mirror of
https://github.com/msberends/AMR.git
synced 2025-07-11 21:01:54 +02:00
styled, unit test fix
This commit is contained in:
@ -28,16 +28,20 @@ library(dplyr)
|
||||
options(knitr.kable.NA = "")
|
||||
|
||||
structure_txt <- function(dataset) {
|
||||
paste0("A data set with ",
|
||||
format(nrow(dataset), big.mark = ","), " rows and ",
|
||||
ncol(dataset), " columns, containing the following column names: \n",
|
||||
AMR:::vector_or(colnames(dataset), quotes = "*", last_sep = " and ", sort = FALSE), ".")
|
||||
paste0(
|
||||
"A data set with ",
|
||||
format(nrow(dataset), big.mark = ","), " rows and ",
|
||||
ncol(dataset), " columns, containing the following column names: \n",
|
||||
AMR:::vector_or(colnames(dataset), quotes = "*", last_sep = " and ", sort = FALSE), "."
|
||||
)
|
||||
}
|
||||
|
||||
download_txt <- function(filename) {
|
||||
msg <- paste0("It was last updated on ",
|
||||
trimws(format(file.mtime(paste0("../data/", filename, ".rda")), "%e %B %Y %H:%M:%S %Z", tz = "UTC")),
|
||||
". Find more info about the structure of this data set [here](https://msberends.github.io/AMR/reference/", ifelse(filename == "antivirals", "antibiotics", filename), ".html).\n")
|
||||
msg <- paste0(
|
||||
"It was last updated on ",
|
||||
trimws(format(file.mtime(paste0("../data/", filename, ".rda")), "%e %B %Y %H:%M:%S %Z", tz = "UTC")),
|
||||
". Find more info about the structure of this data set [here](https://msberends.github.io/AMR/reference/", ifelse(filename == "antivirals", "antibiotics", filename), ".html).\n"
|
||||
)
|
||||
github_base <- "https://github.com/msberends/AMR/raw/main/data-raw/"
|
||||
filename <- paste0("../data-raw/", filename)
|
||||
rds <- paste0(filename, ".rds")
|
||||
@ -50,38 +54,44 @@ download_txt <- function(filename) {
|
||||
stata <- paste0(filename, ".dta")
|
||||
create_txt <- function(filename, type, software, exists) {
|
||||
if (isTRUE(exists)) {
|
||||
paste0("* Download as [", software, "](", github_base, filename, ") (",
|
||||
AMR:::formatted_filesize(filename), ") \n")
|
||||
paste0(
|
||||
"* Download as [", software, "](", github_base, filename, ") (",
|
||||
AMR:::formatted_filesize(filename), ") \n"
|
||||
)
|
||||
} else {
|
||||
paste0("* *(unavailable as ", software, ")*\n")
|
||||
}
|
||||
}
|
||||
|
||||
if (any(file.exists(rds),
|
||||
file.exists(txt),
|
||||
file.exists(excel),
|
||||
file.exists(feather),
|
||||
file.exists(parquet),
|
||||
file.exists(sas),
|
||||
file.exists(spss),
|
||||
file.exists(stata))) {
|
||||
msg <- c(msg, "\n**Direct download links:**\n\n",
|
||||
create_txt(rds, "rds", "original R Data Structure (RDS) file", file.exists(rds)),
|
||||
create_txt(txt, "txt", "tab-separated text file", file.exists(txt)),
|
||||
create_txt(excel, "xlsx", "Microsoft Excel workbook", file.exists(excel)),
|
||||
create_txt(feather, "feather", "Apache Feather file", file.exists(feather)),
|
||||
create_txt(parquet, "parquet", "Apache Parquet file", file.exists(parquet)),
|
||||
create_txt(sas, "sas", "SAS data file", file.exists(sas)),
|
||||
create_txt(spss, "sav", "IBM SPSS Statistics data file", file.exists(spss)),
|
||||
create_txt(stata, "dta", "Stata DTA file", file.exists(stata)))
|
||||
|
||||
if (any(
|
||||
file.exists(rds),
|
||||
file.exists(txt),
|
||||
file.exists(excel),
|
||||
file.exists(feather),
|
||||
file.exists(parquet),
|
||||
file.exists(sas),
|
||||
file.exists(spss),
|
||||
file.exists(stata)
|
||||
)) {
|
||||
msg <- c(
|
||||
msg, "\n**Direct download links:**\n\n",
|
||||
create_txt(rds, "rds", "original R Data Structure (RDS) file", file.exists(rds)),
|
||||
create_txt(txt, "txt", "tab-separated text file", file.exists(txt)),
|
||||
create_txt(excel, "xlsx", "Microsoft Excel workbook", file.exists(excel)),
|
||||
create_txt(feather, "feather", "Apache Feather file", file.exists(feather)),
|
||||
