mirror of
https://github.com/msberends/AMR.git
synced 2025-07-12 02:22:08 +02:00
styled, unit test fix
This commit is contained in:
@ -28,16 +28,20 @@ library(dplyr)
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options(knitr.kable.NA = "")
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structure_txt <- function(dataset) {
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paste0("A data set with ",
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format(nrow(dataset), big.mark = ","), " rows and ",
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ncol(dataset), " columns, containing the following column names: \n",
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AMR:::vector_or(colnames(dataset), quotes = "*", last_sep = " and ", sort = FALSE), ".")
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paste0(
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"A data set with ",
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format(nrow(dataset), big.mark = ","), " rows and ",
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ncol(dataset), " columns, containing the following column names: \n",
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AMR:::vector_or(colnames(dataset), quotes = "*", last_sep = " and ", sort = FALSE), "."
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)
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}
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download_txt <- function(filename) {
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msg <- paste0("It was last updated on ",
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trimws(format(file.mtime(paste0("../data/", filename, ".rda")), "%e %B %Y %H:%M:%S %Z", tz = "UTC")),
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". Find more info about the structure of this data set [here](https://msberends.github.io/AMR/reference/", ifelse(filename == "antivirals", "antibiotics", filename), ".html).\n")
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msg <- paste0(
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"It was last updated on ",
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trimws(format(file.mtime(paste0("../data/", filename, ".rda")), "%e %B %Y %H:%M:%S %Z", tz = "UTC")),
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". Find more info about the structure of this data set [here](https://msberends.github.io/AMR/reference/", ifelse(filename == "antivirals", "antibiotics", filename), ".html).\n"
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)
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github_base <- "https://github.com/msberends/AMR/raw/main/data-raw/"
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filename <- paste0("../data-raw/", filename)
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rds <- paste0(filename, ".rds")
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@ -50,38 +54,44 @@ download_txt <- function(filename) {
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stata <- paste0(filename, ".dta")
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create_txt <- function(filename, type, software, exists) {
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if (isTRUE(exists)) {
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paste0("* Download as [", software, "](", github_base, filename, ") (",
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AMR:::formatted_filesize(filename), ") \n")
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paste0(
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"* Download as [", software, "](", github_base, filename, ") (",
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AMR:::formatted_filesize(filename), ") \n"
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)
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} else {
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paste0("* *(unavailable as ", software, ")*\n")
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}
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}
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if (any(file.exists(rds),
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file.exists(txt),
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file.exists(excel),
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file.exists(feather),
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file.exists(parquet),
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file.exists(sas),
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file.exists(spss),
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file.exists(stata))) {
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msg <- c(msg, "\n**Direct download links:**\n\n",
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create_txt(rds, "rds", "original R Data Structure (RDS) file", file.exists(rds)),
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create_txt(txt, "txt", "tab-separated text file", file.exists(txt)),
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create_txt(excel, "xlsx", "Microsoft Excel workbook", file.exists(excel)),
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create_txt(feather, "feather", "Apache Feather file", file.exists(feather)),
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create_txt(parquet, "parquet", "Apache Parquet file", file.exists(parquet)),
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create_txt(sas, "sas", "SAS data file", file.exists(sas)),
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create_txt(spss, "sav", "IBM SPSS Statistics data file", file.exists(spss)),
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create_txt(stata, "dta", "Stata DTA file", file.exists(stata)))
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if (any(
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file.exists(rds),
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file.exists(txt),
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file.exists(excel),
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file.exists(feather),
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file.exists(parquet),
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file.exists(sas),
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file.exists(spss),
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file.exists(stata)
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)) {
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msg <- c(
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msg, "\n**Direct download links:**\n\n",
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create_txt(rds, "rds", "original R Data Structure (RDS) file", file.exists(rds)),
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create_txt(txt, "txt", "tab-separated text file", file.exists(txt)),
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create_txt(excel, "xlsx", "Microsoft Excel workbook", file.exists(excel)),
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create_txt(feather, "feather", "Apache Feather file", file.exists(feather)),
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create_txt(parquet, "parquet", "Apache Parquet file", file.exists(parquet)),
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create_txt(sas, "sas", "SAS data file", file.exists(sas)),
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create_txt(spss, "sav", "IBM SPSS Statistics data file", file.exists(spss)),
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create_txt(stata, "dta", "Stata DTA file", file.exists(stata))
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)
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}
