The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

AE-Tbls

Vignette Build Datetime

message(paste0('Datetime: ',Sys.Date(),':',Sys.time()))
#> Datetime: 2026-01-21:2026-01-21 09:13:08

Load Libraries

library(repfun)
library(dplyr)
library(DT)
library(kableExtra)

Set Up the Reporting Environment

tmpdr <- tempdir()
datdir <- file.path(gsub("\\","/",tmpdr,fixed=TRUE),"datdir")
dir.create(datdir,showWarnings=FALSE)
repfun::copydata(datdir)
setup <- function(tlfid){
 repfun::rs_setup(
   D_DATADATE=Sys.Date(),
   D_DSPLYNUM=tlfid,
   D_FOOT1='1.) Only treatment emergent events related to lipids are displayed.',
   D_FOOT2='2.) Subjects are only counted once within each body system and preferred term.',
   D_KEEPPOPVARS=c('STUDYID','USUBJID','SAFFL'),
   D_OUTFILE=paste0(tmpdr,"/t_ru_list_",tlfid,".rtf"),
   D_PGMPTH="~/vignettes/AE-Tbls.Rmd",
   D_STUDYID='ABCXYZPDQ',
   D_POP="SAFFL",
   D_POPDATA=repfun::adsl %>% dplyr::filter(SAFFL =='Y') %>% 
             dplyr::mutate(TRT01AN=ifelse(TRT01A=='Placebo',1,ifelse(TRT01A=='Xanomeline Low Dose',2,3))) %>%
             repfun::ru_labels(varlabels=list('TRT01AN'='Actual Treatment for Period 01 (n)')),
   D_POPLBL="Safety",
   D_SUBJID=c("STUDYID","USUBJID"),
   D_TITLE1=paste0('Table ',tlfid,': Summary of Treatment Emergent Adverse Events'),
   R_DDDATA=paste0(tmpdr,'/t_ru_list_',tlfid,'.rds'),
   R_ADAMDATA=datdir)
}

Read in ADAE and Generate Frequency Counts and Percents

setup(1)
tbl1dd <- paste0(tmpdr,"/t_ru_list_1.rds")
aesum <- repfun::ru_freq(repfun:::rfenv$adamdata$adae.rda() %>% dplyr::select(-SAFFL) %>% 
                   repfun::ru_getdata(repfun:::rfenv$G_POPDATA, c("STUDYID", "USUBJID"), keeppopvars=c("TRT01AN", "TRT01A")),
                 dsetindenom=repfun:::rfenv$G_POPDATA,
                 countdistinctvars=c('STUDYID','USUBJID'),
                 groupbyvarsnumer=c('TRT01AN','TRT01A','AEBODSYS','AEDECOD'),
                 anyeventvars = c('AEBODSYS','AEDECOD'),
                 anyeventvalues = c('ANY EVENT','ANY EVENT'),
                 groupbyvarsdenom=c('TRT01AN'),
                 resultstyle="NUMERPCT",
                 totalforvar=c('TRT01AN'),
                 totalid=99,
                 totaldecode='Total',
                 codedecodevarpairs=c("TRT01AN", "TRT01A"),
                 resultpctdps=0) %>% 
  dplyr::arrange(TRT01AN,TRT01A,AEBODSYS,tt_summarylevel,AEDECOD,NUMERCNT,DENOMCNT) %>% 
  repfun::ru_align("tt_result")

Generate Table 1: Summary of Adverse Events [Keywords: NoWidows (Does not fit), Simple Paging Default, OrderVars, Denorm]

repfun::ru_list(aesum,
        columns=c('AEBODSYS','AEDECOD','tt_01','tt_02','tt_03','tt_99'),
        nowidowvar='AEBODSYS',
        widths=c(5.5,4.5,1.75,1.9,1.9,1.75),
        skipvars=c('AEBODSYS'),
        centrevars=c('tt_01','tt_02','tt_03','tt_99'),
        ordervars=c('AEBODSYS','tt_summarylevel','AEDECOD'),
        noprintvars=c('tt_summarylevel'),
        denormyn='Y',
        varsToDenorm=c('tt_result'),
        groupByVars=c('AEBODSYS','tt_summarylevel','AEDECOD'),
        acrossVar="TRT01AN",
        acrossVarLabel="TRT01A",
        acrossColVarPrefix='tt_',
        dddatasetlabel=paste0('DD Dataframe for AE Table ',repfun:::rfenv$G_DSPLYNUM),
        lpp=23)

