Merge branch 'master' of github.com:CC-HIC/cleanEHR

* 'master' of github.com:CC-HIC/cleanEHR: (42 commits)
  Long2short (#145)
  ✏️ install instructions
  paper
  readme
  rename extractInfo
  adding test data
  r cmd check
  update vignette link
  rename
  rename tour
  vignette
  vignettes numerical range filters
  tclean reset to origin
  filters documentation
  fix #88 and more documentation
  more documentation for ccTable; merge spec2fun()
  fix the tests
  tidy up ccRecord
  generic plot episode function
  import evalRcpp only
  ...

DESCRIPTION

@@ -1,18 +1,18 @@
 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
+Version: 0.2
+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
-    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.
+Description: An electronic health care record (EHR) data cleaning and processing
+    platform. It focus on heterogeneous high resolution longitudinal data. It works with 
+    Critical Care Health Informatics Collaborative (CCHIC) dataset. It is
+    created to address various data reliability and accessibility problems of
+    EHRs as such. 
 Depends:
-    R (>= 3.1.0)
+    R (>= 3.1.0) 
+BugReports: https://github.com/CC-HIC/cleanEHR/issues
 License: GPL-3
 LinkingTo: Rcpp
 Suggests:
@@ -22,34 +22,26 @@ Imports:
     XML,
     yaml,
     Rcpp,
-    methods,
-    knitr,
     ggplot2,
+    methods, 
     pander,
-    stats,
-    utils
+    knitr
 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

@@ -3,42 +3,37 @@
 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(extract_info)
 export(file.summary)
 export(for_each_episode)
 export(getEpisodePeriod)
-export(getfilter)
 export(icnarc2diagnosis)
 export(is.demographic)
 export(is.drugs)
 export(is.laboratory)
 export(is.physiology)
 export(lenstay)
+export(long2stname)
 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 +42,36 @@ 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)
+importFrom(ggplot2,aes_string)
+importFrom(ggplot2,annotate)
+importFrom(ggplot2,element_blank)
+importFrom(ggplot2,element_text)
+importFrom(ggplot2,facet_grid)
+importFrom(ggplot2,facet_wrap)
+importFrom(ggplot2,geom_density)
+importFrom(ggplot2,geom_line)
+importFrom(ggplot2,geom_point)
+importFrom(ggplot2,geom_segment)
+importFrom(ggplot2,geom_vline)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,ggtitle)
+importFrom(ggplot2,labs)
+importFrom(ggplot2,scale_colour_manual)
+importFrom(ggplot2,scale_x_datetime)
+importFrom(ggplot2,theme)
+importFrom(ggplot2,xlab)
+importFrom(ggplot2,ylab)
+importFrom(knitr,knit)
+importFrom(pander,pander)
+importFrom(pander,panderOptions)
 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)
 }