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(v0.8.0.9032) fix regex error

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dr. M.S. (Matthijs) Berends 2019-11-15 16:50:46 +01:00
parent 09e2730b53
commit 67f3f4387b
11 changed files with 49 additions and 43 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 0.8.0.9031 Version: 0.8.0.9032
Date: 2019-11-15 Date: 2019-11-15
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

4
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.8.0.9031 # AMR 0.8.0.9032
<small>Last updated: 15-Nov-2019</small> <small>Last updated: 15-Nov-2019</small>
### Breaking ### Breaking
@ -35,7 +35,7 @@
as.mo(c("Stafylococcus aureus", as.mo(c("Stafylococcus aureus",
"staphylokok aureuz")) "staphylokok aureuz"))
#> Warning: #> Warning:
#> Results of two values was guessed with uncertainty. Use mo_uncertainties() to review them. #> Results of two values were guessed with uncertainty. Use mo_uncertainties() to review them.
#> Class 'mo' #> Class 'mo'
#> [1] B_STPHY_AURS B_STPHY_AURS #> [1] B_STPHY_AURS B_STPHY_AURS

34
R/mo.R
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@ -545,7 +545,7 @@ exec_as.mo <- function(x,
x <- gsub("o+", "o+", x) x <- gsub("o+", "o+", x)
x <- gsub("(.)\\1+", "\\1+", x) x <- gsub("(.)\\1+", "\\1+", x)
# allow multiplication of all other consonants # allow multiplication of all other consonants
x <- gsub("([bdghjlnrw]+)", "\\1+", x) x <- gsub("([bdgjlnrw]+)", "\\1+", x)
# allow ending in -en or -us # allow ending in -en or -us
x <- gsub("e\\+n(?![a-z[])", "(e+n|u+(c|k|q|qu|s|z|x|ks)+)", x, perl = TRUE) x <- gsub("e\\+n(?![a-z[])", "(e+n|u+(c|k|q|qu|s|z|x|ks)+)", x, perl = TRUE)
# if the input is longer than 10 characters, allow any forgotten consonant between all characters, as some might just have forgotten one... # if the input is longer than 10 characters, allow any forgotten consonant between all characters, as some might just have forgotten one...
@ -555,10 +555,11 @@ exec_as.mo <- function(x,
# allow au and ou after all these regex implementations # allow au and ou after all these regex implementations
x <- gsub("a+[bcdfghjklmnpqrstvwxyz]?u+[bcdfghjklmnpqrstvwxyz]?", "(a+u+|o+u+)[bcdfghjklmnpqrstvwxyz]?", x, fixed = TRUE) x <- gsub("a+[bcdfghjklmnpqrstvwxyz]?u+[bcdfghjklmnpqrstvwxyz]?", "(a+u+|o+u+)[bcdfghjklmnpqrstvwxyz]?", x, fixed = TRUE)
x <- gsub("o+[bcdfghjklmnpqrstvwxyz]?u+[bcdfghjklmnpqrstvwxyz]?", "(a+u+|o+u+)[bcdfghjklmnpqrstvwxyz]?", x, fixed = TRUE) x <- gsub("o+[bcdfghjklmnpqrstvwxyz]?u+[bcdfghjklmnpqrstvwxyz]?", "(a+u+|o+u+)[bcdfghjklmnpqrstvwxyz]?", x, fixed = TRUE)
# make sure to remove regex overkill (will lead to errors)
x <- gsub("++", "+", x, fixed = TRUE)
} }
x <- strip_whitespace(x, dyslexia_mode) x <- strip_whitespace(x, dyslexia_mode)
# make sure to remove regex overkill (will lead to errors)
x <- gsub("++", "+", x, fixed = TRUE)
x <- gsub("?+", "?", x, fixed = TRUE)
x_trimmed <- x x_trimmed <- x
x_trimmed_species <- paste(x_trimmed, "species") x_trimmed_species <- paste(x_trimmed, "species")
