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(v1.6.0.9062) code consistency

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dr. M.S. (Matthijs) Berends 2021-05-24 00:06:28 +02:00
parent 07939b1a14
commit 06302d296a
23 changed files with 48 additions and 45 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.6.0.9061 Version: 1.6.0.9062
Date: 2021-05-23 Date: 2021-05-24
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

4
NEWS.md
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@ -1,5 +1,5 @@
# `AMR` 1.6.0.9061 # `AMR` 1.6.0.9062
## <small>Last updated: 23 May 2021</small> ## <small>Last updated: 24 May 2021</small>
### Breaking change ### Breaking change
* 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. * 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.

14
R/aa_helper_functions.R
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@ -727,7 +727,7 @@ get_current_data <- function(arg_name, call) {
} }
} }
if (current_R_older_than(3.2)) { if (getRversion() < "3.2") {
# R-3.0 and R-3.1 do not have an `x` element in the call stack, rendering this function useless # R-3.0 and R-3.1 do not have an `x` element in the call stack, rendering this function useless
if (is.na(arg_name)) { if (is.na(arg_name)) {
# like in carbapenems() etc. # like in carbapenems() etc.
@ -893,7 +893,7 @@ has_colour <- function() {
if (Sys.getenv("RSTUDIO", "") == "") { if (Sys.getenv("RSTUDIO", "") == "") {
return(FALSE) return(FALSE)
} }
if ((cols <- Sys.getenv("RSTUDIO_CONSOLE_COLOR", "")) != "" && !is.na(as.numeric(cols))) { if ((cols <- Sys.getenv("RSTUDIO_CONSOLE_COLOR", "")) != "" && !is.na(as.double(cols))) {
return(TRUE) return(TRUE)
} }
tryCatch(get("isAvailable", envir = asNamespace("rstudioapi"))(), error = function(e) return(FALSE)) && tryCatch(get("isAvailable", envir = asNamespace("rstudioapi"))(), error = function(e) return(FALSE)) &&
@ -1186,15 +1186,11 @@ percentage <- function(x, digits = NULL, ...) {
} }
time_start_tracking <- function() { time_start_tracking <- function() {
pkg_env$time_start <- round(as.numeric(Sys.time()) * 1000) pkg_env$time_start <- round(as.double(Sys.time()) * 1000)
} }
time_track <- function(name = NULL) { time_track <- function(name = NULL) {
paste("(until now:", trimws(round(as.numeric(Sys.time()) * 1000) - pkg_env$time_start), "ms)") paste("(until now:", trimws(round(as.double(Sys.time()) * 1000) - pkg_env$time_start), "ms)")
}
current_R_older_than <- function(version) {
as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < version
} }
# prevent dependency on package 'backports' ---- # prevent dependency on package 'backports' ----
@ -1245,7 +1241,7 @@ lengths <- function(x, use.names = TRUE) {
vapply(x, length, FUN.VALUE = NA_integer_, USE.NAMES = use.names) vapply(x, length, FUN.VALUE = NA_integer_, USE.NAMES = use.names)
} }
if (current_R_older_than(3.1)) { if (getRversion() < "3.1") {
# R-3.0 does not contain these functions, set them here to prevent installation failure # R-3.0 does not contain these functions, set them here to prevent installation failure
# (required for extension of the <mic> class) # (required for extension of the <mic> class)
cospi <- function(...) 1 cospi <- function(...) 1

6
R/ab_class_selectors.R
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@ -25,11 +25,11 @@
#' Antibiotic Class Selectors #' Antibiotic Class Selectors
#' #'
#' 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, "."), "")}} #' 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(getRversion() < "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, "."), "")}}
#' @inheritSection lifecycle Stable Lifecycle #' @inheritSection lifecycle Stable Lifecycle
#' @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. #' @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.
#' @param only_rsi_columns a [logical] to indicate whether only columns of class `<rsi>` must be selected (defaults to `FALSE`), see [as.rsi()] #' @param only_rsi_columns a [logical] to indicate whether only columns of class `<rsi>` must be selected (defaults to `FALSE`), see [as.rsi()]
#' @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, "."), "")}} #' @details \strong{\Sexpr{ifelse(getRversion() < "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, "."), "")}}
#' #'
#' #'
#' These functions can be used in data set calls for selecting columns and filtering rows, see *Examples*. They support base R, but work more convenient in dplyr functions such as [`select()`][dplyr::select()], [`filter()`][dplyr::filter()] and [`summarise()`][dplyr::summarise()]. #' These functions can be used in data set calls for selecting columns and filtering rows, see *Examples*. They support base R, but work more convenient in dplyr functions such as [`select()`][dplyr::select()], [`filter()`][dplyr::filter()] and [`summarise()`][dplyr::summarise()].
@ -220,7 +220,7 @@ ab_selector <- function(ab_class,
meet_criteria(function_name, allow_class = "character", has_length = 1, .call_depth = 1) meet_criteria(function_name, allow_class = "character", has_length = 1, .call_depth = 1)
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1, .call_depth = 1) meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1, .call_depth = 1)
if (current_R_older_than(3.2)) { if (getRversion() < "3.2") {
warning_("antibiotic class selectors such as ", function_name, warning_("antibiotic class selectors such as ", function_name,
"() require R version 3.2 or later - you have ", R.version.string, "() require R version 3.2 or later - you have ", R.version.string,
call = FALSE) call = FALSE)

