_true(isDead("dead")) | ||
| testthat::expect_false(isDead(NA)) | ||
| }) | ||
|
|
||
| testthat::test_that("checkAnyDead assigns TRUE correctly", { | ||
| testthat::expect_equal(checkAnyDead(c("dead", NA, NA), c(NA, "dead", NA)), c(TRUE, TRUE, FALSE)) | ||
| }) |