@ -571,21 +572,22 @@ exec_as.mo <- function(x,
# add start en stop regex # add start en stop regex
x <- paste0("^", x, "$") x <- paste0("^", x, "$")
x_withspaces_start_only <- paste0("^", x_withspaces) x_withspaces_start_only <- paste0("^", x_withspaces)
x_withspaces_end_only <- paste0(x_withspaces, "$") x_withspaces_end_only <- paste0(x_withspaces, "$")
x_withspaces_start_end <- paste0("^", x_withspaces, "$") x_withspaces_start_end <- paste0("^", x_withspaces, "$")
if (isTRUE(debug)) { if (isTRUE(debug)) {
cat(paste0('x "', x, '"\n')) cat(paste0(blue('x'), ' "', x, '"\n'))
cat(paste0('x_species "', x_species, '"\n')) cat(paste0(blue('x_species'), ' "', x_species, '"\n'))
cat(paste0('x_withspaces_start_only "', x_withspaces_start_only, '"\n')) cat(paste0(blue('x_withspaces_start_only'), ' "', x_withspaces_start_only, '"\n'))
cat(paste0('x_withspaces_end_only "', x_withspaces_end_only, '"\n')) cat(paste0(blue('x_withspaces_end_only'), ' "', x_withspaces_end_only, '"\n'))
cat(paste0('x_withspaces_start_end "', x_withspaces_start_end, '"\n')) cat(paste0(blue('x_withspaces_start_end'), ' "', x_withspaces_start_end, '"\n'))
cat(paste0('x_backup "', x_backup, '"\n')) cat(paste0(blue('x_backup'), ' "', x_backup, '"\n'))
cat(paste0('x_backup_without_spp "', x_backup_without_spp, '"\n')) cat(paste0(blue('x_backup_without_spp'), ' "', x_backup_without_spp, '"\n'))
cat(paste0('x_trimmed "', x_trimmed, '"\n')) cat(paste0(blue('x_trimmed'), ' "', x_trimmed, '"\n'))
cat(paste0('x_trimmed_species "', x_trimmed_species, '"\n')) cat(paste0(blue('x_trimmed_species'), ' "', x_trimmed_species, '"\n'))
cat(paste0('x_trimmed_without_group "', x_trimmed_without_group, '"\n')) cat(paste0(blue('x_trimmed_without_group'), ' "', x_trimmed_without_group, '"\n'))
} }
progress <- progress_estimated(n = length(x), min_time = 3) progress <- progress_estimated(n = length(x), min_time = 3)
@ -1590,12 +1592,12 @@ exec_as.mo <- function(x,
if (NROW(uncertainties) > 0 & initial_search == TRUE) { if (NROW(uncertainties) > 0 & initial_search == TRUE) {
options(mo_uncertainties = as.list(distinct(uncertainties, input, .keep_all = TRUE))) options(mo_uncertainties = as.list(distinct(uncertainties, input, .keep_all = TRUE)))
plural <- c("", "it") plural <- c("", "it", "was")
if (NROW(uncertainties) > 1) { if (NROW(uncertainties) > 1) {
plural <- c("s", "them") plural <- c("s", "them", "were")
} }
msg <- paste0("\nResult", plural[1], " of ", nr2char(NROW(uncertainties)), " value", plural[1], msg <- paste0("\nResult", plural[1], " of ", nr2char(NROW(uncertainties)), " value", plural[1],
" was guessed with uncertainty. Use mo_uncertainties() to review ", plural[2], ".") " ", plural[3], " guessed with uncertainty. Use mo_uncertainties() to review ", plural[2], ".")
warning(red(msg), warning(red(msg),
call. = FALSE, call. = FALSE,
immediate. = TRUE) # thus will always be shown, even if >= warnings immediate. = TRUE) # thus will always be shown, even if >= warnings

