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(v1.7.1.9010) fix for count_* and proportion_*

This commit is contained in:
dr. M.S. (Matthijs) Berends 2021-07-04 12:00:41 +02:00
parent 3e26929838
commit 3bd50710e8
23 changed files with 147 additions and 47 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.7.1.9009
Date: 2021-07-03
Version: 1.7.1.9010
Date: 2021-07-04
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(
person(role = c("aut", "cre"),

8
NAMESPACE
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@ -20,20 +20,24 @@ S3method("[",ab)
S3method("[",disk)
S3method("[",mic)
S3method("[",mo)
S3method("[",taxonomic_name)
S3method("[<-",ab)
S3method("[<-",disk)
S3method("[<-",mic)
S3method("[<-",mo)
S3method("[<-",rsi)
S3method("[<-",taxonomic_name)
S3method("[[",ab)
S3method("[[",disk)
S3method("[[",mic)
S3method("[[",mo)
S3method("[[",taxonomic_name)
S3method("[[<-",ab)
S3method("[[<-",disk)
S3method("[[<-",mic)
S3method("[[<-",mo)
S3method("[[<-",rsi)
S3method("[[<-",taxonomic_name)
S3method("^",mic)
S3method("|",mic)
S3method(abs,mic)
@ -47,6 +51,7 @@ S3method(any,ab_selector_any_all)
S3method(any,mic)
S3method(as.data.frame,ab)
S3method(as.data.frame,mo)
S3method(as.data.frame,taxonomic_name)
S3method(as.double,mic)
S3method(as.integer,mic)
S3method(as.list,custom_eucast_rules)
@ -72,6 +77,7 @@ S3method(c,disk)
S3method(c,mic)
S3method(c,mo)
S3method(c,rsi)
S3method(c,taxonomic_name)
S3method(ceiling,mic)
S3method(cos,mic)
S3method(cosh,mic)
@ -117,6 +123,7 @@ S3method(print,mo_renamed)
S3method(print,mo_uncertainties)
S3method(print,pca)
S3method(print,rsi)
S3method(print,taxonomic_name)
S3method(prod,mic)
S3method(quantile,mic)
S3method(range,mic)
@ -147,6 +154,7 @@ S3method(unique,disk)
S3method(unique,mic)
S3method(unique,mo)
S3method(unique,rsi)
S3method(unique,taxonomic_name)
export("%like%")
export("%like_case%")
export("%unlike%")

9
NEWS.md
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@ -1,12 +1,12 @@
# `AMR` 1.7.1.9009
## <small>Last updated: 3 July 2021</small>
# `AMR` 1.7.1.9010
## <small>Last updated: 4 July 2021</small>
### Changed
* Antibiotic class selectors (see `ab_class()`)
* They now finally also work in R-3.0 and R-3.1, supporting every version of R since 2013
* Added more selectors: `aminopenicillins()`, `lincosamides()`, `lipoglycopeptides()`, `polymyxins()`, `quinolones()`, `streptogramins()` and `ureidopenicillins()`
* Fix for using selectors multiple times in one call (e.g., using them in `dplyr::filter()` and immediately after in `dplyr::select()`)
* Fixed duplicate ATC codes in the `antibiotics` data set
* Fix for duplicate ATC codes in the `antibiotics` data set
* Added `ggplot2::autoplot()` generic for classes `<mic>`, `<disk>`, `<rsi>` and `<resistance_predict>`
* Fix to prevent introducing `NA`s for old MO codes when running `as.mo()` on them
* Added more informative error messages when any of the `proportion_*()` and `count_*()` functions fail
@ -14,7 +14,8 @@
* Improved automatic column selector when `col_*` arguments are left blank, e.g. in `first_isolate()`
* The right input types for `random_mic()`, `random_disk()` and `random_rsi()` are now enforced
* `as.rsi()` can now correct for textual input (such as "Susceptible", "Resistant") in Dutch, English, French, German, Italian, Portuguese and Spanish
* More informative warnings for all `count_*()`, `proportion_*()` functions (and `resistant()` and `susceptible()`) when they return NA because of too few test results. The warnings now include the official drug name and if used, the `dplyr` group name.
* When warnings are throws because of too few isolates in any `count_*()`, `proportion_*()` function (or `resistant()` or `susceptible()`), the `dplyr` group will be shown, if available
* Taxonomic names now print in italic in tibbles, if created with `mo_name()`, `mo_fullname()`, `mo_shortname()`, `mo_genus()` or `mo_family()`
# `AMR` 1.7.1

