mirror of https://github.com/msberends/AMR.git
(v1.6.0.9061) age() update
This commit is contained in:
parent
fa2f5214b9
commit
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@ -50,17 +50,22 @@ jobs:
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fail-fast: false
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matrix:
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config:
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# these are the developmental version of R - we allow those tests to fail
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- {os: macOS-latest, r: 'devel', allowfail: true}
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- {os: macOS-latest, r: 'release', allowfail: false}
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- {os: macOS-latest, r: 'oldrel', allowfail: false}
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- {os: windows-latest, r: 'devel', allowfail: true}
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- {os: windows-latest, r: 'release', allowfail: false}
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- {os: windows-latest, r: 'oldrel', allowfail: false}
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- {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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# these are the current release of R
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- {os: macOS-latest, r: 'release', allowfail: false}
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- {os: windows-latest, r: 'release', allowfail: false}
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- {os: ubuntu-20.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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# these are the previous release of R
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- {os: macOS-latest, r: 'oldrel', allowfail: false}
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- {os: windows-latest, r: 'oldrel', allowfail: false}
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- {os: ubuntu-20.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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# test against all released versions of R >= 3.0, we support them all!
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- {os: ubuntu-20.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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@ -30,7 +30,6 @@ on:
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- master
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pull_request:
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branches:
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- premaster
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- master
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name: code-coverage
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@ -76,10 +75,9 @@ jobs:
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library(AMR)
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library(tinytest)
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library(covr)
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source_files <- list.files("AMR/R", pattern = ".R$", full.names = TRUE)
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test_files <- list.files("AMR/inst/tinytest", full.names = TRUE)
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cov <- file_coverage(source_files = source_files, test_files = test_files, parent_env = asNamespace("AMR"), line_exclusions = list("AMR/R/atc_online.R", "AMR/R/mo_source.R", "AMR/R/translate.R", "AMR/R/resistance_predict.R", "AMR/R/aa_helper_functions.R", "AMR/R/aa_helper_pm_functions.R", "AMR/R/zzz.R"))
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print(cov)
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source_files <- list.files("R", pattern = ".R$", full.names = TRUE)
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test_files <- list.files("inst/tinytest", full.names = TRUE)
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cov <- file_coverage(source_files = source_files, test_files = test_files, parent_env = asNamespace("AMR"), line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
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attr(cov, which = "package") <- list(path = ".") # until https://github.com/r-lib/covr/issues/478 is solved
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codecov(coverage = cov, quiet = FALSE)
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shell: Rscript {0}
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.6.0.9060
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Date: 2021-05-22
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Version: 1.6.0.9061
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Date: 2021-05-23
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Title: Antimicrobial Resistance Data Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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5
NEWS.md
5
NEWS.md
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@ -1,5 +1,5 @@
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# `AMR` 1.6.0.9060
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## <small>Last updated: 22 May 2021</small>
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# `AMR` 1.6.0.9061
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## <small>Last updated: 23 May 2021</small>
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### Breaking change
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* All antibiotic class selectors (such as `carbapenems()`, `aminoglycosides()`) can now be used for filtering as well, making all their accompanying `filter_*()` functions redundant (such as `filter_carbapenems()`, `filter_aminoglycosides()`). These functions are now deprecated and will be removed in a next release.
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@ -64,6 +64,7 @@
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* Updated join functions to always use `dplyr` join functions if the `dplyr` package is installed - now also preserving grouped variables
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* Antibiotic class selectors (such as `cephalosporins()`) now maintain the column order from the original data
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* Fix for selecting columns using `fluoroquinolones()`
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* `age()` now vectorises over both `x` and `reference`
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### Other
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* All unit tests are now processed by the `tinytest` package, instead of the `testthat` package. The `testthat` package unfortunately requires tons of dependencies that are also heavy and only usable for recent R versions, disallowing developers to test a package under any R 3.* version. On the contrary, the `tinytest` package is very lightweight and dependency-free.
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@ -27,7 +27,7 @@
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#'
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#' These functions help to filter and select columns with antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
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#' @inheritSection lifecycle Stable Lifecycle
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#' @param ab_class an antimicrobial class, like `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value.
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#' @param ab_class an antimicrobial class, such as `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value.
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#' @param only_rsi_columns a [logical] to indicate whether only columns of class `<rsi>` must be selected (defaults to `FALSE`), see [as.rsi()]
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#' @details \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
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#'
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23
R/age.R
23
R/age.R
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@ -27,12 +27,14 @@
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#'
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#' Calculates age in years based on a reference date, which is the sytem date at default.
