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keyab fixes
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NEWS.md
19
NEWS.md
@ -1,18 +1,16 @@
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# 0.2.0.90xx (development version)
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#### New
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* **BREAKING**: `rsi_df` was removed in favour of new functions `resistance` and `susceptibility`. Now, all functions used to calculate resistance (`resistance` and `susceptibility`) or count isolates (`n_rsi`) use **hybrid evaluation**. This means calculations are not done in R directly but rather in C++ using the `Rcpp` package, making them 25 to 30 times faster. The function `rsi` still works, but is deprecated.
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* **BREAKING**: the methodology for determining first weighted isolates was changed. The antibiotics (call *key antibiotics*) that are compared between isolated to include more first isolates (called first *weighted* isolates) are now as follows:
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* **BREAKING**: `rsi_df` was removed in favour of new functions `resistance` and `susceptibility`. Now, all functions used to calculate resistance (`resistance` and `susceptibility`) use **hybrid evaluation**. This means calculations are not done in R directly but rather in C++ using the `Rcpp` package, making them 25 to 30 times faster. The function `rsi` still works, but is deprecated.
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* **BREAKING**: the methodology for determining first weighted isolates was changed. The antibiotics that are compared between isolates (call *key antibiotics*) to include more first isolates (afterwards called first *weighted* isolates) are now as follows:
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* Gram-positive: amoxicillin, amoxicillin/clavlanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole, vancomycin, teicoplanin, tetracycline, erythromycin, oxacillin, rifampicin
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* Gram-negative: amoxicillin, amoxicillin/clavlanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole, gentamicin, tobramycin, colistin, cefotaxime, ceftazidime, meropenem
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* Support for Addins menu in RStudio to quickly insert `%in%` or `%like%` (and give them keyboard shortcuts), or to view the datasets that come with this package
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* For convience, new descriptive statistical functions `kurtosis` and `skewness` that are lacking in base R - they are generic functions and have support for vectors, data.frames and matrices
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* Function `g.test` as added to perform the Χ<sup>2</sup> distributed [*G*-test](https://en.wikipedia.org/wiki/G-test), which use is the same as `chisq.test`
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* Function `ratio` was added to transform a vector of values to a preset ratio. For example:
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```r
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ratio(c(772, 1611, 737), ratio = "1:2:1")
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# [1] 780 1560 780
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```
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* Function `p.symbol` was added to transform p values to their related symbols: `0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1`
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* Function `g.test` to perform the Χ<sup>2</sup> distributed [*G*-test](https://en.wikipedia.org/wiki/G-test), which use is the same as `chisq.test`
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* Function `ratio` to transform a vector of values to a preset ratio
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* For example: `ratio(c(10, 500, 10), ratio = "1:2:1")` would return `130, 260, 130`
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* Support for Addins menu in RStudio to quickly insert `%in%` or `%like%` (and give them keyboard shortcuts), or to view the datasets that come with this package
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* Function `p.symbol` to transform p values to their related symbols: `0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1`
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* Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS. These functions use the `clipr` package, but are a little altered to also support headless Linux servers (so you can use it in RStudio Server)
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* New for frequency tables (function `freq`):
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* A vignette to explain its usage
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* Support for `table` to use as input: `freq(table(x, y))`
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@ -22,7 +20,6 @@ ratio(c(772, 1611, 737), ratio = "1:2:1")
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* Function `top_freq` function to return the top/below *n* items as vector
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* Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)
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* Possibility to globally set the default for the amount of items to print, with `options(max.print.freq = n)` where *n* is your preset value
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* Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS. These functions use the `clipr` package, but are a little altered to also support headless Linux servers (so you can use it in RStudio Server).
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#### Changed
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* Pretty printing for tibbles removed as it is not really the scope of this package
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@ -136,7 +136,8 @@ key_antibiotics <- function(tbl,
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# format
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key_abs <- tbl %>%
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pull(key_ab) %>%
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gsub('(NA|NULL)', '-', .)