7
R/ab_class_selectors.R
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@ -266,12 +266,13 @@ ab_selector <- function(function_name,
meet_criteria(function_name, allow_class = "character", has_length = 1, allow_NULL = TRUE, .call_depth = 1)
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1, .call_depth = 1)
meet_criteria(ab_class, allow_class = "character", has_length = 1, allow_NULL = TRUE, .call_depth = 1)
# get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
# but it only takes a couple of milliseconds
vars_df <- get_current_data(arg_name = NA, call = -3)
# to improve speed, get_column_abx() will only run once when e.g. in a select or group call
ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)
if (length(ab_in_data) == 0) {
message_("No antimicrobial agents found in the data.")
return(NULL)
@ -312,7 +313,7 @@ ab_selector <- function(function_name,
paste0("\"", ab_class, "\""),
""),
")` using ",
ifelse(length(agents) == 1, "column: ", "columns: "),
ifelse(length(agents) == 1, "column ", "columns "),
vector_and(agents_formatted, quotes = FALSE, sort = FALSE))
}
remember_thrown_message(paste0(function_name, ".", paste(pkg_env$get_column_abx.out, collapse = "|")))

111
R/mo_property.R
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@ -222,9 +222,12 @@ mo_shortname <- function(x, language = get_locale(), ...) {
shortnames[is.na(x.mo)] <- NA_character_
load_mo_failures_uncertainties_renamed(metadata)
translate_AMR(shortnames, language = language, only_unknown = FALSE, only_affect_mo_names = TRUE)
out <- translate_AMR(shortnames, language = language, only_unknown = FALSE, only_affect_mo_names = TRUE)
set_clean_class(out, new_class = c("taxonomic_name", "character"))
}
#' @rdname mo_property
#' @export
mo_subspecies <- function(x, language = get_locale(), ...) {
@ -723,20 +726,24 @@ mo_validate <- function(x, property, language, ...) {
if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$mo) & !has_Becker_or_Lancefield, error = function(e) FALSE)) {
# special case for mo_* functions where class is already <mo>
return(MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE])
}
# try to catch an error when inputting an invalid argument
# so the 'call.' can be set to FALSE
tryCatch(x[1L] %in% MO_lookup[1, property, drop = TRUE],
error = function(e) stop(e$message, call. = FALSE))
x <- MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE]
if (!all(x[!is.na(x)] %in% MO_lookup[, property, drop = TRUE]) | has_Becker_or_Lancefield) {
x <- exec_as.mo(x, property = property, language = language, ...)
} else {
# try to catch an error when inputting an invalid argument
# so the 'call.' can be set to FALSE
tryCatch(x[1L] %in% MO_lookup[1, property, drop = TRUE],
error = function(e) stop(e$message, call. = FALSE))
if (!all(x[!is.na(x)] %in% MO_lookup[, property, drop = TRUE]) | has_Becker_or_Lancefield) {
x <- exec_as.mo(x, property = property, language = language, ...)
}
}
if (property == "mo") {
return(set_clean_class(x, new_class = c("mo", "character")))
} else if (property %in% c("fullname", "genus", "family")) {
# shortname is considered in mo_shortname()
return(set_clean_class(x, new_class = c("taxonomic_name", "character")))
} else if (property == "snomed") {
return(as.double(eval(parse(text = x))))
} else {
@ -762,3 +769,87 @@ find_mo_col <- function(fn) {
stop_("argument `x` is missing and no column with info about microorganisms could be found.", call = -2)
}
}
#' @method print taxonomic_name
#' @export
#' @noRd
print.taxonomic_name <- function(x, ...) {
print(unclass(x), ...)
}
#' @method as.data.frame taxonomic_name
#' @export
#' @noRd
as.data.frame.taxonomic_name <- function(x, ...) {
nm <- deparse1(substitute(x))
if (!"nm" %in% names(list(...))) {
as.data.frame.vector(x, ..., nm = nm)
} else {
as.data.frame.vector(x, ...)
}
}
# will be exported using s3_register() in R/zzz.R
type_sum.taxonomic_name <- function(x, ...) {
"chr"
}
# will be exported using s3_register() in R/zzz.R
pillar_shaft.taxonomic_name <- function(x, ...) {
out <- format(x)
hits <- tolower(x) %in% MO_lookup$fullname_lower | tolower(gsub("[^a-zA-Z ]", "", x)) %in% c(MO_lookup$g_species)
# grey out the kingdom (part until first "_")
out[hits] <- font_italic(x[hits], collapse = NULL)
out[is.na(x)] <- font_na(out[is.na(x)], collapse = NULL)
create_pillar_column(out, align = "left")
}
#' @method [ taxonomic_name
#' @export
#' @noRd
"[.taxonomic_name" <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
}
#' @method [[ taxonomic_name
#' @export
#' @noRd
"[[.taxonomic_name" <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
}
#' @method [<- taxonomic_name
#' @export
#' @noRd
"[<-.taxonomic_name" <- function(i, j, ..., value) {
value <- set_clean_class(value, c("taxonomic_name", "character"))
y <- NextMethod()
attributes(y) <- attributes(i)
y
}
#' @method [[<- taxonomic_name
#' @export
#' @noRd
"[[<-.taxonomic_name" <- function(i, j, ..., value) {
value <- set_clean_class(value, c("taxonomic_name", "character"))
y <- NextMethod()
attributes(y) <- attributes(i)
y
}
#' @method c taxonomic_name
#' @export
#' @noRd
c.taxonomic_name <- function(...) {
set_clean_class(unlist(lapply(list(...), as.character)), c("taxonomic_name", "character"))
}
#' @method unique taxonomic_name
#' @export
#' @noRd
unique.taxonomic_name <- function(x, incomparables = FALSE, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
}

