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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.
#' @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_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_species column name of the species of the microorganisms
#' @param col_testcode column name of the test codes, see Details
@ -84,7 +84,7 @@
#' }
first_isolate <- function(tbl,
col_date,
col_patid,
col_patient_id,
col_genus,
col_species,
col_testcode = NA,
@ -113,7 +113,7 @@ first_isolate <- function(tbl,
}
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_species)
check_columns_existance(col_testcode)
@ -162,7 +162,10 @@ first_isolate <- function(tbl,
mutate(first_isolate_row_index = 1:nrow(tbl),
eersteisolaatbepaling = 0,
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))
if (filter_specimen == '') {
@ -172,7 +175,7 @@ first_isolate <- function(tbl,
cat('Isolates from ICU will *NOT* be ignored.\n')
}
tbl <- tbl %>%
arrange_at(c(col_patid,
arrange_at(c(col_patient_id,
col_genus,
col_species,
col_date))
@ -184,7 +187,7 @@ first_isolate <- function(tbl,
}
tbl <- tbl %>%
arrange_at(c(col_icu,
col_patid,
col_patient_id,
col_genus,
col_species,
col_date))
@ -205,7 +208,7 @@ first_isolate <- function(tbl,
}
tbl <- tbl %>%
arrange_at(c(col_specimen,
col_patid,
col_patient_id,
col_genus,
col_species,
col_date))
@ -222,7 +225,7 @@ first_isolate <- function(tbl,
tbl <- tbl %>%
arrange_at(c(col_icu,
col_specimen,
col_patid,
col_patient_id,
col_genus,
col_species,
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).
#### Latest stable version from CRAN (recommended)
RStudio:
- Click on `Tools` and then `Install Packages..`
### Latest stable version from CRAN (recommended)
For RStudio:
- Click on `Tools` and then `Install Packages...`
- Type in `AMR` and press <kbd>Install</kbd>
Other:
Or in the R console:
```r
install.packages("AMR")
```
#### Latest development version from GitHub
### Latest development version from GitHub
```r
devtools::install_github("msberends/AMR")
```

4
man/first_isolate.Rd
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@ -4,7 +4,7 @@
\alias{first_isolate}
\title{Determine first (weighted) isolates}
\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,
episode_days = 365, testcodes_exclude = "", icu_exclude = FALSE,
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_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}