17
R/age.R
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@ -75,11 +75,16 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
# add decimals # add decimals
if (exact == TRUE) { if (exact == TRUE) {
# get dates of `x` when `x` would have the year of `reference` # get dates of `x` when `x` would have the year of `reference`
x_in_reference_year <- as.POSIXlt(paste0(format(as.Date(reference), "%Y"), format(as.Date(x), "-%m-%d"))) x_in_reference_year <- as.POSIXlt(paste0(format(as.Date(reference), "%Y"),
format(as.Date(x), "-%m-%d")),
format = "%Y-%m-%d")
# get differences in days # get differences in days
n_days_x_rest <- as.double(difftime(as.Date(reference), as.Date(x_in_reference_year), units = "days")) n_days_x_rest <- as.double(difftime(as.Date(reference),
as.Date(x_in_reference_year),
units = "days"))
# get numbers of days the years of `reference` has for a reliable denominator # get numbers of days the years of `reference` has for a reliable denominator
n_days_reference_year <- as.POSIXlt(paste0(format(as.Date(reference), "%Y"), "-12-31"))$yday + 1 n_days_reference_year <- as.POSIXlt(paste0(format(as.Date(reference), "%Y"), "-12-31"),
format = "%Y-%m-%d")$yday + 1
# add decimal parts of year # add decimal parts of year
mod <- n_days_x_rest / n_days_reference_year mod <- n_days_x_rest / n_days_reference_year
# negative mods are cases where `x_in_reference_year` > `reference` - so 'add' a year # negative mods are cases where `x_in_reference_year` > `reference` - so 'add' a year
@ -100,7 +105,11 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
ages <- ages[!is.na(ages)] ages <- ages[!is.na(ages)]
} }
ages if (exact == TRUE) {
as.double(ages)
} else {
as.integer(ages)
}
} }
#' Split Ages into Age Groups #' Split Ages into Age Groups

2
R/disk.R
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@ -85,7 +85,7 @@ as.disk <- function(x, na.rm = FALSE) {
fixed = TRUE) fixed = TRUE)
x_clean <- gsub(remove, "", x, ignore.case = TRUE, fixed = fixed) x_clean <- gsub(remove, "", x, ignore.case = TRUE, fixed = fixed)
# remove everything that is not a number or dot # remove everything that is not a number or dot
as.numeric(gsub("[^0-9.]+", "", x_clean)) as.double(gsub("[^0-9.]+", "", x_clean))
} }
# round up and make it an integer # round up and make it an integer

2
R/pca.R
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@ -120,7 +120,7 @@ pca <- function(x,
message_("Columns selected for PCA: ", vector_and(font_bold(colnames(pca_data), collapse = NULL), quotes = TRUE), message_("Columns selected for PCA: ", vector_and(font_bold(colnames(pca_data), collapse = NULL), quotes = TRUE),
". Total observations available: ", nrow(pca_data), ".") ". Total observations available: ", nrow(pca_data), ".")
if (current_R_older_than(3.4)) { if (getRversion() < "3.4.0") {
# stats::prcomp prior to 3.4.0 does not have the 'rank.' argument # stats::prcomp prior to 3.4.0 does not have the 'rank.' argument
pca_model <- prcomp(pca_data, retx = retx, center = center, scale. = scale., tol = tol) pca_model <- prcomp(pca_data, retx = retx, center = center, scale. = scale., tol = tol)
} else { } else {

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data-raw/AMR_latest.tar.gz
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2
docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a> <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">1.6.0.9061</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9062</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.6.0.9061</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9062</span>
</span> </span>
</div> </div>

4
docs/articles/datasets.html
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@ -39,7 +39,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.6.0.9061</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9062</span>
</span> </span>
</div> </div>
@ -192,7 +192,7 @@
<div class="page-header toc-ignore"> <div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1> <h1 data-toc-skip>Data sets for download / own use</h1>
<h4 class="date">23 May 2021</h4> <h4 class="date">24 May 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div> <div class="hidden name"><code>datasets.Rmd</code></div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.6.0.9061</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9062</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.6.0.9061</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9062</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -42,7 +42,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.6.0.9061</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9062</span>
</span> </span>
</div> </div>

