mirror of https://github.com/msberends/AMR.git
fix freq length calculation
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parent
30ff770c93
commit
ae44b185e6
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 0.5.0.9017
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Date: 2019-02-12
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Date: 2019-02-13
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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38
R/freq.R
38
R/freq.R
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@ -352,6 +352,14 @@ frequency_tbl <- function(x,
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NAs <- x[is.na(x)]
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}
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if (mult.columns > 0) {
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header_list <- list(columns = mult.columns)
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} else {
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header_list <- list(class = class(x),
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mode = mode(x))
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}
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header_list$length <- length(x)
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if (na.rm == TRUE) {
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x_class <- class(x)
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x <- x[!x %in% NAs]
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@ -364,13 +372,6 @@ frequency_tbl <- function(x,
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}
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x_align <- "l"
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if (mult.columns > 0) {
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header_list <- list(columns = mult.columns)
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} else {
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header_list <- list(class = class(x),
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mode = mode(x))
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}
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if (!is.null(levels(x))) {
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header_list$levels <- levels(x)
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header_list$ordered <- is.ordered(x)
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@ -381,7 +382,6 @@ frequency_tbl <- function(x,
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}
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}
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header_list$length <- length(x)
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header_list$na_length <- length(NAs)
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header_list$unique <- n_distinct(x)
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@ -559,7 +559,7 @@ format_header <- function(x, markdown = FALSE, decimal.mark = ".", big.mark = ",
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header <- header(x)
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x_class <- header$class
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has_length <- header$length + header$na_length > 0
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has_length <- header$length > 0
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# FORMATTING
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# rsi
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@ -633,23 +633,25 @@ format_header <- function(x, markdown = FALSE, decimal.mark = ".", big.mark = ",
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}
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# levels
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if (!is.null(header$levels)) {
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n_levels <- header$levels %>% length()
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n_levels_list <- header$levels
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if (n_levels > 5) {
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n_levels_list <- c(n_levels_list[1:5], "...")
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if (markdown == TRUE) {
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header$levels <- paste0("`", header$levels, "`")
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}
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if (header$ordered == TRUE) {
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n_levels_list <- paste0(n_levels_list, collapse = " < ")
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levels_text <- paste0(header$levels, collapse = " < ")
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} else {
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n_levels_list <- paste0(n_levels_list, collapse = ", ")
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levels_text <- paste0(header$levels, collapse = ", ")
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}
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header$levels <- n_levels_list
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if (nchar(levels_text) > 70) {
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# levels text wider than half the console
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levels_text <- paste0(substr(levels_text, 1, 70 - 3), "...")
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}
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header$levels <- paste0(length(header$levels), ": ", levels_text)
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header <- header[names(header) != "ordered"]
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}
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# length and NAs
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if (has_length == TRUE) {
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na_txt <- paste0(header$na_length %>% format(decimal.mark = decimal.mark, big.mark = big.mark), " = ",
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(header$na_length / (header$na_length + header$length)) %>% percent(force_zero = TRUE, round = digits, decimal.mark = decimal.mark) %>%
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(header$na_length / header$length) %>% percent(force_zero = TRUE, round = digits, decimal.mark = decimal.mark) %>%
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sub("NaN", "0", ., fixed = TRUE))
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if (!na_txt %like% "^0 =") {
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na_txt <- red(na_txt)
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@ -660,7 +662,7 @@ format_header <- function(x, markdown = FALSE, decimal.mark = ".", big.mark = ",
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} else {
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na_txt <- ""
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}
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header$length <- paste((header$na_length + header$length) %>% format(decimal.mark = decimal.mark, big.mark = big.mark),
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header$length <- paste(format(header$length, decimal.mark = decimal.mark, big.mark = big.mark),
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na_txt)
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header <- header[names(header) != "na_length"]
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@ -38,9 +38,9 @@ $( document ).ready(function() {
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if ($(".template-article").length > 0) {
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$('#sidebar').prepend(
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'<div id="r4ds">' +
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' <a href="https://r4ds.had.co.nz/">Learn R reading this great book: R for Data Science.' +
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' <br>' +
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' <br>' +
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' <a target="_blank" href="https://r4ds.had.co.nz/">' +
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' Learn R reading this great book: R for Data Science.' +
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' <br><br>' +
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' Click to read it online - it was published for free.' +
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' <img src="../../AMR/cover_r4ds.png" height="100px">' +
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' </a> ' +
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@ -261,7 +261,7 @@
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<h4 class="hasAnchor">
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<a href="#whonet--ears-net" class="anchor"></a>WHONET / EARS-Net</h4>
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<p><img src="./whonet.png"></p>
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<p>We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a> with the exact same structure and a WHONET export file. Furthermore, this package also contains a <a href="./reference/antibiotics.html">data set <code>antibiotics</code></a> with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.</p>
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<p>We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a> with the exact same structure as a WHONET export file. Furthermore, this package also contains a <a href="./reference/antibiotics.html">data set <code>antibiotics</code></a> with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.</p>
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<p>Read our tutorial about <a href="./articles/WHONET.html">how to work with WHONET data here</a>.</p>
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</div>
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<div id="antimicrobial-reference-data" class="section level4">
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2
index.md
2
index.md
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@ -81,7 +81,7 @@ To find out how to conduct AMR analysis, please [continue reading here to get st
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<img src="./whonet.png">
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We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an [example data set `WHONET`](./reference/WHONET.html) with the exact same structure and a WHONET export file. Furthermore, this package also contains a [data set `antibiotics`](./reference/antibiotics.html) with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.
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We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an [example data set `WHONET`](./reference/WHONET.html) with the exact same structure as a WHONET export file. Furthermore, this package also contains a [data set `antibiotics`](./reference/antibiotics.html) with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.
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Read our tutorial about [how to work with WHONET data here](./articles/WHONET.html).
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@ -38,9 +38,9 @@ $( document ).ready(function() {
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if ($(".template-article").length > 0) {
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$('#sidebar').prepend(
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'<div id="r4ds">' +
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' <a href="https://r4ds.had.co.nz/">Learn R reading this great book: R for Data Science.' +
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' <br>' +
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' <br>' +
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' <a target="_blank" href="https://r4ds.had.co.nz/">' +
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' Learn R reading this great book: R for Data Science.' +
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' <br><br>' +
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' Click to read it online - it was published for free.' +
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' <img src="../../AMR/cover_r4ds.png" height="100px">' +
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' </a> ' +
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