Select Page(s) of Table 1 (1)

Table 1 (pg 1) Image
Table 1 (pg 1) Image

DDDATA for Table 1 (First few obs)

t1 <- readRDS(repfun:::rfenv$G_DDDATA) %>% dplyr::filter(AEDECOD != '') %>% dplyr::filter(row_number()<=10)
lbls <- sapply(t1,function(x){attr(x,"label")})
names(t1) <- paste(names(lbls),lbls,sep=": ")
DT::datatable(
  t1, extensions = 'FixedColumns',
  options = list(
  dom = 't',
  pageLength=1000,
  scrollY = 300,
  scrollX = TRUE,
  scrollCollapse = TRUE
))

Table 1 RTF

Download

Table 1 PDF

View

Generate Table 2: Summary of Adverse Events [Keywords: NoWidows, SkipVars, OrderVars, Denorm]

setup(2)
SOCterms <- aesum %>% distinct(AEBODSYS,AEDECOD)
SOCcnts <- table(SOCterms$AEBODSYS)
repfun::ru_list(aesum %>% dplyr::filter(!(AEBODSYS %in% names(SOCcnts[SOCcnts>=20]))),
        columns=c('AEBODSYS','AEDECOD','tt_01','tt_02','tt_03','tt_99'),
        nowidowvar='AEBODSYS',
        widths=c(5.5,4.5,1.75,1.9,1.9,1.75),
        skipvars=c('AEBODSYS'),
        centrevars=c('tt_01','tt_02','tt_03','tt_99'),
        ordervars=c('AEBODSYS','tt_summarylevel','AEDECOD'),
        noprintvars=c('tt_summarylevel'),
        denormyn='Y',
        varsToDenorm=c('tt_result'),
        groupByVars=c('AEBODSYS','tt_summarylevel','AEDECOD'),
        acrossVar="TRT01AN",
        acrossVarLabel="TRT01A",
        acrossColVarPrefix='tt_',
        dddatasetlabel=paste0('DD Dataframe for AE Table ',repfun:::rfenv$G_DSPLYNUM),
        lpp=24)

Select Page(s) of Table 2 (1)

Table 2 (pg 1) Image
Table 2 (pg 1) Image

DDDATA for Table 2 (First few obs)

t2 <- readRDS(repfun:::rfenv$G_DDDATA) %>% dplyr::filter(AEDECOD != '') %>% dplyr::filter(row_number()<=10)
lbls <- sapply(t2,function(x){attr(x,"label")})
names(t2) <- paste(names(lbls),lbls,sep=": ")
datatable(
  t2, extensions = 'FixedColumns',
  options = list(
  dom = 't',
  pageLength=1000,
  scrollY = 300,
  scrollX = TRUE,
  scrollCollapse = TRUE
))

Table 2 RTF

Download

Table 2 PDF

View

Generate Table 3: Summary of Adverse Events by Gender [Keywords: Pageby, NoWidows, Skipvars, ShareColVars, NoData]