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#' @inheritSection lifecycle Stable Lifecycle
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#' @param x date(s), will be coerced with [as.POSIXlt()]
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#' @param reference reference date(s) (defaults to today), will be coerced with [as.POSIXlt()]
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#' @param x date(s), [character] (vectors) will be coerced with [as.POSIXlt()]
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#' @param reference reference date(s) (defaults to today), [character] (vectors) will be coerced with [as.POSIXlt()]
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#' @param exact a [logical] to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of [year-to-date](https://en.wikipedia.org/wiki/Year-to-date) (YTD) of `x` by the number of days in the year of `reference` (either 365 or 366).
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#' @param na.rm a [logical] to indicate whether missing values should be removed
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#' @param ... arguments passed on to [as.POSIXlt()], such as `origin`
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#' @details Ages below 0 will be returned as `NA` with a warning. Ages above 120 will only give a warning.
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#'
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#' This function vectorises over both `x` and `reference`, meaning that either can have a length of 1 while the other argument has a larger length.
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#' @return An [integer] (no decimals) if `exact = FALSE`, a [double] (with decimals) otherwise
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#' @seealso To split ages into groups, use the [age_groups()] function.
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#' @inheritSection AMR Read more on Our Website!
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@ -53,8 +55,13 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
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meet_criteria(na.rm, allow_class = "logical", has_length = 1)
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if (length(x) != length(reference)) {
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stop_if(length(reference) != 1, "`x` and `reference` must be of same length, or `reference` must be of length 1.")
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reference <- rep(reference, length(x))
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if (length(x) == 1) {
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x <- rep(x, length(reference))
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} else if (length(reference) == 1) {
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reference <- rep(reference, length(x))
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} else {
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stop_("`x` and `reference` must be of same length, or `reference` must be of length 1.")
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}
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}
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x <- as.POSIXlt(x, ...)
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reference <- as.POSIXlt(reference, ...)
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@ -68,15 +75,15 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
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# add decimals
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if (exact == TRUE) {
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# get dates of `x` when `x` would have the year of `reference`
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x_in_reference_year <- as.POSIXlt(paste0(format(reference, "%Y"), format(x, "-%m-%d")))
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x_in_reference_year <- as.POSIXlt(paste0(format(as.Date(reference), "%Y"), format(as.Date(x), "-%m-%d")))
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# get differences in days
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n_days_x_rest <- as.double(difftime(reference, x_in_reference_year, units = "days"))
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n_days_x_rest <- as.double(difftime(as.Date(reference), as.Date(x_in_reference_year), units = "days"))
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# get numbers of days the years of `reference` has for a reliable denominator
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n_days_reference_year <- as.POSIXlt(paste0(format(reference, "%Y"), "-12-31"))$yday + 1
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n_days_reference_year <- as.POSIXlt(paste0(format(as.Date(reference), "%Y"), "-12-31"))$yday + 1
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# add decimal parts of year
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mod <- n_days_x_rest / n_days_reference_year
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# negative mods are cases where `x_in_reference_year` > `reference` - so 'add' a year
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mod[mod < 0] <- 1 + mod[mod < 0]
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mod[mod < 0] <- mod[mod < 0] + 1
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# and finally add to ages
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ages <- ages + mod
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}
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Binary file not shown.
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9060</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9060</span>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9060</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
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</span>
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</div>
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@ -192,7 +192,7 @@
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<div class="page-header toc-ignore">
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<h1 data-toc-skip>Data sets for download / own use</h1>
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<h4 class="date">22 May 2021</h4>
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<h4 class="date">23 May 2021</h4>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
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<div class="hidden name"><code>datasets.Rmd</code></div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9060</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9060</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
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</span>
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</div>
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@ -222,6 +222,9 @@ table a:not(.btn) {
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table a:not(.btn):hover {
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text-decoration: underline;
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}
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.template-article thead th {
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text-align: inherit;
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}
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/* text below header in manual overview */
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.template-reference-index h2 ~ p {
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9060</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9060</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
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</span>
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</div>
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@ -236,12 +236,12 @@
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1609060" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9060">
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<a href="#amr-1609060" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9060</h1>