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gsub('(NA|NULL)', '.', .) %>%
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gsub('[^SIR]', '.', ., ignore.case = TRUE)
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key_abs
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@ -162,22 +163,24 @@ key_antibiotics_equal <- function(x,
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if (type == "keyantibiotics") {
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if (ignore_I == TRUE) {
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# evaluation using regular expression will treat '?' as any character
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# evaluation using regular expression will treat '.' as any character
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# so I is actually ignored then
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x <- gsub('I', '?', x, ignore.case = TRUE)
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y <- gsub('I', '?', y, ignore.case = TRUE)
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x <- gsub('I', '.', x, ignore.case = TRUE)
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y <- gsub('I', '.', y, ignore.case = TRUE)
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}
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for (i in 1:length(x)) {
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result[i] <- grepl(x = x[i],
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pattern = y[i],
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ignore.case = TRUE) |
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grepl(x = y[i],
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pattern = x[i],
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ignore.case = TRUE)
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result[i] <- nchar(x[i]) == nchar(y[i]) &
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(x[i] %like% paste0("^", y[i], "$") |
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y[i] %like% paste0("^", x[i], "$"))
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}
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return(result)
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} else {
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if (type != 'points') {
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stop('`', type, '` is not a valid value for type, must be "points" or "keyantibiotics". See ?first_isolate.')
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}
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if (info == TRUE) {
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p <- dplyr::progress_estimated(length(x))
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}
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@ -208,7 +211,6 @@ key_antibiotics_equal <- function(x,
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x2 <- strsplit(x[i], "")[[1]]
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y2 <- strsplit(y[i], "")[[1]]
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if (type == 'points') {
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# count points for every single character:
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# - no change is 0 points
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# - I <-> S|R is 0.5 point
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@ -220,10 +222,6 @@ key_antibiotics_equal <- function(x,
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points <- (x2 - y2) %>% abs() %>% sum(na.rm = TRUE)
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result[i] <- ((points / 2) >= points_threshold)
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} else {
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stop('`', type, '` is not a valid value for type, must be "points" or "keyantibiotics". See ?first_isolate.')
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}
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}
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}
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if (info == TRUE) {
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@ -14,6 +14,8 @@ test_that("clipboard works", {
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clipboard_import())
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clipboard_export(septic_patients[1:100,])
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expect_identical(as.data.frame(tbl_parse_guess(septic_patients[1:100,]), stringsAsFactors = FALSE),
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clipboard_import(guess_col_types = TRUE, stringsAsFactors = FALSE))
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expect_identical(as.data.frame(tbl_parse_guess(septic_patients[1:100,]),
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stringsAsFactors = FALSE),
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clipboard_import(guess_col_types = TRUE,
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stringsAsFactors = FALSE))
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})
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@ -3,6 +3,7 @@ context("first_isolates.R")
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test_that("keyantibiotics work", {
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expect_equal(length(key_antibiotics(septic_patients, info = FALSE)), nrow(septic_patients))
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expect_true(key_antibiotics_equal("SSS", "SSS"))
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expect_false(key_antibiotics_equal("SSS", "SRS"))
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expect_true(key_antibiotics_equal("SSS", "SIS", ignore_I = TRUE))
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expect_false(key_antibiotics_equal("SSS", "SIS", ignore_I = FALSE))
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})
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@ -19,7 +20,7 @@ test_that("first isolates work", {
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na.rm = TRUE),
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1959)
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# septic_patients contains 1963 out of 2000 first *weighted* isolates
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# septic_patients contains 1962 out of 2000 first *weighted* isolates
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expect_equal(
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suppressWarnings(
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sum(
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@ -31,7 +32,7 @@ test_that("first isolates work", {
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type = "keyantibiotics",
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info = TRUE),
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na.rm = TRUE)),
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1963)
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1962)
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# and 1997 when using points
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expect_equal(
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suppressWarnings(
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@ -18,3 +18,8 @@ test_that("functions missing in older R versions work", {
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expect_equal(trimws(" test ", "l"), "test ")
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expect_equal(trimws(" test ", "r"), " test")
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})
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test_that("generic dates work", {
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expect_equal(date_generic("yyyy-mm-dd"), "%Y-%m-%d")
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expect_equal(date_generic("dddd d mmmm yyyy"), "%A %e %B %Y")
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})
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