setup(3)
df <- readRDS(file=tbl1dd) %>% 
  dplyr::select(-PAGEVAR) %>% dplyr::filter(!(AEDECOD == '')) %>% 
  dplyr::filter(!(AEBODSYS %in% names(SOCcnts[SOCcnts>=15])))
dfpg <- rbind(df %>% dplyr::mutate(AESER='Yes'), df %>% dplyr::mutate(AESER='No')) 
attr(dfpg[['AESER']],'label') <- 'Serious AE (Y/N)'
mytbls <- list('Gender: Male'=dfpg[0,], 'Gender: Female'=dfpg)
repfun::ru_list(dsetin=mytbls,
        columns=c('AESER','AEBODSYS','AEDECOD','tt_01','tt_02','tt_03','tt_99'),
        nowidowvar='AEBODSYS',
        sharecolvars=c('AESER','AEBODSYS','AEDECOD'),
        widths=c(7,1.65,1.9,1.9,1.65),
        skipvars=c('AEBODSYS'),
        centrevars=c('tt_01','tt_02','tt_03','tt_99'),
        lpp = 30,
        dddatasetlabel=paste0('DD Dataframe for AE Table ',repfun:::rfenv$G_DSPLYNUM))

Select Page(s) of Table 3 (1)

Table 3 (pg 1) Image
Table 3 (pg 1) Image

DDDATA for Table 3 (First few obs)

t3 <- readRDS(repfun:::rfenv$G_DDDATA) %>% dplyr::filter(gsub("\\s+", "",STACKVAR) != '') %>% dplyr::filter(row_number()<=10)
lbls <- sapply(t3,function(x){attr(x,"label")})
names(t3) <- paste(names(lbls),lbls,sep=": ")
datatable(
  t3, extensions = 'FixedColumns',
  options = list(
  dom = 't',
  pageLength=1000,
  scrollY = 300,
  scrollX = TRUE,
  scrollCollapse = TRUE
))

Table 3 RTF

Download

Table 3 PDF

View

Generate Table 4: Summary of Adverse Events when Data Frame is Empty [Keywords: NoData]

setup(4)
df <- readRDS(file=tbl1dd) %>% dplyr::select(-PAGEVAR) %>% dplyr::filter(!(AEDECOD == '')) 
repfun::ru_list(dsetin=df[0,], 
        columns=c('AEBODSYS','AEDECOD','tt_01','tt_02','tt_03','tt_99'), 
        ordervars=c('AEBODSYS','AEDECOD'), 
        orderdata=TRUE, 
        widths=c(7,5,2,2,2,2), 
        dddatasetlabel=paste0('DD Dataframe for AE Table ',repfun:::rfenv$G_DSPLYNUM))

Select Page(s) of Table 4 (1)

Table 4 (pg 1) Image
Table 4 (pg 1) Image

Note: There is no DDDATA for Table 4

Table 4 RTF

Download

Table 4 PDF

View

Generate Table 5: Summary of Adverse Events [Keywords: Stackvars, NoWidows, SkipVars, PageByVar, PageVar]

setup(5)

df <- readRDS(file=tbl1dd) %>% 
  dplyr::select(-PAGEVAR,-tt_99) %>% dplyr::filter(!(AEDECOD == '')) %>%
  dplyr::filter(!(AEBODSYS %in% names(SOCcnts[SOCcnts>=15]))) %>%
  dplyr::group_by(AEBODSYS) %>% 
  dplyr::mutate(AESOC=ifelse(row_number()==1,paste0(AEBODSYS,': '),gsub('.',' ',paste0(AEBODSYS,': ')))) %>%
  dplyr::mutate(AESOC=ifelse(nchar(AEBODSYS)>55,gsub('^[ ][ ]*','  ',AESOC),AESOC)) %>% 
  dplyr::select(AEBODSYS,AESOC,everything())
dfpg <- rbind(df %>% dplyr::mutate(MYPAGEVAR=1),
              df %>% dplyr::mutate(MYPAGEVAR=2)) %>% 
        repfun::ru_labels(varlabels=list('AESOC'='Body System: ','MYPAGEVAR'='My Page Variable'))

mytbls <- list('Gender: Male'=dfpg,
               'Gender: Female'=dfpg %>%
                                repfun::ru_labels(varlabels=lapply(sapply(dfpg,function(x){attr(x,"label")}),function(x) gsub('X','Y',x))))

repfun::ru_list(dsetin=mytbls,
               stackvar1=list(varsin=c('AESOC','AEDECOD'), varout='SYSPREF', sepc='', splitc=''),
               noprintvars=c('AEBODSYS'),
               columns=c('AEBODSYS','SYSPREF','tt_01','tt_02','tt_03'),
               nowidowvar='AEBODSYS',
               widths=c(13,2,2.3,2.3),
               skipvars=c('AEBODSYS'),
               centrevars=c('tt_01','tt_02','tt_03'),
               pagevars=c('MYPAGEVAR'),
               computebeforepagelines="paste0('This is page value: ',MYPAGEVAR)",
               lpp = 25,
               dddatasetlabel=paste0('DD Dataframe for AE Table ',repfun:::rfenv$G_DSPLYNUM))

