P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2024-12-26 08:06:12 +01:00
Code Releases Activity

first isolates

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends 2018-02-26 14:06:31 +01:00
parent d36a391747
commit 6fa05fe33b
No known key found for this signature in database
GPG Key ID: AE86720DBCDA4567
3 changed files with 18 additions and 15 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

19
R/first_isolates.R
View File

@ -21,7 +21,7 @@
#' Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. #' Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type.
#' @param tbl a \code{data.frame} containing isolates. #' @param tbl a \code{data.frame} containing isolates.
#' @param col_date column name of the result date (or date that is was received on the lab) #' @param col_date column name of the result date (or date that is was received on the lab)
#' @param col_patid column name of the unique IDs of the patients #' @param col_patient_id column name of the unique IDs of the patients
#' @param col_genus column name of the genus of the microorganisms #' @param col_genus column name of the genus of the microorganisms
#' @param col_species column name of the species of the microorganisms #' @param col_species column name of the species of the microorganisms
#' @param col_testcode column name of the test codes, see Details #' @param col_testcode column name of the test codes, see Details
@ -84,7 +84,7 @@
#' } #' }
first_isolate <- function(tbl, first_isolate <- function(tbl,
col_date, col_date,
col_patid, col_patient_id,
col_genus, col_genus,
col_species, col_species,
col_testcode = NA, col_testcode = NA,
@ -113,7 +113,7 @@ first_isolate <- function(tbl,
} }
check_columns_existance(col_date) check_columns_existance(col_date)
check_columns_existance(col_patid) check_columns_existance(col_patient_id)
check_columns_existance(col_genus) check_columns_existance(col_genus)
check_columns_existance(col_species) check_columns_existance(col_species)
check_columns_existance(col_testcode) check_columns_existance(col_testcode)
@ -162,7 +162,10 @@ first_isolate <- function(tbl,
mutate(first_isolate_row_index = 1:nrow(tbl), mutate(first_isolate_row_index = 1:nrow(tbl),
eersteisolaatbepaling = 0, eersteisolaatbepaling = 0,
date_lab = tbl %>% pull(col_date), date_lab = tbl %>% pull(col_date),
species = if_else(is.na(species), '', species), patient_id = tbl %>% pull(col_patient_id),
species = tbl %>% pull(col_species),
genus = tbl %>% pull(col_genus)) %>%
mutate(species = if_else(is.na(species), '', species),
genus = if_else(is.na(genus), '', genus)) genus = if_else(is.na(genus), '', genus))
if (filter_specimen == '') { if (filter_specimen == '') {
@ -172,7 +175,7 @@ first_isolate <- function(tbl,
cat('Isolates from ICU will *NOT* be ignored.\n') cat('Isolates from ICU will *NOT* be ignored.\n')
} }
tbl <- tbl %>% tbl <- tbl %>%
arrange_at(c(col_patid, arrange_at(c(col_patient_id,
col_genus, col_genus,
col_species, col_species,
col_date)) col_date))
@ -184,7 +187,7 @@ first_isolate <- function(tbl,
} }
tbl <- tbl %>% tbl <- tbl %>%
arrange_at(c(col_icu, arrange_at(c(col_icu,
col_patid, col_patient_id,
col_genus, col_genus,
col_species, col_species,
col_date)) col_date))
@ -205,7 +208,7 @@ first_isolate <- function(tbl,
} }
tbl <- tbl %>% tbl <- tbl %>%
arrange_at(c(col_specimen, arrange_at(c(col_specimen,
col_patid, col_patient_id,
col_genus, col_genus,
col_species, col_species,
col_date)) col_date))
@ -222,7 +225,7 @@ first_isolate <- function(tbl,
tbl <- tbl %>% tbl <- tbl %>%
arrange_at(c(col_icu, arrange_at(c(col_icu,
col_specimen, col_specimen,
col_patid, col_patient_id,
col_genus, col_genus,
col_species, col_species,
col_date)) col_date))

10
README.md
View File

@ -17,17 +17,17 @@ It also contains functions to translate antibiotic codes from the lab (like `"AM
This package is available on CRAN (latest stable version) and also here on GitHub (latest development version). This package is available on CRAN (latest stable version) and also here on GitHub (latest development version).
#### Latest stable version from CRAN (recommended) ### Latest stable version from CRAN (recommended)
RStudio: For RStudio:
- Click on `Tools` and then `Install Packages..` - Click on `Tools` and then `Install Packages...`
- Type in `AMR` and press <kbd>Install</kbd> - Type in `AMR` and press <kbd>Install</kbd>
Other: Or in the R console:
```r ```r
install.packages("AMR") install.packages("AMR")
``` ```
#### Latest development version from GitHub ### Latest development version from GitHub
```r ```r
devtools::install_github("msberends/AMR") devtools::install_github("msberends/AMR")
``` ```

4
man/first_isolate.Rd
View File

@ -4,7 +4,7 @@
\alias{first_isolate} \alias{first_isolate}
\title{Determine first (weighted) isolates} \title{Determine first (weighted) isolates}
\usage{ \usage{
first_isolate(tbl, col_date, col_patid, col_genus, col_species, first_isolate(tbl, col_date, col_patient_id, col_genus, col_species,
col_testcode = NA, col_specimen, col_icu, col_keyantibiotics = NA, col_testcode = NA, col_specimen, col_icu, col_keyantibiotics = NA,
episode_days = 365, testcodes_exclude = "", icu_exclude = FALSE, episode_days = 365, testcodes_exclude = "", icu_exclude = FALSE,
filter_specimen = NA, output_logical = TRUE, ignore_I = TRUE, filter_specimen = NA, output_logical = TRUE, ignore_I = TRUE,
@ -15,7 +15,7 @@ first_isolate(tbl, col_date, col_patid, col_genus, col_species,
\item{col_date}{column name of the result date (or date that is was received on the lab)} \item{col_date}{column name of the result date (or date that is was received on the lab)}
\item{col_patid}{column name of the unique IDs of the patients} \item{col_patient_id}{column name of the unique IDs of the patients}
\item{col_genus}{column name of the genus of the microorganisms} \item{col_genus}{column name of the genus of the microorganisms}