12
docs/news/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.6.0.9061</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9062</span>
</span> </span>
</div> </div>
@ -236,12 +236,12 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1609061" class="section level1"> <div id="amr-1609062" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9061"> <h1 class="page-header" data-toc-text="1.6.0.9062">
<a href="#amr-1609061" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9061</h1> <a href="#amr-1609062" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9062</h1>
<div id="last-updated-23-may-2021" class="section level2"> <div id="last-updated-24-may-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-23-may-2021" class="anchor"></a><small>Last updated: 23 May 2021</small> <a href="#last-updated-24-may-2021" class="anchor"></a><small>Last updated: 24 May 2021</small>
</h2> </h2>
<div id="breaking-change" class="section level3"> <div id="breaking-change" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-05-23T20:10Z last_built: 2021-05-23T22:05Z
urls: urls:
reference: https://msberends.github.io/AMR//reference reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles article: https://msberends.github.io/AMR//articles

2
docs/reference/antibiotic_class_selectors.html
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@ -83,7 +83,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.6.0.9061</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9062</span>
</span> </span>
</div> </div>

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.6.0.9061</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9062</span>
</span> </span>
</div> </div>

2
docs/survey.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.6.0.9061</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9062</span>
</span> </span>
</div> </div>

2
inst/tinytest/test-ab_class_selectors.R
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@ -23,7 +23,7 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== # # ==================================================================== #
if (!AMR:::current_R_older_than(3.2)) { if (getRversion() >= "3.2") {
# antibiotic class selectors require at least R-3.2 # antibiotic class selectors require at least R-3.2
expect_true(ncol(example_isolates[, aminoglycosides(), drop = FALSE]) < ncol(example_isolates)) expect_true(ncol(example_isolates[, aminoglycosides(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, betalactams(), drop = FALSE]) < ncol(example_isolates)) expect_true(ncol(example_isolates[, betalactams(), drop = FALSE]) < ncol(example_isolates))

2
inst/tinytest/test-mic.R
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@ -85,7 +85,7 @@ suppressWarnings(expect_identical(log1p(x), log1p(x_double)))
suppressWarnings(expect_identical(cos(x), cos(x_double))) suppressWarnings(expect_identical(cos(x), cos(x_double)))
suppressWarnings(expect_identical(sin(x), sin(x_double))) suppressWarnings(expect_identical(sin(x), sin(x_double)))
suppressWarnings(expect_identical(tan(x), tan(x_double))) suppressWarnings(expect_identical(tan(x), tan(x_double)))
if (!AMR:::current_R_older_than(3.1)) { if (getRversion() >= "3.1") {
suppressWarnings(expect_identical(cospi(x), cospi(x_double))) suppressWarnings(expect_identical(cospi(x), cospi(x_double)))
suppressWarnings(expect_identical(sinpi(x), sinpi(x_double))) suppressWarnings(expect_identical(sinpi(x), sinpi(x_double)))
suppressWarnings(expect_identical(tanpi(x), tanpi(x_double))) suppressWarnings(expect_identical(tanpi(x), tanpi(x_double)))

4
man/antibiotic_class_selectors.Rd
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@ -58,10 +58,10 @@ tetracyclines(only_rsi_columns = FALSE)
\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()}}} \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()}}}
} }
\description{ \description{
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, "."), "")}} 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(getRversion() < "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, "."), "")}}
} }
\details{ \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, "."), "")}} \strong{\Sexpr{ifelse(getRversion() < "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, "."), "")}}
These functions can be used in data set calls for selecting columns and filtering rows, see \emph{Examples}. They support base R, but work more convenient in dplyr functions such as \code{\link[dplyr:select]{select()}}, \code{\link[dplyr:filter]{filter()}} and \code{\link[dplyr:summarise]{summarise()}}. These functions can be used in data set calls for selecting columns and filtering rows, see \emph{Examples}. They support base R, but work more convenient in dplyr functions such as \code{\link[dplyr:select]{select()}}, \code{\link[dplyr:filter]{filter()}} and \code{\link[dplyr:summarise]{summarise()}}.

2
tests/tinytest.R
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@ -27,9 +27,7 @@
if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) { if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
# env var 'R_LIBS_USER' got overwritten during 'R CMD check' in GitHub Actions, so: # env var 'R_LIBS_USER' got overwritten during 'R CMD check' in GitHub Actions, so:
.libPaths(c(Sys.getenv("R_LIBS_USER_GH_ACTIONS"), .libPaths())) .libPaths(c(Sys.getenv("R_LIBS_USER_GH_ACTIONS"), .libPaths()))
print("here")
if (AMR:::pkg_is_available("tinytest")) { if (AMR:::pkg_is_available("tinytest")) {
print("here2")
library(AMR) library(AMR)
out <- test_package("AMR", out <- test_package("AMR",
testdir = ifelse(AMR:::dir.exists("inst/tinytest"), testdir = ifelse(AMR:::dir.exists("inst/tinytest"),