Merge branch 'main' of github.com:shajoezhu/pharmaverse_examples

Author: shajoezhu

DESCRIPTION

@@ -13,7 +13,9 @@ Authors@R:
     person("Daniel D.", "Sjoberg", , "danield.sjoberg@gmail.com", role = "aut", comment = c(ORCID = "0000-0003-0862-2018")),
     person("Fanny", "Gautier", role = "aut", comment = c(ORCID = "0009-0004-3581-0131")),
     person("Joe", "Zhu", role = "aut", comment = c(ORCID = "0000-0001-7566-2787")),
-    person("Aksel", "Thomsen", , "oath@novonordisk.com", role = "aut")
+    person("Aksel", "Thomsen", , "oath@novonordisk.com", role = "aut"),
+    person("Shiyu", "Chen", , "shiyu.chen@atorusresearch.com", role = "aut"),
+    person("Rammprasad", "Ganapathy", , "rammprasad.ganapathy@gene.com", role = "aut")
 Description: This is not a package, but we just use this file to declare
     the dependencies of the site.
 URL: https://github.com/pharmaverse/examples
@@ -31,6 +33,7 @@ Imports:
     metacore,
     metatools,
     nestcolor,
+    pharmaverseraw,
     pharmaversesdtm,
     pharmaverseadam,
     pkglite,
@@ -39,6 +42,7 @@ Imports:
     rtables,
     rtables.officer,
     rlistings,
+    sdtm.oak,
     sparkline,
     stringr,
     shinylive,

README.md

@@ -15,8 +15,8 @@ increasingly simple.
 
 This book contains end-to-end examples of using pharmaverse packages
 together to achieve common clinical reporting analyses, such as ADaM and
-Tables/Listings/Graphs. The examples use consistent source test SDTMs
-and ADaMs from {pharmaversesdtm} and {pharmaverseadam} respectively.
+Tables/Listings/Graphs. The examples use consistent source test raw data, SDTMs
+and ADaMs from {pharmaverseraw}, {pharmaversesdtm} and {pharmaverseadam} respectively.
 
 We'll endeavour to include a selection of examples here over time, e.g.
 to help users when trying out the packages for PK/PD or Therapeutic Area

index.qmd

@@ -9,9 +9,9 @@ will ever completely cover all your needs, but by piecing them together we can
 make complex tasks increasingly simple.
 
 This book contains end-to-end examples of using pharmaverse packages together to
-achieve common clinical reporting analyses, such as ADaM and Tables/Listings/Graphs.
-The examples use consistent source test SDTMs and ADaMs from `{pharmaversesdtm}`
-and `{pharmaverseadam}` respectively.
+achieve common clinical reporting analyses, such as SDTM, ADaM and Tables/Listings/Graphs.
+The examples use consistent source test raw datasets from `{pharmaverseraw}`, 
+SDTMs and ADaMs from `{pharmaversesdtm}` and `{pharmaverseadam}` respectively.
 
 We'll endeavour to include a selection of examples here over time, e.g. to help
 users when trying out the packages for PK/PD or Therapeutic Area specific

