JOSS review

DESCRIPTION

@@ -2,8 +2,7 @@ Package: cleanEHR
 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
+Author: Sinan Shi, David Perez-Suarez, 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
@@ -13,43 +12,36 @@ Description: A toolset to deal with the Critical Care Health Informatics
     anonymisation, cleaning and validation.
 Depends:
     R (>= 3.1.0)
+BugReports: http://github.com/cleanEHR/issues
 License: GPL-3
 LinkingTo: Rcpp
 Suggests:
-    testthat
+    testthat,
 Imports:
     data.table,
     XML,
     yaml,
     Rcpp,
     methods,
-    knitr,
-    ggplot2,
-    pander,
     stats,
-    utils
+    utils,
+    pander
 VignetteBuilder: knitr
 URL: https://github.com/CC-HIC/cleanEHR, http://www.hic.nihr.ac.uk
 RoxygenNote: 5.0.1
 Collate:
     'RcppExports.R'
     'ccRecord.R'
     'ccTable.R'
-    'create2dclean.R'
+    'cchic_xml.R'
+    'data.R'
     'data.quality.report.R'
     'deltaTime.R'
     'demographics.R'
     'filter.categorical.R'
     'filter.missingness.R'
     'filter.range.R'
     'imputation.R'
-    'pipeline.R'
-    'reallocateTime.R'
-    'selectTable.R'
-    'sql_demographic.R'
     'stdid.R'
-    'summary.R'
-    'unique.spell.R'
     'utilities.R'
-    'xml2ccdata.R'
     'zzz.R'

NAMESPACE

@@ -3,22 +3,21 @@
 export(StdId)
 export(as.number)
 export(ccRecord)
-export(ccRecord_subset_files)
+export(ccd_demographic_spell)
+export(ccd_demographic_table)
+export(ccd_unique_spell)
 export(code2stname)
-export(create.cctable)
 export(create2dclean)
+export(create_cctable)
 export(data.quality.report)
 export(data.quality.report.brc)
 export(deltaTime)
 export(demg.distribution)
 export(demographic.data.completeness)
-export(demographic.patient.spell)
-export(episode.graph)
 export(extractInfo)
 export(file.summary)
 export(for_each_episode)
 export(getEpisodePeriod)
-export(getfilter)
 export(icnarc2diagnosis)
 export(is.demographic)
 export(is.drugs)
@@ -28,17 +27,12 @@ export(lenstay)
 export(lookup.items)
 export(new.episode)
 export(physio.distribution)
-export(reallocateTimeRecord)
 export(samplerate2d)
-export(selectTable)
 export(site.info)
-export(sql.demographic.table)
 export(stname2code)
 export(stname2longname)
 export(table1)
 export(total.data.point)
-export(unique_spell)
-export(update_database)
 export(which.classification)
 export(xml.file.duration.plot)
 export(xml.site.duration.plot)
@@ -47,16 +41,17 @@ export(xmlTime2POSIX)
 exportClasses(ccEpisode)
 exportClasses(ccRecord)
 exportClasses(ccTable)
+exportMethods("+")
 exportMethods("[")
 exportMethods("[[")
-import(Rcpp)
+exportMethods(plot)
+exportMethods(subset)
 import(XML)
 import(data.table)
 import(ggplot2)
 import(knitr)
 import(methods)
 import(pander)
-import(parallel)
 import(yaml)
 importFrom(Rcpp,evalCpp)
 useDynLib(cleanEHR)

R/RcppExports.R

@@ -2,6 +2,6 @@
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 reallocateTime_ <- function(d, t_discharge, frequency) {
-    .Call('cleanEHR_reallocateTime_', PACKAGE = 'cleanEHR', d, t_discharge, frequency)
+    .Call('_cleanEHR_reallocateTime_', PACKAGE = 'cleanEHR', d, t_discharge, frequency)
 }