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AMR
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(v1.4.0.9002) bugfix

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v1.8.2
dr. M.S. (Matthijs) Berends 2 years ago
parent 4e9ccb4435
commit ddae8085e1
14 changed files with 50 additions and 50 deletions
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  1. 2
      DESCRIPTION
  2. 2
      NEWS.md
  3. 2
      R/ab.R
  4. 4
      R/mo.R
  5. 66
      R/mo_property.R
  6. 2
      docs/404.html
  7. 2
      docs/LICENSE-text.html
  8. 2
      docs/articles/index.html
  9. 2
      docs/authors.html
  10. 2
      docs/index.html
  11. 8
      docs/news/index.html
  12. 2
      docs/pkgdown.yml
  13. 2
      docs/reference/index.html
  14. 2
      docs/survey.html

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.4.0.9001
Version: 1.4.0.9002
Date: 2020-10-19
Title: Antimicrobial Resistance Analysis
Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.4.0.9001
# AMR 1.4.0.9002
## <small>Last updated: 19 October 2020</small>
### New

2
R/ab.R
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@ -82,7 +82,7 @@
#' ab_name("J01FA01") # "Erythromycin"
#' ab_name("eryt") # "Erythromycin"
as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
meet_criteria(x, allow_class = c("character", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_class = c("character", "numeric", "integer", "factor"), allow_NA = TRUE)
meet_criteria(flag_multiple_results, allow_class = "logical", has_length = 1)
meet_criteria(info, allow_class = "logical", has_length = 1)

4
R/mo.R
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@ -158,7 +158,7 @@ as.mo <- function(x,
ignore_pattern = getOption("AMR_ignore_pattern"),
language = get_locale(),
...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(Becker, allow_class = c("logical", "character"), has_length = 1)
meet_criteria(Lancefield, allow_class = c("logical", "character"), has_length = 1)
meet_criteria(allow_uncertain, allow_class = c("logical", "numeric", "integer"), has_length = 1)
@ -275,7 +275,7 @@ exec_as.mo <- function(x,
actual_uncertainty = 1,
actual_input = NULL,
language = get_locale()) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(Becker, allow_class = c("logical", "character"), has_length = 1)
meet_criteria(Lancefield, allow_class = c("logical", "character"), has_length = 1)
meet_criteria(allow_uncertain, allow_class = c("logical", "numeric", "integer"), has_length = 1)