30
R/zzz.R
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@ -49,23 +49,27 @@
#' @importFrom data.table as.data.table setkey #' @importFrom data.table as.data.table setkey
#' @importFrom dplyr %>% mutate case_when #' @importFrom dplyr %>% mutate case_when
make_DT <- function() { make_DT <- function() {
microorganismsDT <- as.data.table(AMR::microorganisms %>% microorganismsDT <- AMR::microorganisms %>%
mutate(kingdom_index = case_when(kingdom == "Bacteria" ~ 1, mutate(kingdom_index = case_when(kingdom == "Bacteria" ~ 1,
kingdom == "Fungi" ~ 2, kingdom == "Fungi" ~ 2,
kingdom == "Protozoa" ~ 3, kingdom == "Protozoa" ~ 3,
kingdom == "Archaea" ~ 4, kingdom == "Archaea" ~ 4,
TRUE ~ 99), TRUE ~ 99),
# for fullname_lower: keep only dots, letters, # for fullname_lower: keep only dots, letters,
# numbers, slashes, spaces and dashes # numbers, slashes, spaces and dashes
fullname_lower = gsub("[^.a-z0-9/ \\-]+", "", fullname_lower = gsub("[^.a-z0-9/ \\-]+", "",
# use this paste instead of `fullname` to # use this paste instead of `fullname` to
# work with Viridans Group Streptococci, etc. # work with Viridans Group Streptococci, etc.
tolower(trimws(paste(genus, species, subspecies)))))) tolower(trimws(ifelse(genus == "",
fullname,
paste(genus, species, subspecies)))))) %>%
as.data.table()
# so arrange data on prevalence first, then kingdom, then full name # so arrange data on prevalence first, then kingdom, then full name
setkey(microorganismsDT, setkey(microorganismsDT,
prevalence, prevalence,
kingdom_index, kingdom_index,
fullname) fullname_lower)
microorganismsDT microorganismsDT
} }

2
docs/404.html
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@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9031</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -84,7 +84,7 @@
</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">0.8.0.9031</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -84,7 +84,7 @@
</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">0.8.0.9031</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -84,7 +84,7 @@
</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">0.8.0.9031</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -45,7 +45,7 @@
</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">0.8.0.9031</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
</span> </span>
</div> </div>

10
docs/news/index.html
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@ -84,7 +84,7 @@
</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">0.8.0.9031</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
</span> </span>
</div> </div>
@ -231,9 +231,9 @@
</div> </div>
<div id="amr-0-8-0-9031" class="section level1"> <div id="amr-0-8-0-9032" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-8-0-9031" class="anchor"></a>AMR 0.8.0.9031<small> Unreleased </small> <a href="#amr-0-8-0-9032" class="anchor"></a>AMR 0.8.0.9032<small> Unreleased </small>
</h1> </h1>
<p><small>Last updated: 15-Nov-2019</small></p> <p><small>Last updated: 15-Nov-2019</small></p>
<div id="breaking" class="section level3"> <div id="breaking" class="section level3">
@ -286,7 +286,7 @@
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Stafylococcus aureus"</span>,</a> <div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Stafylococcus aureus"</span>,</a>
<a class="sourceLine" id="cb4-2" data-line-number="2"> <span class="st">"staphylokok aureuz"</span>))</a> <a class="sourceLine" id="cb4-2" data-line-number="2"> <span class="st">"staphylokok aureuz"</span>))</a>
<a class="sourceLine" id="cb4-3" data-line-number="3"><span class="co">#&gt; Warning: </span></a> <a class="sourceLine" id="cb4-3" data-line-number="3"><span class="co">#&gt; Warning: </span></a>
<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="co">#&gt; Results of two values was guessed with uncertainty. Use mo_uncertainties() to review them.</span></a> <a class="sourceLine" id="cb4-4" data-line-number="4"><span class="co">#&gt; Results of two values were guessed with uncertainty. Use mo_uncertainties() to review them.</span></a>
<a class="sourceLine" id="cb4-5" data-line-number="5"><span class="co">#&gt; Class 'mo'</span></a> <a class="sourceLine" id="cb4-5" data-line-number="5"><span class="co">#&gt; Class 'mo'</span></a>
<a class="sourceLine" id="cb4-6" data-line-number="6"><span class="co">#&gt; [1] B_STPHY_AURS B_STPHY_AURS</span></a> <a class="sourceLine" id="cb4-6" data-line-number="6"><span class="co">#&gt; [1] B_STPHY_AURS B_STPHY_AURS</span></a>
<a class="sourceLine" id="cb4-7" data-line-number="7"></a> <a class="sourceLine" id="cb4-7" data-line-number="7"></a>
@ -1385,7 +1385,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-8-0-9031">0.8.0.9031</a></li> <li><a href="#amr-0-8-0-9032">0.8.0.9032</a></li>
<li><a href="#amr-0-8-0">0.8.0</a></li> <li><a href="#amr-0-8-0">0.8.0</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li> <li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li> <li><a href="#amr-0-7-0">0.7.0</a></li>

2
docs/reference/index.html
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@ -84,7 +84,7 @@
</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">0.8.0.9031</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
</span> </span>
</div> </div>