7
R/rsi_calc.R
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@ -27,12 +27,7 @@ dots2vars <- function(...) {
# this function is to give more informative output about
# variable names in count_* and proportion_* functions
dots <- substitute(list(...))
agents <- as.character(dots)[2:length(dots)]
agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'")
agents_names <- ab_name(agents, tolower = TRUE, language = NULL)
need_name <- generalise_antibiotic_name(agents) != agents_names
agents_formatted[need_name] <- paste0(agents_formatted[need_name], " (", agents_names[need_name], ")")
vector_and(agents_formatted, quotes = FALSE)
as.character(dots)[2:length(dots)]
}
rsi_calc <- function(...,

2
R/zzz.R
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@ -48,11 +48,13 @@ if (utf8_supported && !is_latex) {
s3_register("pillar::pillar_shaft", "rsi")
s3_register("pillar::pillar_shaft", "mic")
s3_register("pillar::pillar_shaft", "disk")
s3_register("pillar::pillar_shaft", "taxonomic_name")
s3_register("tibble::type_sum", "ab")
s3_register("tibble::type_sum", "mo")
s3_register("tibble::type_sum", "rsi")
s3_register("tibble::type_sum", "mic")
s3_register("tibble::type_sum", "disk")
s3_register("tibble::type_sum", "taxonomic_name")
# Support for frequency tables from the cleaner package
s3_register("cleaner::freq", "mo")
s3_register("cleaner::freq", "rsi")

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data-raw/rsi.md5
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1a7fe52f8185c9bb2c470712863d1887
7c7f6a0ecfc2e122c4547c0ebed09346

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docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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">1.7.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9010</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -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">1.7.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9010</span>
</span>
</div>

4
docs/articles/datasets.html
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@ -39,7 +39,7 @@
</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">1.7.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9010</span>
</span>
</div>
@ -192,7 +192,7 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 class="date">03 July 2021</h4>
<h4 class="date">04 July 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>
<div class="hidden name"><code>datasets.Rmd</code></div>