inst/WORDLIST

@@ -2,6 +2,7 @@ aarch
 ABLFL
 ACTARM
 ACTARMCD
+aCRF
 adae
 ADAE
 adam
@@ -38,20 +39,50 @@ ADVS
 ADY
 ae
 AE
+AEACN
+AEBDSYCD
 AEBODSYS
 AEDECOD
+AEDIS
+AEDTC
+AEDTCOL
+AEENDAT
 AEENDTC
+AEENDY
+AEHLGT
+AEHLGTCD
+AEHLT
+AEHLTCD
+AELLT
+AELLTCD
 AEN
 AENDT
 AENDTF
 AENDTM
 AENDY
 AEOUT
+AEOUTCOME
+AEPTCD
+AEREL
 AEs
+AESCAN
+AESCNO
+AESCONG
+AESDISAB
+AESDTH
 AESEQ
+AESER
 AESEV
 AESEVN
+AESHOSP
+AESLIFE
+AESOC
+AESOCCD
+AESOD
+AESTDAT
 AESTDTC
+AESTDY
+AETERM
 AETHNIC
 AETHNICN
 AFRLT
@@ -86,6 +117,7 @@ args
 ARMCD
 arrlt
 ARRLT
+articlehere
 aseq
 ASEQ
 ASEVN
@@ -147,16 +179,19 @@ callr
 categorizationvars
 cdisc
 CDISC
+CDISCPILOT
 chgpchg
 CKD
 cli
+clst
 CMT
 CNSDTDSC
 codebases
 codelist
 codelists
 COHORTC
 colcounts
+conf
 config
 COUNTRYL
 COUNTRYN
@@ -169,13 +204,16 @@ creat
 CREAT
 CREATBL
 creatu
+CRF
 css
+csv
 ctype
 cust
 cv
 cyclocomp
 cyl
 darwin
+dat
 datacutr
 dataname
 datanames
@@ -185,20 +223,27 @@ Datetime
 datetimes
 davidblair
 de
+DEATHDT
 deathvars
 deliverables
 demog
+der
+derivedvars
 desc
 devtools
 df
 DF
+dformat
+DIA
 diabp
 DIABP
 dir
 disp
 dispovars
 dm
 DM
+DMDTC
+DMDY
 dmvars
 DOSEA
 DOSEP
@@ -208,10 +253,12 @@ ds
 DS
 DSCAT
 DSDECOD
+DSDTCOL
 DSST
 DSSTDT
 DSSTDTC
 DSTERM
+DSTMCOL
 dt
 dtc
 DTC
@@ -238,6 +285,9 @@ DVL
 dy
 dylib
 DYTPE
+ec
+ECENDAT
+ECSTDAT
 ectd
 egfr
 EGFRBL
@@ -295,6 +345,7 @@ grp
 gsub
 gts
 gtsummary
+hardcode
 HashSum
 hia
 hjust
@@ -303,7 +354,9 @@ HTBLU
 htmltools
 htmlwidgets
 httpuv
+IC
 iconv
+ifelse
 iframe
 init
 inputId
@@ -339,6 +392,7 @@ lintR
 lm
 loaddata
 loadspecs
+LOC
 localdomain
 lockfile
 logr
@@ -352,6 +406,9 @@ lwr
 lyt
 macOS
 magrittr
+maprest
+maptopic
+mapvars
 maxdate
 MDV
 MedDRA
@@ -360,7 +417,9 @@ metacore
 Metacore
 metatools
 miniUI
+minumum
 mmHg
+mmm
 Mosteller
 MRRLT
 mtcars
@@ -389,8 +448,10 @@ nSampling
 nTime
 num
 NXRLT
+oakidvars
 OCC
 occflags
+OID
 onco
 ONCO
 ontrtfl
@@ -414,6 +475,7 @@ params
 paramval
 paramvars
 PARCAT
+PATNUM
 pc
 PCDTC
 pchg
@@ -439,6 +501,7 @@ Pharmacokinetic
 pharmaverse
 Pharmaverse
 pharmaverseadam
+pharmaverseraw
 pharmaversesdtm
 PHUSE
 pkgbuild
@@ -485,24 +548,33 @@ rangeind
 Rcpp
 rds
 reactable
+readct
+readdata
 readline
 README
 readr
 recist
 RECIST
 RECSEQ
+refdates
+refdt
 REGIONCAT
 REGIONx
 renderPlot
 renderUI
 renv
 Renv
+repeatsteps
 repo
 reproducibility
 req
 rex
 RFENDTC
+RFICDTC
+RFPENDTC
 RFSTDTC
+RFXENDTC
+RFXSTDTC
 rlang
 rlistings
 RLTU
@@ -525,6 +597,7 @@ sas
 SCRFDT
 sd
 sdi
+sdtm
 SDTM
 sdtmchecks
 SDTMs
@@ -563,19 +636,26 @@ SUBJIDN
 SUBJTYP
 SUBJTYPC
 subperiods
+SUBPOS
+substr
 summarise
 summaryrec
 suppdm
 SUPPDM
 suppressWarnings
+SYS
 sysbp
 SYSBP
 tabset
 TBILBL
 tbl
 tcl
 tempdir
+TEMPLOC
 TESTCD
+tformat
+tgdt
+tgt
 thevalidatoR
 tibble
 tidyr
@@ -589,8 +669,11 @@ TLGs
 tm
 tmc
 tmp
+TMPTC
 topleft
 toupper
+TPT
+TPTNUM
 traceback
 TRE
 treatmentvars
@@ -640,16 +723,28 @@ viewerHeight
 VISITDY
 VISITNUM
 VSBLFL
+VSCAT
 VSDTC
+VSDY
+VSELTM
 vslb
+VSLOC
+VSORRES
+VSORRESU
+VSORRRES
+VSPOS
 VSSEQ
+VSSRESC
 VSSTAT
+VSSTRESC
 VSSTRESN
 VSSTRESU
 VSTEST
 VSTESTCD
 VSTPT
 VSTPTNUM
+VSTPTREF
+VTLD
 WebR
 WG
 withr
@@ -671,6 +766,7 @@ xz
 yaml
 yml
 yn
+yyyy
 zlib
 zzzadlb
 AESER