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set_mo_source
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitab.io/AMR. #
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# ==================================================================== #
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#' Use predefined reference data set
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#'
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#' These functions can be used to predefine your own reference to be used in \code{\link{as.mo}} and consequently all \code{mo_*} functions like \code{\link{mo_genus}} and \code{\link{mo_gramstain}}.
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#' @param path location of your reference file, see Details
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#' @rdname mo_source
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#' @name mo_source
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#' @aliases set_mo_source get_mo_source
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#' @details The reference file can be a text file seperated with commas (CSV) or pipes, an Excel file (old 'xls' format or new 'xlsx' format) or an R object file (extension '.rds'). To use an Excel file, you need to have the \code{readxl} package installed.
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#'
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#' \code{set_mo_source} will check the file for validity: it must be a \code{data.frame}, must have a column named \code{"mo"} which contains values from \code{microorganisms$mo} and must have a reference column with your own defined values. If all tests pass, \code{set_mo_source} will read the file into R and export it to \code{"~/.mo_source.rds"}. This compressed data file will then be used at default for MO determination (function \code{\link{as.mo}} and consequently all \code{mo_*} functions like \code{\link{mo_genus}} and \code{\link{mo_gramstain}}). The location of the original file will be saved as option with \code{\link{options}(mo_source = path)}. Its timestamp will be saved with \code{\link{options}(mo_source_datetime = ...)}.
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#'
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#' \code{get_mo_source} will return the data set by reading \code{"~/.mo_source.rds"} with \code{\link{readRDS}}. If the original file has changed (the file defined with \code{path}), it will call \code{set_mo_source} to update the data file automatically.
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#'
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#' Reading an Excel file (\code{.xlsx}) with only one row has a size of 8-9 kB. The compressed file will have a size of 0.1 kB and can be read by \code{get_mo_source} in only a couple of microseconds (a millionth of a second).
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#' @importFrom dplyr select everything
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#' @export
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' \dontrun{
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#'
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#' # imagine this Excel file (mo codes looked up in `microorganisms` data set):
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#' # A B
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#' # 1 our code mo
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#' # 2 lab_mo_ecoli B_ESCHR_COL
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#' # 3 lab_mo_kpneumoniae B_KLBSL_PNE
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#'
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#' # 1. We save it as 'home/me/ourcodes.xlsx'
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#'
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#' # 2. We use it for input:
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#' set_mo_source("C:\path\ourcodes.xlsx")
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#' #> Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
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#'
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#' # 3. And use it in our functions:
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#' as.mo("lab_mo_ecoli")
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#' #> B_ESCHR_COL
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#'
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#' mo_genus("lab_mo_kpneumoniae")
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#' #> "Klebsiella"
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#'
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#' # 4. It will look for changes itself:
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#' # (add new row to the Excel file and save it)
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#'
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#' mo_genus("lab_mo_kpneumoniae")
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#' #> Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
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#' #> "Klebsiella"
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#' }
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set_mo_source <- function(path) {
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if (!is.character(path) | length(path) > 1) {
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stop("`path` must be a character of length 1.")
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}
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if (path == "") {
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options(mo_source = NULL)
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options(mo_source_timestamp = NULL)
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if (file.exists("~/.mo_source.rds")) {
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unlink("~/.mo_source.rds")
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message("Removed mo_source file '~/.mo_source.rds'.")
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}
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return(invisible())
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}
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if (!file.exists(path)) {
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stop("File not found: ", path)
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}
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is_valid <- function(df) {
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valid <- TRUE
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if (!is.data.frame(df)) {
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valid <- FALSE
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} else if (!"mo" %in% colnames(df)) {
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valid <- FALSE
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} else if (!all(df$mo %in% AMR::microorganisms$mo)) {
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valid <- FALSE
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} else if (NCOL(df) < 2) {
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valid <- FALSE
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}
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valid
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}
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if (path %like% '[.]rds$') {
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df <- readRDS(path)
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} else if (path %like% '[.]xlsx?$') {
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# is Excel file (old or new)
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if (!"readxl" %in% utils::installed.packages()) {
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stop("Install the 'readxl' package first.")
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}
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if (path %like% '[.]xlsx$') {
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df <- readxl::read_xlsx(path)
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} else {
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df <- readxl::read_xls(path)
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}
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} else {
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# try comma first
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try(
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df <- utils::read.table(header = TRUE, sep = ",", stringsAsFactors = FALSE),
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silent = TRUE)
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if (!is_valid(df)) {
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# try pipe
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try(
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df <- utils::read.table(header = TRUE, sep = "|", stringsAsFactors = FALSE),
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silent = TRUE)
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}
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}
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if (!is_valid(df)) {
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stop("File must contain a column with self-defined values and a reference column `mo` with valid values from the `microorganisms` data set.")
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}
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if (colnames(df)[1] == "mo") {
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# put mo to the end
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df <- df %>% select(-"mo", everything(), "mo")
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}
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df <- as.data.frame(df, stringAsFactors = FALSE)
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# success
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if (file.exists("~/.mo_source.rds")) {
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action <- "Updated"
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} else {
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action <- "Created"
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}
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saveRDS(df, "~/.mo_source.rds")
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options(mo_source = path)
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options(mo_source_timestamp = as.character(file.info(path)$mtime))
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message(action, " mo_source file '~/.mo_source.rds' from '", path, "'.")
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}
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#' @rdname mo_source
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#' @export
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get_mo_source <- function() {
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if (is.null(getOption("mo_source", NULL))) {
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return(NULL)
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} else {
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old_time <- as.POSIXct(getOption("mo_source_timestamp"))
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new_time <- as.POSIXct(as.character(file.info(getOption("mo_source", ""))$mtime))
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if (is.na(new_time)) {
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# source file was deleted, remove reference too
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set_mo_source("")
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return(NULL)
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}
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if (new_time != old_time) {
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# set updated source
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set_mo_source(getOption("mo_source"))
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}
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}
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readRDS("~/.mo_source.rds")
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}
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<h1>Translation table for microorganism codes</h1>
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<div class="hidden name"><code>microorganisms.codes.Rd</code></div>
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<div class="ref-description">
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<p>A data set containing commonly used codes for microorganisms. Define your own with <code><a href='mo_source.html'>set_mo_source</a></code>.</p>
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<pre class="usage"><span class='no'>microorganisms.codes</span></pre>
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<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
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<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 3,303 observations and 2 variables:</p><dl class='dl-horizontal'>
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<dt><code>certe</code></dt><dd><p>Commonly used code of a microorganism</p></dd>
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<dt><code>mo</code></dt><dd><p>Code of microorganism in <code><a href='microorganisms.html'>microorganisms</a></code></p></dd>
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</dl>
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<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
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<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
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On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a omprehensive tutorial</a> about how to conduct AMR analysis and find <a href='https://msberends.gitlab.io/AMR/reference'>the complete documentation of all functions</a>, which reads a lot easier than in R.</p>
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<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
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<div class='dont-index'><p><code><a href='as.mo.html'>as.mo</a></code> <code><a href='microorganisms.html'>microorganisms</a></code></p></div>
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