P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2024-12-25 07:26:12 +01:00
Code Releases Activity

(v1.4.0.9021) more robust class setting

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends 2020-11-16 16:57:55 +01:00
parent 05fb213a7c
commit deefce9520
29 changed files with 98 additions and 85 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
.github/workflows/check.yaml vendored
View File

@ -64,8 +64,7 @@ jobs:
- {os: ubuntu-16.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.4', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.3', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
# older R versions cannot be tested, since tidyverse only supports last 4 R x.x versions
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}

2
DESCRIPTION
View File

@ -1,5 +1,5 @@
Package: AMR
Version: 1.4.0.9020
Version: 1.4.0.9021
Date: 2020-11-16
Title: Antimicrobial Resistance Analysis
Authors@R: c(

2
NEWS.md
View File

@ -1,4 +1,4 @@
# AMR 1.4.0.9020
# AMR 1.4.0.9021
## <small>Last updated: 16 November 2020</small>
### New

17
R/aa_helper_functions.R
View File

@ -670,7 +670,7 @@ progress_ticker <- function(n = 1, n_min = 0, ...) {
pb$kill <- function() {
invisible()
}
structure(pb, class = "txtProgressBar")
set_clean_class(pb, new_class = "txtProgressBar")
} else if (n >= n_min) {
pb <- utils::txtProgressBar(max = n, style = 3)
pb$tick <- function() {
@ -680,6 +680,21 @@ progress_ticker <- function(n = 1, n_min = 0, ...) {
}
}
set_clean_class <- function(x, new_class) {
if (is.null(x)) {
x <- NA_character_
}
if (is.factor(x)) {
lvls <- levels(x)
attributes(x) <- NULL
levels(x) <- lvls
} else {
attributes(x) <- NULL
}
class(x) <- new_class
x
}
create_pillar_column <- function(x, ...) {
new_pillar_shaft_simple <- import_fn("new_pillar_shaft_simple", "pillar", error_on_fail = FALSE)
if (!is.null(new_pillar_shaft_simple)) {

8
R/ab.R
View File

@ -97,8 +97,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
if (all(toupper(x) %in% antibiotics$ab)) {
# valid AB code, but not yet right class
return(structure(.Data = toupper(x),
class = c("ab", "character")))
return(set_clean_class(toupper(x),
new_class = c("ab", "character")))
}
x_bak <- x
@ -455,8 +455,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
x_result <- NA_character_
}
structure(.Data = x_result,
class = c("ab", "character"))
set_clean_class(x_result,
new_class = c("ab", "character"))
}
#' @rdname as.ab

2
R/ab_property.R
View File

@ -263,7 +263,7 @@ ab_validate <- function(x, property, ...) {
pm_pull(property)
}
if (property == "ab") {
return(structure(x, class = property))
return(set_clean_class(x, new_class = c("ab", "character")))
} else if (property == "cid") {
return(as.integer(x))
} else if (property %like% "ddd") {

15
R/age.R
View File

@ -139,13 +139,14 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
#'
#' \donttest{
#' # resistance of ciprofloxacin per age group
#' library(dplyr)
#' example_isolates %>%
#' filter_first_isolate() %>%
#' filter(mo == as.mo("E. coli")) %>%
#' group_by(age_group = age_groups(age)) %>%
#' select(age_group, CIP) %>%
#' ggplot_rsi(x = "age_group", minimum = 0)
#' if (require("dplyr")) {
#' example_isolates %>%
#' filter_first_isolate() %>%
#' filter(mo == as.mo("E. coli")) %>%
#' group_by(age_group = age_groups(age)) %>%
#' select(age_group, CIP) %>%
#' ggplot_rsi(x = "age_group", minimum = 0)
#' }
#' }
age_groups <- function(x, split_at = c(12, 25, 55, 75), na.rm = FALSE) {
meet_criteria(x, allow_class = c("numeric", "integer"))

6
R/bug_drug_combinations.R
View File

@ -106,7 +106,8 @@ bug_drug_combinations <- function(x,
out <- rbind(out, out_group, stringsAsFactors = FALSE)
}
structure(.Data = out, class = c("bug_drug_combinations", x_class))
set_clean_class(out,
new_class = c("bug_drug_combinations", x_class))
}
#' @method format bug_drug_combinations
@ -245,7 +246,8 @@ format.bug_drug_combinations <- function(x,
#' @export
print.bug_drug_combinations <- function(x, ...) {
x_class <- class(x)
print(structure(x, class = x_class[x_class != "bug_drug_combinations"]),
print(set_clean_class(x,
new_class = x_class[x_class != "bug_drug_combinations"]),
...)
message_("Use 'format()' on this result to get a publishable/printable format.", as_note = FALSE)
}

4
R/catalogue_of_life.R
View File

@ -107,8 +107,8 @@ catalogue_of_life_version <- function() {
n_total_species = nrow(microorganisms),
n_total_synonyms = nrow(microorganisms.old)))
structure(.Data = lst,
class = c("catalogue_of_life_version", "list"))
set_clean_class(lst,
new_class = c("catalogue_of_life_version", "list"))
}
#' @method print catalogue_of_life_version