Select Page(s) of Table 5 (1)

Table 5 (pg 1) Image
Table 5 (pg 1) Image

DDDATA for Table 5 (First few obs)

t5 <- readRDS(repfun:::rfenv$G_DDDATA) %>% dplyr::filter(SYSPREF != '') %>% dplyr::filter(row_number()<=10)
lbls <- sapply(t5,function(x){attr(x,"label")})
names(t5) <- paste(names(lbls),lbls,sep=": ")
datatable(
  t5, extensions = 'FixedColumns',
  options = list(
  dom = 't',
  pageLength=1000,
  scrollY = 300,
  scrollX = TRUE,
  scrollCollapse = TRUE
))

Table 5 RTF

Download

Table 5 PDF

View

Generate Table 6: Summary of Adverse Events [Keywords: NoWidows, SkipVars, PageByVar, PageByLabel]

setup(6)

df <- readRDS(file=tbl1dd) %>% dplyr::select(-PAGEVAR) %>% 
  dplyr::filter(!(AEDECOD == '') & !(AEBODSYS %in% names(SOCcnts[SOCcnts>=15]))) 
dfpg <- rbind(df %>% dplyr::mutate(MYPAGEVAR=1),df %>% dplyr::mutate(MYPAGEVAR=2)) %>% repfun::ru_labels(varlabels=list('MYPAGEVAR'='My Page Variable'))

repfun::ru_list(dsetin=dfpg,
        columns=c('AEBODSYS','AEDECOD','tt_01','tt_02','tt_03','tt_99'),
        widths=c(5.5,4.5,2,2,2,2),
        nowidowvar='AEBODSYS',
        skipvars=c('AEBODSYS'),
        centrevars=c('tt_01','tt_02','tt_03','tt_99'),
        pagevars=c('MYPAGEVAR'),
        computebeforepagelines="paste0('This is page value: ',MYPAGEVAR)",
        lpp=23,
        dddatasetlabel=paste0('DD Dataframe for AE Table ',repfun:::rfenv$G_DSPLYNUM))

Select Page(s) of Table 6 (1)

Table 6 (pg 1) Image
Table 6 (pg 1) Image

DDDATA for Table 6 (First few obs)

t6 <- readRDS(repfun:::rfenv$G_DDDATA) %>% dplyr::filter(AEDECOD != '') %>% dplyr::filter(row_number()<=10)
lbls <- sapply(t6,function(x){attr(x,"label")})
names(t6) <- paste(names(lbls),lbls,sep=": ")
datatable(
  t6, extensions = 'FixedColumns',
  options = list(
  dom = 't',
  pageLength=1000,
  scrollY = 300,
  scrollX = TRUE,
  scrollCollapse = TRUE
))

Table 6 RTF

Download

Table 6 PDF

View

Generate Table 7: Summary of Adverse Events [Keywords: NoWidows, SkipVars, ByVars, PageVars, ComputeBeforePageLines (2 page-by variables)]

setup(7)

df <- readRDS(file=tbl1dd) %>% dplyr::select(-PAGEVAR) %>%
  dplyr::filter(!(AEDECOD == '') & !(AEBODSYS %in% names(SOCcnts[SOCcnts>=15])))

dfpg <- rbind(df %>% dplyr::mutate(MYPAGEVAR1=1,MYPAGEVAR2=1),
              df %>% dplyr::mutate(MYPAGEVAR1=1,MYPAGEVAR2=2),
              df %>% dplyr::mutate(MYPAGEVAR1=2,MYPAGEVAR2=3),
              df %>% dplyr::mutate(MYPAGEVAR1=2,MYPAGEVAR2=4)) %>%
  repfun::ru_labels(varlabels=list('MYPAGEVAR'='My Page Variable'))