create_txt(parquet, "parquet", "Apache Parquet file", file.exists(parquet)),
|
||||
create_txt(sas, "sas", "SAS data file", file.exists(sas)),
|
||||
create_txt(spss, "sav", "IBM SPSS Statistics data file", file.exists(spss)),
|
||||
create_txt(stata, "dta", "Stata DTA file", file.exists(stata))
|
||||
)
|
||||
}
|
||||
paste0(msg, collapse = "")
|
||||
}
|
||||
|
||||
print_df <- function(x, rows = 6) {
|
||||
x %>%
|
||||
as.data.frame(stringsAsFactors = FALSE) %>%
|
||||
head(n = rows) %>%
|
||||
x %>%
|
||||
as.data.frame(stringsAsFactors = FALSE) %>%
|
||||
head(n = rows) %>%
|
||||
mutate_all(function(x) {
|
||||
if (is.list(x)) {
|
||||
sapply(x, function(y) {
|
||||
@ -128,10 +138,10 @@ Our full taxonomy of microorganisms is based on the authoritative and comprehens
|
||||
Included (sub)species per taxonomic kingdom:
|
||||
|
||||
```{r, echo = FALSE}
|
||||
microorganisms %>%
|
||||
count(kingdom) %>%
|
||||
mutate(n = format(n, big.mark = ",")) %>%
|
||||
setNames(c("Kingdom", "Number of (sub)species")) %>%
|
||||
microorganisms %>%
|
||||
count(kingdom) %>%
|
||||
mutate(n = format(n, big.mark = ",")) %>%
|
||||
setNames(c("Kingdom", "Number of (sub)species")) %>%
|
||||
print_df()
|
||||
```
|
||||
|
||||
@ -139,7 +149,7 @@ Example rows when filtering on genus *Escherichia*:
|
||||
|
||||
```{r, echo = FALSE}
|
||||
microorganisms %>%
|
||||
filter(genus == "Escherichia") %>%
|
||||
filter(genus == "Escherichia") %>%
|
||||
print_df()
|
||||
```
|
||||
|
||||
@ -166,7 +176,7 @@ Example rows when filtering on *Escherichia*:
|
||||
|
||||
```{r, echo = FALSE}
|
||||
microorganisms.old %>%
|
||||
filter(fullname %like% "^Escherichia") %>%
|
||||
filter(fullname %like% "^Escherichia") %>%
|
||||
print_df()
|
||||
```
|
||||
|
||||
@ -191,7 +201,7 @@ This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET,
|
||||
|
||||
```{r, echo = FALSE}
|
||||
antibiotics %>%
|
||||
filter(ab %in% colnames(example_isolates)) %>%
|
||||
filter(ab %in% colnames(example_isolates)) %>%
|
||||
print_df()
|
||||
```
|
||||
|
||||
@ -233,9 +243,9 @@ This data set contains interpretation rules for MIC values and disk diffusion di
|
||||
### Example content
|
||||
|
||||
```{r, echo = FALSE}
|
||||
rsi_translation %>%
|
||||
mutate(mo_name = mo_name(mo, language = NULL), .after = mo) %>%
|
||||
mutate(ab_name = ab_name(ab, language = NULL), .after = ab) %>%
|
||||
rsi_translation %>%
|
||||
mutate(mo_name = mo_name(mo, language = NULL), .after = mo) %>%
|
||||
mutate(ab_name = ab_name(ab, language = NULL), .after = ab) %>%
|
||||
print_df()
|
||||
```
|
||||
|
||||
@ -258,9 +268,11 @@ Example rows when filtering on *Enterobacter cloacae*:
|
||||
|
||||
```{r, echo = FALSE}
|
||||
intrinsic_resistant %>%
|
||||
transmute(microorganism = mo_name(mo),
|
||||
antibiotic = ab_name(ab)) %>%
|
||||
filter(microorganism == "Enterobacter cloacae") %>%
|
||||
transmute(
|
||||
microorganism = mo_name(mo),
|
||||
antibiotic = ab_name(ab)
|
||||
) %>%
|
||||
filter(microorganism == "Enterobacter cloacae") %>%
|
||||
arrange(antibiotic) %>%
|
||||
print_df(rows = Inf)
|
||||
```
|
||||
@ -283,7 +295,7 @@ Currently included dosages in the data set are meant for: `r AMR:::format_eucast
|
||||
### Example content
|
||||
|
||||
```{r, echo = FALSE}
|
||||
dosage %>%
|
||||
dosage %>%
|
||||
print_df()
|
||||
```
|
||||
|
||||
@ -303,7 +315,7 @@ This data set contains randomised fictitious data, but reflects reality and can
|
||||
### Example content
|
||||
|
||||
```{r, echo = FALSE}
|
||||
example_isolates %>%
|
||||
example_isolates %>%
|
||||
print_df()
|
||||
```
|
||||
|
||||
@ -322,6 +334,6 @@ This data set contains randomised fictitious data, but reflects reality and can
|
||||
### Example content
|
||||
|
||||
```{r, echo = FALSE}
|
||||
example_isolates_unclean %>%
|
||||
example_isolates_unclean %>%
|
||||
print_df()
|
||||
```
|
||||
|
||||
Reference in New Issue
Block a user