5
R/disk.R
View File

@ -39,7 +39,6 @@
#' @examples
#' \donttest{
#' # transform existing disk zones to the `disk` class
#' library(dplyr)
#' df <- data.frame(microorganism = "E. coli",
#' AMP = 20,
#' CIP = 14,
@ -107,8 +106,8 @@ as.disk <- function(x, na.rm = FALSE) {
list_missing, call = FALSE)
}
}
structure(as.integer(x),
class = c("disk", "integer"))
set_clean_class(as.integer(x),
new_class = c("disk", "integer"))
}
all_valid_disks <- function(x) {

4
R/mic.R
View File

@ -131,8 +131,8 @@ as.mic <- function(x, na.rm = FALSE) {
list_missing, call = FALSE)
}
structure(.Data = factor(x, levels = lvls, ordered = TRUE),
class = c("mic", "ordered", "factor"))
set_clean_class(factor(x, levels = lvls, ordered = TRUE),
new_class = c("mic", "ordered", "factor"))
}
}

25
R/mo.R
View File

@ -175,7 +175,7 @@ as.mo <- function(x,
& isFALSE(Lancefield), error = function(e) FALSE)) {
# don't look into valid MO codes, just return them
# is.mo() won't work - MO codes might change between package versions
return(to_class_mo(x))
return(set_clean_class(x, new_class = c("mo", "character")))
}
if (tryCatch(all(x == "" | gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE) %in% MO_lookup$fullname_lower, na.rm = TRUE)
@ -228,12 +228,8 @@ as.mo <- function(x,
...)
}
to_class_mo(y)
}
to_class_mo <- function(x) {
structure(.Data = x,
class = c("mo", "character"))
set_clean_class(y,
new_class = c("mo", "character"))
}
#' @rdname as.mo
@ -399,7 +395,8 @@ exec_as.mo <- function(x,
# all empty
if (all(identical(trimws(x_input), "") | is.na(x_input) | length(x) == 0)) {
if (property == "mo") {
return(to_class_mo(rep(NA_character_, length(x_input))))
return(set_clean_class(rep(NA_character_, length(x_input)),
new_class = c("mo", "character")))
} else {
return(rep(NA_character_, length(x_input)))
}
@ -1499,7 +1496,7 @@ exec_as.mo <- function(x,
x <- df_found$found[match(df_input$input, df_found$input)]
if (property == "mo") {
x <- to_class_mo(x)
x <- set_clean_class(x, new_class = c("mo", "character"))
}
if (length(mo_renamed()) > 0) {
@ -1740,8 +1737,9 @@ mo_uncertainties <- function() {
if (is.null(getOption("mo_uncertainties"))) {
return(NULL)
}
structure(.Data = as.data.frame(getOption("mo_uncertainties"), stringsAsFactors = FALSE),
class = c("mo_uncertainties", "data.frame"))
set_clean_class(as.data.frame(getOption("mo_uncertainties"),
stringsAsFactors = FALSE),
new_class = c("mo_uncertainties", "data.frame"))
}
#' @method print mo_uncertainties
@ -1814,8 +1812,9 @@ mo_renamed <- function() {
} else {
items <- pm_distinct(items, old_name, .keep_all = TRUE)
}
structure(.Data = items,
class = c("mo_renamed", "data.frame"))
set_clean_class(as.data.frame(items,
stringsAsFactors = FALSE),
new_class = c("mo_renamed", "data.frame"))
}
#' @method print mo_renamed

24
R/rsi.R
View File

@ -223,17 +223,15 @@ is.rsi.eligible <- function(x, threshold = 0.05) {
#' @export
as.rsi.default <- function(x, ...) {
if (is.rsi(x)) {
x
} else if (all(is.na(x)) || identical(levels(x), c("S", "I", "R"))) {
structure(.Data = factor(x, levels = c("S", "I", "R"), ordered = TRUE),
class = c("rsi", "ordered", "factor"))
} else if (inherits(x, "integer") & all(x %in% c(1:3, NA))) {
return(x)
}
if (inherits(x, "integer") & all(x %in% c(1:3, NA))) {
x[x == 1] <- "S"
x[x == 2] <- "I"
x[x == 3] <- "R"
structure(.Data = factor(x, levels = c("S", "I", "R"), ordered = TRUE),
class = c("rsi", "ordered", "factor"))
} else {
} else if (!all(is.na(x)) && !identical(levels(x), c("S", "I", "R"))) {
if (!any(x %like% "(R|S|I)", na.rm = TRUE)) {
# check if they are actually MICs or disks now that the antibiotic name is valid
@ -280,10 +278,10 @@ as.rsi.default <- function(x, ...) {
list_missing, call = FALSE)
}
}
structure(.Data = factor(x, levels = c("S", "I", "R"), ordered = TRUE),
class = c("rsi", "ordered", "factor"))
}
set_clean_class(factor(x, levels = c("S", "I", "R"), ordered = TRUE),
new_class = c("rsi", "ordered", "factor"))
}
#' @rdname as.rsi
@ -804,8 +802,8 @@ exec_as.rsi <- function(method,
load_mo_failures_uncertainties_renamed(metadata_mo)
structure(.Data = factor(new_rsi, levels = c("S", "I", "R"), ordered = TRUE),
class = c("rsi", "ordered", "factor"))
set_clean_class(factor(new_rsi, levels = c("S", "I", "R"), ordered = TRUE),
new_class = c("rsi", "ordered", "factor"))
}
# will be exported using s3_register() in R/zzz.R

