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https://github.com/msberends/AMR.git
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(v1.7.1.9037) dplyr grouping fix on windows?
This commit is contained in:
parent
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commit
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42
.github/workflows/check.yaml
vendored
42
.github/workflows/check.yaml
vendored
@ -52,35 +52,33 @@ jobs:
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fail-fast: false
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fail-fast: false
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matrix:
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matrix:
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config:
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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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# test all systems against all released versions of R >= 3.0, we support them all!
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# - {os: macOS-latest, r: 'devel', allowfail: false}
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- {os: macOS-latest, r: 'devel', allowfail: true}
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# - {os: windows-latest, r: 'devel', allowfail: false}
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- {os: macOS-latest, r: '4.1', allowfail: false}
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# - {os: ubuntu-20.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: macOS-latest, r: '4.0', allowfail: false}
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#
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- {os: macOS-latest, r: '3.6', allowfail: false}
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# # test all systems against all released versions of R >= 3.0, we support them all!
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- {os: macOS-latest, r: '3.5', allowfail: false}
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# - {os: macOS-latest, r: '4.1', allowfail: false}
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- {os: macOS-latest, r: '3.4', allowfail: false}
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- {os: macOS-latest, r: '3.3', allowfail: false}
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- {os: macOS-latest, r: '3.2', 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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- {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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- {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: windows-latest, r: 'devel', allowfail: true}
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- {os: windows-latest, r: '4.1', allowfail: false}
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- {os: windows-latest, r: '4.1', allowfail: false}
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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: macOS-latest, r: '4.0', allowfail: false}
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- {os: windows-latest, r: '4.0', allowfail: false}
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- {os: windows-latest, r: '4.0', allowfail: false}
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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: macOS-latest, r: '3.6', allowfail: false}
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- {os: windows-latest, r: '3.6', allowfail: false}
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- {os: windows-latest, r: '3.6', allowfail: false}
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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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# - {os: macOS-latest, r: '3.5', allowfail: false}
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- {os: windows-latest, r: '3.5', allowfail: false}
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- {os: windows-latest, r: '3.5', allowfail: false}
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# - {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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# - {os: macOS-latest, r: '3.4', allowfail: false}
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- {os: windows-latest, r: '3.4', allowfail: false}
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- {os: windows-latest, r: '3.4', allowfail: false}
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# - {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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# - {os: macOS-latest, r: '3.3', allowfail: false}
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- {os: windows-latest, r: '3.3', allowfail: false}
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- {os: windows-latest, r: '3.3', allowfail: false}
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# - {os: ubuntu-20.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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# - {os: macOS-latest, r: '3.2', allowfail: false}
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- {os: windows-latest, r: '3.2', allowfail: false}
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- {os: windows-latest, r: '3.2', allowfail: false}
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# - {os: ubuntu-20.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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# - {os: ubuntu-20.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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# - {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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env:
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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@ -1,6 +1,6 @@
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Package: AMR
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Package: AMR
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Version: 1.7.1.9036
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Version: 1.7.1.9037
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Date: 2021-08-30
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Date: 2021-08-31
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Title: Antimicrobial Resistance Data Analysis
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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data analysis and to work with microbial and antimicrobial properties by
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4
NEWS.md
4
NEWS.md
@ -1,5 +1,5 @@
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# `AMR` 1.7.1.9036
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# `AMR` 1.7.1.9037
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## <small>Last updated: 30 August 2021</small>
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## <small>Last updated: 31 August 2021</small>
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### Breaking changes
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### Breaking changes
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* Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version
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* Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version
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@ -728,18 +728,14 @@ meet_criteria <- function(object,
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return(invisible())
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return(invisible())
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}
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}
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get_current_data <- function(arg_name, call, requires_cur_data = FALSE) {
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get_current_data <- function(arg_name, call) {
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# try dplyr::cur_data_all() first to support dplyr groups
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# try dplyr::cur_data_all() first to support dplyr groups
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# only useful for e.g. dplyr::filter(), dplyr::mutate() and dplyr::summarise()
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# only useful for e.g. dplyr::filter(), dplyr::mutate() and dplyr::summarise()
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# not useful (throws error) with e.g. dplyr::select() - but that will be caught later in this function
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# not useful (throws error) with e.g. dplyr::select() - but that will be caught later in this function
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cur_data_all <- import_fn("cur_data_all", "dplyr", error_on_fail = FALSE)
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cur_data_all <- import_fn("cur_data_all", "dplyr", error_on_fail = FALSE)
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if (isTRUE(requires_cur_data)) {
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print(cur_data_all())
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}
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if (!is.null(cur_data_all)) {
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if (!is.null(cur_data_all)) {
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out <- tryCatch(cur_data_all(), error = function(e) NULL)
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out <- tryCatch(cur_data_all(), error = function(e) NULL)
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if (is.data.frame(out)) {
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if (is.data.frame(out)) {
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message("==> RETURNING cur_data_all()")
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return(structure(out, type = "dplyr_cur_data_all"))
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return(structure(out, type = "dplyr_cur_data_all"))
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}
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}
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}
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}
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@ -752,17 +748,14 @@ get_current_data <- function(arg_name, call, requires_cur_data = FALSE) {
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if (!is.null(env$`.data`) && is.data.frame(env$`.data`)) {
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if (!is.null(env$`.data`) && is.data.frame(env$`.data`)) {
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# an element `.data` will be in the environment when using `dplyr::select()`