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<div id="last-updated-22-may-2021" class="section level2">
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<div id="amr-1609061" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9061">
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<a href="#amr-1609061" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9061</h1>
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<div id="last-updated-23-may-2021" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-22-may-2021" class="anchor"></a><small>Last updated: 22 May 2021</small>
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<a href="#last-updated-23-may-2021" class="anchor"></a><small>Last updated: 23 May 2021</small>
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</h2>
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<div id="breaking-change" class="section level3">
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<h3 class="hasAnchor">
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@ -335,6 +335,9 @@
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<li>Antibiotic class selectors (such as <code><a href="../reference/antibiotic_class_selectors.html">cephalosporins()</a></code>) now maintain the column order from the original data</li>
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<li>Fix for selecting columns using <code><a href="../reference/antibiotic_class_selectors.html">fluoroquinolones()</a></code>
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</li>
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<li>
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<code><a href="../reference/age.html">age()</a></code> now vectorises over both <code>x</code> and <code>reference</code>
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</li>
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</ul>
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</div>
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<div id="other" class="section level3">
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datasets: datasets.html
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resistance_predict: resistance_predict.html
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welcome_to_AMR: welcome_to_AMR.html
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last_built: 2021-05-22T07:53Z
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last_built: 2021-05-23T20:10Z
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urls:
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reference: https://msberends.github.io/AMR//reference
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article: https://msberends.github.io/AMR//articles
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
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</span>
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</div>
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<colgroup><col class="name" /><col class="desc" /></colgroup>
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<tr>
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<th>x</th>
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<td><p>date(s), will be coerced with <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXlt()</a></code></p></td>
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<td><p>date(s), <a href='https://rdrr.io/r/base/character.html'>character</a> (vectors) will be coerced with <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXlt()</a></code></p></td>
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</tr>
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<tr>
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<th>reference</th>
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<td><p>reference date(s) (defaults to today), will be coerced with <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXlt()</a></code></p></td>
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<td><p>reference date(s) (defaults to today), <a href='https://rdrr.io/r/base/character.html'>character</a> (vectors) will be coerced with <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXlt()</a></code></p></td>
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</tr>
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<tr>
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<th>exact</th>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>Ages below 0 will be returned as <code>NA</code> with a warning. Ages above 120 will only give a warning.</p>
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<p>This function vectorises over both <code>x</code> and <code>reference</code>, meaning that either can have a length of 1 while the other argument has a larger length.</p>
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<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
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||||
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|
|
|||
|
|
@ -83,7 +83,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -281,7 +281,7 @@
|
|||
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
||||
<tr>
|
||||
<th>ab_class</th>
|
||||
<td><p>an antimicrobial class, like <code>"carbapenems"</code>. The columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code> of the <a href='antibiotics.html'>antibiotics</a> data set will be searched (case-insensitive) for this value.</p></td>
|
||||
<td><p>an antimicrobial class, such as <code>"carbapenems"</code>. The columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code> of the <a href='antibiotics.html'>antibiotics</a> data set will be searched (case-insensitive) for this value.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>only_rsi_columns</th>
|
||||
|
|
|
|||
|
|
@ -81,7 +81,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9060</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -81,7 +81,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9060</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -7,9 +7,9 @@
|
|||
age(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...)
|
||||
}
|
||||
\arguments{
|
||||
\item{x}{date(s), will be coerced with \code{\link[=as.POSIXlt]{as.POSIXlt()}}}
|
||||
\item{x}{date(s), \link{character} (vectors) will be coerced with \code{\link[=as.POSIXlt]{as.POSIXlt()}}}
|
||||
|
||||
\item{reference}{reference date(s) (defaults to today), will be coerced with \code{\link[=as.POSIXlt]{as.POSIXlt()}}}
|
||||
\item{reference}{reference date(s) (defaults to today), \link{character} (vectors) will be coerced with \code{\link[=as.POSIXlt]{as.POSIXlt()}}}
|
||||
|
||||
\item{exact}{a \link{logical} to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of \href{https://en.wikipedia.org/wiki/Year-to-date}{year-to-date} (YTD) of \code{x} by the number of days in the year of \code{reference} (either 365 or 366).}
|
||||
|
||||
|
|
@ -25,6 +25,8 @@ Calculates age in years based on a reference date, which is the sytem date at de
|
|||
}
|
||||
\details{
|
||||
Ages below 0 will be returned as \code{NA} with a warning. Ages above 120 will only give a warning.
|
||||
|
||||
This function vectorises over both \code{x} and \code{reference}, meaning that either can have a length of 1 while the other argument has a larger length.
|
||||
}
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
|
|
|
|||
|
|
@ -53,7 +53,7 @@ penicillins(only_rsi_columns = FALSE)
|
|||
tetracyclines(only_rsi_columns = FALSE)
|
||||
}
|
||||
\arguments{
|
||||
\item{ab_class}{an antimicrobial class, like \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.}
|
||||
\item{ab_class}{an antimicrobial class, such as \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.}
|
||||
|
||||
\item{only_rsi_columns}{a \link{logical} to indicate whether only columns of class \verb{<rsi>} must be selected (defaults to \code{FALSE}), see \code{\link[=as.rsi]{as.rsi()}}}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -222,6 +222,9 @@ table a:not(.btn) {
|
|||
table a:not(.btn):hover {
|
||||
text-decoration: underline;
|
||||
}
|
||||
.template-article thead th {
|
||||
text-align: inherit;
|
||||
}
|
||||
|
||||
/* text below header in manual overview */
|
||||
.template-reference-index h2 ~ p {
|
||||
|
|
|
|||
Loading…
Reference in New Issue