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mirror of https://github.com/msberends/AMR.git synced 2024-12-25 20:46:11 +01:00

fix freq length calculation

This commit is contained in:
dr. M.S. (Matthijs) Berends 2019-02-13 17:14:59 +01:00
parent 30ff770c93
commit ae44b185e6
6 changed files with 29 additions and 27 deletions

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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.5.0.9017 Version: 0.5.0.9017
Date: 2019-02-12 Date: 2019-02-13
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person( person(

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@ -352,6 +352,14 @@ frequency_tbl <- function(x,
NAs <- x[is.na(x)] NAs <- x[is.na(x)]
} }
if (mult.columns > 0) {
header_list <- list(columns = mult.columns)
} else {
header_list <- list(class = class(x),
mode = mode(x))
}
header_list$length <- length(x)
if (na.rm == TRUE) { if (na.rm == TRUE) {
x_class <- class(x) x_class <- class(x)
x <- x[!x %in% NAs] x <- x[!x %in% NAs]
@ -364,13 +372,6 @@ frequency_tbl <- function(x,
} }
x_align <- "l" x_align <- "l"
if (mult.columns > 0) {
header_list <- list(columns = mult.columns)
} else {
header_list <- list(class = class(x),
mode = mode(x))
}
if (!is.null(levels(x))) { if (!is.null(levels(x))) {
header_list$levels <- levels(x) header_list$levels <- levels(x)
header_list$ordered <- is.ordered(x) header_list$ordered <- is.ordered(x)
@ -381,7 +382,6 @@ frequency_tbl <- function(x,
} }
} }
header_list$length <- length(x)
header_list$na_length <- length(NAs) header_list$na_length <- length(NAs)
header_list$unique <- n_distinct(x) header_list$unique <- n_distinct(x)
@ -559,7 +559,7 @@ format_header <- function(x, markdown = FALSE, decimal.mark = ".", big.mark = ",
header <- header(x) header <- header(x)
x_class <- header$class x_class <- header$class
has_length <- header$length + header$na_length > 0 has_length <- header$length > 0
# FORMATTING # FORMATTING
# rsi # rsi
@ -633,23 +633,25 @@ format_header <- function(x, markdown = FALSE, decimal.mark = ".", big.mark = ",
} }
# levels # levels
if (!is.null(header$levels)) { if (!is.null(header$levels)) {
n_levels <- header$levels %>% length() if (markdown == TRUE) {
n_levels_list <- header$levels header$levels <- paste0("`", header$levels, "`")
if (n_levels > 5) {
n_levels_list <- c(n_levels_list[1:5], "...")
} }
if (header$ordered == TRUE) { if (header$ordered == TRUE) {
n_levels_list <- paste0(n_levels_list, collapse = " < ") levels_text <- paste0(header$levels, collapse = " < ")
} else { } else {
n_levels_list <- paste0(n_levels_list, collapse = ", ") levels_text <- paste0(header$levels, collapse = ", ")
} }
header$levels <- n_levels_list if (nchar(levels_text) > 70) {
# levels text wider than half the console
levels_text <- paste0(substr(levels_text, 1, 70 - 3), "...")
}
header$levels <- paste0(length(header$levels), ": ", levels_text)
header <- header[names(header) != "ordered"] header <- header[names(header) != "ordered"]
} }
# length and NAs # length and NAs
if (has_length == TRUE) { if (has_length == TRUE) {
na_txt <- paste0(header$na_length %>% format(decimal.mark = decimal.mark, big.mark = big.mark), " = ", na_txt <- paste0(header$na_length %>% format(decimal.mark = decimal.mark, big.mark = big.mark), " = ",
(header$na_length / (header$na_length + header$length)) %>% percent(force_zero = TRUE, round = digits, decimal.mark = decimal.mark) %>% (header$na_length / header$length) %>% percent(force_zero = TRUE, round = digits, decimal.mark = decimal.mark) %>%
sub("NaN", "0", ., fixed = TRUE)) sub("NaN", "0", ., fixed = TRUE))
if (!na_txt %like% "^0 =") { if (!na_txt %like% "^0 =") {
na_txt <- red(na_txt) na_txt <- red(na_txt)
@ -660,7 +662,7 @@ format_header <- function(x, markdown = FALSE, decimal.mark = ".", big.mark = ",
} else { } else {
na_txt <- "" na_txt <- ""
} }
header$length <- paste((header$na_length + header$length) %>% format(decimal.mark = decimal.mark, big.mark = big.mark), header$length <- paste(format(header$length, decimal.mark = decimal.mark, big.mark = big.mark),
na_txt) na_txt)
header <- header[names(header) != "na_length"] header <- header[names(header) != "na_length"]

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@ -38,9 +38,9 @@ $( document ).ready(function() {
if ($(".template-article").length > 0) { if ($(".template-article").length > 0) {
$('#sidebar').prepend( $('#sidebar').prepend(
'<div id="r4ds">' + '<div id="r4ds">' +
' <a href="https://r4ds.had.co.nz/">Learn R reading this great book: R for Data Science.' + ' <a target="_blank" href="https://r4ds.had.co.nz/">' +
' <br>' + ' Learn R reading this great book: R for Data Science.' +
' <br>' + ' <br><br>' +
' Click to read it online - it was published for free.' + ' Click to read it online - it was published for free.' +
' <img src="../../AMR/cover_r4ds.png" height="100px">' + ' <img src="../../AMR/cover_r4ds.png" height="100px">' +
' </a> ' + ' </a> ' +

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@ -261,7 +261,7 @@
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#whonet--ears-net" class="anchor"></a>WHONET / EARS-Net</h4> <a href="#whonet--ears-net" class="anchor"></a>WHONET / EARS-Net</h4>
<p><img src="./whonet.png"></p> <p><img src="./whonet.png"></p>
<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> <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>
<p>Read our tutorial about <a href="./articles/WHONET.html">how to work with WHONET data here</a>.</p> <p>Read our tutorial about <a href="./articles/WHONET.html">how to work with WHONET data here</a>.</p>
</div> </div>
<div id="antimicrobial-reference-data" class="section level4"> <div id="antimicrobial-reference-data" class="section level4">

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@ -81,7 +81,7 @@ To find out how to conduct AMR analysis, please [continue reading here to get st
<img src="./whonet.png"> <img src="./whonet.png">
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. 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.
Read our tutorial about [how to work with WHONET data here](./articles/WHONET.html). Read our tutorial about [how to work with WHONET data here](./articles/WHONET.html).

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@ -38,9 +38,9 @@ $( document ).ready(function() {
if ($(".template-article").length > 0) { if ($(".template-article").length > 0) {
$('#sidebar').prepend( $('#sidebar').prepend(
'<div id="r4ds">' + '<div id="r4ds">' +
' <a href="https://r4ds.had.co.nz/">Learn R reading this great book: R for Data Science.' + ' <a target="_blank" href="https://r4ds.had.co.nz/">' +
' <br>' + ' Learn R reading this great book: R for Data Science.' +
' <br>' + ' <br><br>' +
' Click to read it online - it was published for free.' + ' Click to read it online - it was published for free.' +
' <img src="../../AMR/cover_r4ds.png" height="100px">' + ' <img src="../../AMR/cover_r4ds.png" height="100px">' +
' </a> ' + ' </a> ' +