function to calculate the length of ICU stay

DESCRIPTION

@@ -3,13 +3,13 @@ Type: Package
 Title: The Critical Care Clinical Data Processing Tools
 Version: 0.1
 Date: 2017-01-30
-Author: Sinan Shi, David Pérez-Suárez, Steve Harris, Niall MacCallum, David Brealey, Mervyn Singer, James Hetherington
+Author: Sinan Shi, David Pérez-Suárez, Steve Harris, Niall MacCallum, David
+    Brealey, Mervyn Singer, James Hetherington
 Maintainer: Sinan Shi <[email protected]>
-Description: 
-    A toolset to deal with the Critical Care Health Informatics Collaborative
-    dataset. It is created to address various data reliability and accessibility
-    problems of electronic healthcare records (EHR). It provides a unique
-    platform which enables data manipulation, transformation, reduction,
+Description: A toolset to deal with the Critical Care Health Informatics
+    Collaborative dataset. It is created to address various data reliability and
+    accessibility problems of electronic healthcare records (EHR). It provides a
+    unique platform which enables data manipulation, transformation, reduction,
     anonymisation, cleaning and validation.
 Depends:
     R (>= 3.1.0)
@@ -25,7 +25,7 @@ Imports:
     methods,
     knitr,
     ggplot2,
-    pander, 
+    pander,
     stats,
     utils
 VignetteBuilder: knitr
@@ -38,6 +38,7 @@ Collate:
     'create2dclean.R'
     'data.quality.report.R'
     'deltaTime.R'
+    'demographics.R'
     'filter.categorical.R'
     'filter.missingness.R'
     'filter.range.R'

NAMESPACE

@@ -25,6 +25,7 @@ export(is.demographic)
 export(is.drugs)
 export(is.laboratory)
 export(is.physiology)
+export(lenstay)
 export(lookup.items)
 export(new.episode)
 export(physio.distribution)

R/demographics.R

@@ -0,0 +1,16 @@
+#' Calculate the lenght of stay in the ICU. 
+#'
+#' Calculate the lenght of stay in the ICU and append it to the original demographic
+#' table. 
+#' @param demg data.table the demograhic table which should at least contain
+#' column DAICU and DDICU
+#' @param units character The unit of lenstay column, by default the output will be in hours 
+#' @return data.table It is the original data.table with lenstay column (in 
+#' difftime) appended. 
+#' @export lenstay
+lenstay <- function(demg, units="hours") {
+    len <- difftime(xmlTime2POSIX(demg$DDICU, allow=T), 
+             xmlTime2POSIX(demg$DAICU, allow=T),
+             units=units)
+    return(cbind(demg, lenstay = len))
+}

tests/testthat/test_demographics.r

@@ -0,0 +1,26 @@
+context("Testing functionalities for the demographic table")
+
+test_that("calculate length of stay in the ICU",{
+    demg <- data.table(DAICU="2007-01-01", DDICU="2007-01-02")
+    demg_ <- lenstay(demg)
+    expect_true(is.data.frame(demg_))
+    expect_equal(ncol(demg) + 1, ncol(demg_))
+    expect_equal(as.numeric(demg_$lenstay), 24)
+
+    demg <- data.table(DAICU="2007-01-01T00:00:00", DDICU="2007-01-01T22:00:00")
+    demg_ <- lenstay(demg)
+    expect_equal(as.numeric(demg_$lenstay), 22)
+
+    demg <- data.table(DAICU="2007-01-01", DDICU="wrong_format")
+    demg_ <- lenstay(demg)
+    expect_true(is.na(demg_$lenstay))
+
+    demg <- data.table(DAICU="wrong_format1", DDICU="wrong_format1")
+    demg_ <- lenstay(demg)
+    expect_true(is.na(demg_$lenstay))
+
+    demg <- data.table(DAICU="2007-01-01T00:00:00", DDICU="2007-01-01T22:00:00")
+    demg_ <- lenstay(demg, "days")
+    expect_equal(as.numeric(demg_$lenstay), 1-2/24)
+})
+