2
docs/articles/index.html
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@ -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">1.7.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9010</span>
</span>
</div>

2
docs/authors.html
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@ -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">1.7.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9010</span>
</span>
</div>

2
docs/index.html
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@ -42,7 +42,7 @@
</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">1.7.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9010</span>
</span>
</div>

24
docs/news/index.html
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@ -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">1.7.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9010</span>
</span>
</div>
@ -236,12 +236,12 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1719009" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9009">
<a href="#amr-1719009" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9009</h1>
<div id="last-updated-3-july-2021" class="section level2">
<div id="amr-1719010" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9010">
<a href="#amr-1719010" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9010</h1>
<div id="last-updated-4-july-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-3-july-2021" class="anchor"></a><small>Last updated: 3 July 2021</small>
<a href="#last-updated-4-july-2021" class="anchor"></a><small>Last updated: 4 July 2021</small>
</h2>
<div id="changed" class="section level3">
<h3 class="hasAnchor">
@ -255,7 +255,7 @@
<li>Fix for using selectors multiple times in one call (e.g., using them in <code><a href="https://dplyr.tidyverse.org/reference/filter.html">dplyr::filter()</a></code> and immediately after in <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code>)</li>
</ul>
</li>
<li>Fixed duplicate ATC codes in the <code>antibiotics</code> data set</li>
<li>Fix for duplicate ATC codes in the <code>antibiotics</code> data set</li>
<li>Added <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html">ggplot2::autoplot()</a></code> generic for classes <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code>, <code>&lt;rsi&gt;</code> and <code>&lt;resistance_predict&gt;</code>
</li>
<li>Fix to prevent introducing <code>NA</code>s for old MO codes when running <code><a href="../reference/as.mo.html">as.mo()</a></code> on them</li>
@ -267,7 +267,9 @@
<li>The right input types for <code><a href="../reference/random.html">random_mic()</a></code>, <code><a href="../reference/random.html">random_disk()</a></code> and <code><a href="../reference/random.html">random_rsi()</a></code> are now enforced</li>
<li>
<code><a href="../reference/as.rsi.html">as.rsi()</a></code> can now correct for textual input (such as “Susceptible”, “Resistant”) in Dutch, English, French, German, Italian, Portuguese and Spanish</li>
<li>More informative warnings for all <code>count_*()</code>, <code>proportion_*()</code> functions (and <code>resistant()</code> and <code>susceptible()</code>) when they return NA because of too few test results. The warnings now include the official drug name and if used, the <code>dplyr</code> group name.</li>
<li>When warnings are throws because of too few isolates in any <code>count_*()</code>, <code>proportion_*()</code> function (or <code>resistant()</code> or <code>susceptible()</code>), the <code>dplyr</code> group will be shown, if available</li>
<li>Taxonomic names now print in italic in tibbles, if created with <code><a href="../reference/mo_property.html">mo_name()</a></code>, <code><a href="../reference/mo_property.html">mo_fullname()</a></code>, <code><a href="../reference/mo_property.html">mo_shortname()</a></code>, <code><a href="../reference/mo_property.html">mo_genus()</a></code> or <code><a href="../reference/mo_property.html">mo_family()</a></code>
</li>
</ul>
</div>
</div>
@ -321,7 +323,7 @@
</ul>
</li>
<li>Function <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> as additional antbiotic column selector and function <code><a href="../reference/AMR-deprecated.html">filter_betalactams()</a></code> as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.</li>
<li>A <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
<li>A <code>ggplot()</code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
</li>
</ul>
</div>
@ -422,7 +424,7 @@
<span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
</li>
<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li><p><code>ggplot()</code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li>
<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
@ -479,7 +481,7 @@
<li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
</ul>
</li>
<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-07-03T19:56Z
last_built: 2021-07-04T09:59Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

2
docs/reference/index.html
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@ -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">1.7.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9010</span>
</span>
</div>

2
docs/survey.html
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@ -81,7 +81,7 @@
</button>
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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">1.7.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9010</span>
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