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# an element `.data` will be in the environment when using `dplyr::select()`
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# (but not when using `dplyr::filter()`, `dplyr::mutate()` or `dplyr::summarise()`)
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# (but not when using `dplyr::filter()`, `dplyr::mutate()` or `dplyr::summarise()`)
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message("==> RETURNING dplyr_selector")
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return(structure(env$`.data`, type = "dplyr_selector"))
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return(structure(env$`.data`, type = "dplyr_selector"))
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} else if (!is.null(env$xx) && is.data.frame(env$xx)) {
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} else if (!is.null(env$xx) && is.data.frame(env$xx)) {
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# an element `xx` will be in the environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
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# an element `xx` will be in the environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
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message("==> RETURNING base_R 1")
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return(structure(env$xx, type = "base_R"))
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return(structure(env$xx, type = "base_R"))
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} else if (!is.null(env$x) && is.data.frame(env$x)) {
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} else if (!is.null(env$x) && is.data.frame(env$x)) {
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# an element `x` will be in the environment for only cols, e.g. `example_isolates[, carbapenems()]`
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# an element `x` will be in the environment for only cols, e.g. `example_isolates[, carbapenems()]`
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message("==> RETURNING base_R 2")
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return(structure(env$x, type = "base_R"))
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return(structure(env$x, type = "base_R"))
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}
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}
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}
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}
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Binary file not shown.
@ -40,7 +40,7 @@ if (length(to_install) == 0) {
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for (i in seq_len(length(to_install))) {
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for (i in seq_len(length(to_install))) {
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cat("Installing package", to_install[i], "\n")
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cat("Installing package", to_install[i], "\n")
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tryCatch(install.packages(to_install[i],
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tryCatch(install.packages(to_install[i],
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type = ifelse(.Platform$OS.type == "unix", "source", "binary"),
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# type = ifelse(.Platform$OS.type == "unix", "source", "binary"),
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repos = "https://cran.rstudio.com/",
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repos = "https://cran.rstudio.com/",
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dependencies = c("Depends", "Imports"),
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dependencies = c("Depends", "Imports"),
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quiet = FALSE),
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quiet = FALSE),
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.7.1.9036</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9037</span>
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</span>
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</span>
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</div>
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</div>
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<div class="page-header toc-ignore">
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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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<h1 data-toc-skip>Data sets for download / own use</h1>
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<h4 data-toc-skip class="date">30 August 2021</h4>
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<h4 data-toc-skip class="date">31 August 2021</h4>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
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<div class="hidden name"><code>datasets.Rmd</code></div>
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<div class="hidden name"><code>datasets.Rmd</code></div>
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.7.1.9036</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9037</span>
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</span>
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</span>
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</div>
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</div>
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@ -240,12 +240,12 @@
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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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<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>
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<div id="amr-1719036" class="section level1">
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<div id="amr-1719037" class="section level1">
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<h1 class="page-header" data-toc-text="1.7.1.9036">
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<h1 class="page-header" data-toc-text="1.7.1.9037">
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<a href="#amr-1719036" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9036</h1>
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<a href="#amr-1719037" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9037</h1>
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<div id="last-updated-30-august-2021" class="section level2">
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<div id="last-updated-31-august-2021" class="section level2">
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<h2 class="hasAnchor">
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<h2 class="hasAnchor">
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<a href="#last-updated-30-august-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 30 August 2021</small>
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<a href="#last-updated-31-august-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 31 August 2021</small>
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</h2>
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</h2>
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<div id="breaking-changes" class="section level3">
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<div id="breaking-changes" class="section level3">
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<h3 class="hasAnchor">
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<h3 class="hasAnchor">
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@ -117,14 +117,12 @@ if (AMR:::pkg_is_available("dplyr")) {
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first_isolate(col_date = "date",
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first_isolate(col_date = "date",
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col_mo = "mo",
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col_mo = "mo",
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col_patient_id = "patient_id",
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col_patient_id = "patient_id",
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info = FALSE,
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info = FALSE),
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require_cur_data = TRUE),
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example_isolates %>%
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example_isolates %>%
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first_isolate(col_date = "date",
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first_isolate(col_date = "date",
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col_mo = "mo",
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col_mo = "mo",
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col_patient_id = "patient_id",
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col_patient_id = "patient_id",
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info = FALSE,
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info = FALSE))
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require_cur_data = TRUE))
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# support for WHONET
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# support for WHONET
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expect_message(example_isolates %>%
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expect_message(example_isolates %>%
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@ -135,8 +133,8 @@ if (AMR:::pkg_is_available("dplyr")) {
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first_isolate(info = TRUE))
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first_isolate(info = TRUE))
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# groups
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# groups
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x <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate(require_cur_data = TRUE))
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x <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate())
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y <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate(., require_cur_data = TRUE))
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y <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate(.))
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expect_identical(x, y)
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expect_identical(x, y)
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}
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}
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