2
docs/404.html
View File

@ -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">1.4.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9021</span>
</span>
</div>

2
docs/LICENSE-text.html
View File

@ -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">1.4.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9021</span>
</span>
</div>

2
docs/articles/index.html
View File

@ -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">1.4.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9021</span>
</span>
</div>

2
docs/authors.html
View File

@ -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">1.4.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9021</span>
</span>
</div>

2
docs/index.html
View File

@ -43,7 +43,7 @@
</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">1.4.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9021</span>
</span>
</div>

8
docs/news/index.html
View File

@ -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">1.4.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9021</span>
</span>
</div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1409020" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9020">
<a href="#amr-1409020" class="anchor"></a>AMR 1.4.0.9020<small> Unreleased </small>
<div id="amr-1409021" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9021">
<a href="#amr-1409021" class="anchor"></a>AMR 1.4.0.9021<small> Unreleased </small>
</h1>
<div id="last-updated-16-november-2020" class="section level2">
<h2 class="hasAnchor">

2
docs/pkgdown.yml
View File

@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2020-11-16T09:57Z
last_built: 2020-11-16T15:57Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

17
docs/reference/age_groups.html
View File

@ -82,7 +82,7 @@
</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">1.4.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9021</span>
</span>
</div>
@ -316,13 +316,14 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># \donttest{</span>
<span class='co'># resistance of ciprofloxacin per age group</span>
<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://dplyr.tidyverse.org'>dplyr</a></span><span class='op'>)</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span>age_group <span class='op'>=</span> <span class='fu'>age_groups</span><span class='op'>(</span><span class='va'>age</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>age_group</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span><span class='op'>(</span>x <span class='op'>=</span> <span class='st'>"age_group"</span>, minimum <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span>age_group <span class='op'>=</span> <span class='fu'>age_groups</span><span class='op'>(</span><span class='va'>age</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>age_group</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span><span class='op'>(</span>x <span class='op'>=</span> <span class='st'>"age_group"</span>, minimum <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</div>

2
docs/reference/antibiotic_class_selectors.html
View File

@ -82,7 +82,7 @@
</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">1.4.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9021</span>
</span>
</div>

3
docs/reference/as.disk.html
View File

@ -82,7 +82,7 @@
</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">1.4.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9021</span>
</span>
</div>
@ -284,7 +284,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># \donttest{</span>
<span class='co'># transform existing disk zones to the `disk` class</span>
<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://dplyr.tidyverse.org'>dplyr</a></span><span class='op'>)</span>
<span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>microorganism <span class='op'>=</span> <span class='st'>"E. coli"</span>,
AMP <span class='op'>=</span> <span class='fl'>20</span>,
CIP <span class='op'>=</span> <span class='fl'>14</span>,

2
docs/reference/as.mo.html
View File

@ -82,7 +82,7 @@
</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">1.4.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9021</span>
</span>
</div>

2
docs/reference/index.html
View File

@ -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">1.4.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9021</span>
</span>
</div>

2
docs/reference/mo_property.html
View File

@ -82,7 +82,7 @@
</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">1.4.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9021</span>
</span>
</div>

2
docs/survey.html
View File

@ -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">1.4.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9021</span>
</span>
</div>

15
man/age_groups.Rd
View File

@ -69,13 +69,14 @@ age_groups(ages, "children")
\donttest{
# resistance of ciprofloxacin per age group
library(dplyr)
example_isolates \%>\%
filter_first_isolate() \%>\%
filter(mo == as.mo("E. coli")) \%>\%
group_by(age_group = age_groups(age)) \%>\%
select(age_group, CIP) \%>\%
ggplot_rsi(x = "age_group", minimum = 0)
if (require("dplyr")) {
example_isolates \%>\%
filter_first_isolate() \%>\%
filter(mo == as.mo("E. coli")) \%>\%
group_by(age_group = age_groups(age)) \%>\%
select(age_group, CIP) \%>\%
ggplot_rsi(x = "age_group", minimum = 0)
}
}
}
\seealso{

1
man/as.disk.Rd
View File

@ -40,7 +40,6 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
\examples{
\donttest{
# transform existing disk zones to the `disk` class
library(dplyr)
df <- data.frame(microorganism = "E. coli",
AMP = 20,
CIP = 14,