66
R/mo_property.R
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@ -146,7 +146,7 @@
#' mo_info("E. coli")
#' }
mo_name <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = "fullname", language = language, ...), language = language, only_unknown = FALSE)
@ -159,7 +159,7 @@ mo_fullname <- mo_name
#' @rdname mo_property
#' @export
mo_shortname <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
x.mo <- as.mo(x, language = language, ...)
@ -192,7 +192,7 @@ mo_shortname <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_subspecies <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = "subspecies", language = language, ...), language = language, only_unknown = TRUE)
@ -201,7 +201,7 @@ mo_subspecies <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_species <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = "species", language = language, ...), language = language, only_unknown = TRUE)
@ -210,7 +210,7 @@ mo_species <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_genus <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = "genus", language = language, ...), language = language, only_unknown = TRUE)
@ -219,7 +219,7 @@ mo_genus <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_family <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = "family", language = language, ...), language = language, only_unknown = TRUE)
@ -228,7 +228,7 @@ mo_family <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_order <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = "order", language = language, ...), language = language, only_unknown = TRUE)
@ -237,7 +237,7 @@ mo_order <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_class <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = "class", language = language, ...), language = language, only_unknown = TRUE)
@ -246,7 +246,7 @@ mo_class <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_phylum <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = "phylum", language = language, ...), language = language, only_unknown = TRUE)
@ -255,7 +255,7 @@ mo_phylum <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_kingdom <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = "kingdom", language = language, ...), language = language, only_unknown = TRUE)
@ -268,7 +268,7 @@ mo_domain <- mo_kingdom
#' @rdname mo_property
#' @export
mo_type <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = "kingdom", language = language, ...), language = language, only_unknown = FALSE)
@ -277,7 +277,7 @@ mo_type <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_gramstain <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
x.mo <- as.mo(x, language = language, ...)
@ -311,7 +311,7 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
is_gram_negative <- function(x, ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
grams <- mo_gramstain(x, language = NULL, ...)
"Gram-negative" == grams & !is.na(grams)
}
@ -319,7 +319,7 @@ is_gram_negative <- function(x, ...) {
#' @rdname mo_property
#' @export
is_gram_positive <- function(x, ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
grams <- mo_gramstain(x, language = NULL, ...)
"Gram-positive" == grams & !is.na(grams)
}
@ -327,7 +327,7 @@ is_gram_positive <- function(x, ...) {
#' @rdname mo_property
#' @export
mo_snomed <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
mo_validate(x = x, property = "snomed", language = language, ...)
@ -336,7 +336,7 @@ mo_snomed <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_ref <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
mo_validate(x = x, property = "ref", language = language, ...)
@ -345,7 +345,7 @@ mo_ref <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_authors <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
x <- mo_validate(x = x, property = "ref", language = language, ...)
@ -357,7 +357,7 @@ mo_authors <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_year <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
x <- mo_validate(x = x, property = "ref", language = language, ...)
@ -369,7 +369,7 @@ mo_year <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_rank <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
mo_validate(x = x, property = "rank", language = language, ...)
@ -378,20 +378,20 @@ mo_rank <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_taxonomy <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
x <- as.mo(x, language = language, ...)
metadata <- get_mo_failures_uncertainties_renamed()
result <- list(kingdom = mo_kingdom(x, language = language),
phylum = mo_phylum(x, language = language),
class = mo_class(x, language = language),
order = mo_order(x, language = language),
family = mo_family(x, language = language),
genus = mo_genus(x, language = language),
species = mo_species(x, language = language),
subspecies = mo_subspecies(x, language = language))
phylum = mo_phylum(x, language = language),
class = mo_class(x, language = language),
order = mo_order(x, language = language),
family = mo_family(x, language = language),
genus = mo_genus(x, language = language),
species = mo_species(x, language = language),
subspecies = mo_subspecies(x, language = language))
load_mo_failures_uncertainties_renamed(metadata)
result
@ -400,7 +400,7 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_synonyms <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
x <- as.mo(x, language = language, ...)
@ -429,7 +429,7 @@ mo_synonyms <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_info <- function(x, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
x <- as.mo(x, language = language, ...)
@ -455,7 +455,7 @@ mo_info <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(open, allow_class = "logical", has_length = 1)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -464,7 +464,7 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
metadata <- get_mo_failures_uncertainties_renamed()
df <- data.frame(mo, stringsAsFactors = FALSE) %pm>%
pm_left_join(pm_select(microorganisms, mo, source, species_id), by = "mo")
pm_left_join(pm_select(microorganisms, mo, source, species_id), by = "mo")
df$url <- ifelse(df$source == "CoL",
paste0(catalogue_of_life$url_CoL, "details/species/id/", df$species_id, "/"),
ifelse(df$source == "DSMZ",
@ -488,10 +488,10 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_property <- function(x, property = "fullname", language = get_locale(), ...) {
meet_criteria(x, allow_class = c("character", "data.frame", "list", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(x, allow_NA = TRUE)
meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(microorganisms))
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
translate_AMR(mo_validate(x = x, property = property, language = language, ...), language = language, only_unknown = TRUE)
}

2
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">1.4.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</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">1.4.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</span>
</span>
</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">1.4.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</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">1.4.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</span>
</span>
</div>

2
docs/index.html
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@ -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">1.4.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</span>
</span>
</div>

8
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">1.4.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</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-1409001" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9001">
<a href="#amr-1409001" class="anchor"></a>AMR 1.4.0.9001<small> Unreleased </small>
<div id="amr-1409002" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9002">
<a href="#amr-1409002" class="anchor"></a>AMR 1.4.0.9002<small> Unreleased </small>
</h1>
<div id="last-updated-19-october-2020" class="section level2">
<h2 class="hasAnchor">

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: 2020-10-19T15:08Z
last_built: 2020-10-19T18:44Z
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">1.4.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</span>
</span>
</div>

2
docs/survey.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">1.4.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9002</span>
</span>
</div>

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