From 6fa05fe33bfd0ee8a8bbcc0c93c5c0f718827f27 Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Mon, 26 Feb 2018 14:06:31 +0100
Subject: [PATCH] first isolates

---
 R/first_isolates.R   | 19 +++++++++++--------
 README.md            | 10 +++++-----
 man/first_isolate.Rd |  4 ++--
 3 files changed, 18 insertions(+), 15 deletions(-)

diff --git a/R/first_isolates.R b/R/first_isolates.R
index efc67f0b..cc8c999e 100644
--- a/R/first_isolates.R
+++ b/R/first_isolates.R
@@ -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))
diff --git a/README.md b/README.md
index d5e7a40d..ec2b1a74 100644
--- a/README.md
+++ b/README.md
@@ -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")
 ```
diff --git a/man/first_isolate.Rd b/man/first_isolate.Rd
index 0ea54ef8..ca9e344d 100644
--- a/man/first_isolate.Rd
+++ b/man/first_isolate.Rd
@@ -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}