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paste0(msg, collapse = "")
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}
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print_df <- function(x, rows = 6) {
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x %>%
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as.data.frame(stringsAsFactors = FALSE) %>%
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head(n = rows) %>%
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x %>%
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as.data.frame(stringsAsFactors = FALSE) %>%
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head(n = rows) %>%
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mutate_all(function(x) {
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if (is.list(x)) {
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sapply(x, function(y) {
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@ -128,10 +138,10 @@ Our full taxonomy of microorganisms is based on the authoritative and comprehens
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Included (sub)species per taxonomic kingdom:
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```{r, echo = FALSE}
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microorganisms %>%
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count(kingdom) %>%
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mutate(n = format(n, big.mark = ",")) %>%
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setNames(c("Kingdom", "Number of (sub)species")) %>%
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microorganisms %>%
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count(kingdom) %>%
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mutate(n = format(n, big.mark = ",")) %>%
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setNames(c("Kingdom", "Number of (sub)species")) %>%
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print_df()
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```
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@ -139,7 +149,7 @@ Example rows when filtering on genus *Escherichia*:
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```{r, echo = FALSE}
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microorganisms %>%
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filter(genus == "Escherichia") %>%
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filter(genus == "Escherichia") %>%
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print_df()
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```
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@ -166,7 +176,7 @@ Example rows when filtering on *Escherichia*:
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```{r, echo = FALSE}
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microorganisms.old %>%
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filter(fullname %like% "^Escherichia") %>%
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filter(fullname %like% "^Escherichia") %>%
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print_df()
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```
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@ -191,7 +201,7 @@ This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET,
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```{r, echo = FALSE}
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antibiotics %>%
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filter(ab %in% colnames(example_isolates)) %>%
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filter(ab %in% colnames(example_isolates)) %>%
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print_df()
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```
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@ -233,9 +243,9 @@ This data set contains interpretation rules for MIC values and disk diffusion di
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### Example content
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```{r, echo = FALSE}
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rsi_translation %>%
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mutate(mo_name = mo_name(mo, language = NULL), .after = mo) %>%
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mutate(ab_name = ab_name(ab, language = NULL), .after = ab) %>%
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rsi_translation %>%
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mutate(mo_name = mo_name(mo, language = NULL), .after = mo) %>%
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mutate(ab_name = ab_name(ab, language = NULL), .after = ab) %>%
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print_df()
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```
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@ -258,9 +268,11 @@ Example rows when filtering on *Enterobacter cloacae*:
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```{r, echo = FALSE}
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intrinsic_resistant %>%
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transmute(microorganism = mo_name(mo),
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antibiotic = ab_name(ab)) %>%
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filter(microorganism == "Enterobacter cloacae") %>%
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transmute(
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microorganism = mo_name(mo),
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antibiotic = ab_name(ab)
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) %>%
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filter(microorganism == "Enterobacter cloacae") %>%
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arrange(antibiotic) %>%
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print_df(rows = Inf)
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```
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@ -283,7 +295,7 @@ Currently included dosages in the data set are meant for: `r AMR:::format_eucast
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### Example content
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```{r, echo = FALSE}
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dosage %>%
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dosage %>%
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print_df()
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```
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@ -303,7 +315,7 @@ This data set contains randomised fictitious data, but reflects reality and can
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### Example content
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```{r, echo = FALSE}
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example_isolates %>%
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example_isolates %>%
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print_df()
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```
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@ -322,6 +334,6 @@ This data set contains randomised fictitious data, but reflects reality and can
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### Example content
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```{r, echo = FALSE}
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example_isolates_unclean %>%
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example_isolates_unclean %>%
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print_df()
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```
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