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first isolates

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dr. M.S. (Matthijs) Berends 2018-02-26 14:06:31 +01:00
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commit 6fa05fe33b
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3 changed files with 18 additions and 15 deletions
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19
R/first_isolates.R
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@ -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
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@ -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
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@ -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}