repfun::ru_list(dsetin=dfpg,
        columns=c('AEBODSYS','AEDECOD','tt_01','tt_02','tt_03','tt_99'),
        nowidowvar='AEBODSYS',
        widths=c(6,4,2,2,2,2),
        skipvars=c('AEBODSYS'),
        centrevars=c('tt_01','tt_02','tt_03','tt_99'),
        byvars=c('MYPAGEVAR2'),
        pagevars=c('MYPAGEVAR1'),
        computebeforepagelines="paste0('This is page value 1: ',MYPAGEVAR1,' and this is page value 2: ',MYPAGEVAR2)",
        lpp=23,
        dddatasetlabel=paste0('DD Dataframe for AE Table ',repfun:::rfenv$G_DSPLYNUM))

Select Page(s) of Table 7 (1)

Table 7 (pg 1) Image
Table 7 (pg 1) Image

DDDATA for Table 7 (First few obs)

t7 <- readRDS(repfun:::rfenv$G_DDDATA) %>% dplyr::filter(AEDECOD != '') %>% dplyr::filter(row_number()<=10)
lbls <- sapply(t7,function(x){attr(x,"label")})
names(t7) <- paste(names(lbls),lbls,sep=": ")
datatable(
  t7, extensions = 'FixedColumns',
  options = list(
  dom = 't',
  pageLength=1000,
  scrollY = 300,
  scrollX = TRUE,
  scrollCollapse = TRUE
))

Table 7 RTF

Download

Table 7 PDF

View

Generate Table 8: Summary of Adverse Events [Keywords: NoWidows, SkipVars, ShareColVars, PageBy (w/Changing Column Headers)]

setup(8)
df <- readRDS(file=tbl1dd) %>%
  dplyr::select(-PAGEVAR) %>%
  dplyr::filter(!(AEDECOD == '') & !(AEBODSYS %in% names(SOCcnts[SOCcnts>=15])))

mytbls <- list('Gender: Male'=df,
               'Gender: Female'=df %>% 
                 repfun::ru_labels(varlabels=lapply(sapply(df,function(x){attr(x,"label")}),function(x) gsub('X','Y',x))))

repfun::ru_list(dsetin=mytbls,
        columns=c('AEBODSYS','AEDECOD','tt_01','tt_02','tt_03','tt_99'),
        nowidowvar='AEBODSYS',
        sharecolvars=c('AEBODSYS','AEDECOD'),
        widths=c(8.0,2,2,2,2),
        skipvars=c('AEBODSYS'),
        centrevars=c('tt_01','tt_02','tt_03','tt_99'),
        lpp=28,
        dddatasetlabel=paste0('DD Dataframe for AE Table ',repfun:::rfenv$G_DSPLYNUM))

Select Page(s) of Table 8 (1)

Table 8 (pg 1) Image
Table 8 (pg 1) Image

DDDATA for Table 8 (First few obs)

t8 <- readRDS(repfun:::rfenv$G_DDDATA) %>% dplyr::filter(gsub("\\s+", "", STACKVAR) != '') %>% dplyr::filter(row_number()<=10)
lbls <- sapply(t8,function(x){attr(x,"label")})
names(t8) <- paste(names(lbls),lbls,sep=": ")
datatable(
  t8, extensions = 'FixedColumns',
  options = list(
  dom = 't',
  pageLength=1000,
  scrollY = 300,
  scrollX = TRUE,
  scrollCollapse = TRUE
))

Table 8 RTF

Download

Table 8 PDF

View

Generate Table 9: Summary of Adverse Events [Keywords: NoWidows, SkipVars, ShareColVars, Update Column Labels]

setup(9)

df <- readRDS(file=tbl1dd) %>%
  dplyr::select(-PAGEVAR) %>%
  dplyr::filter(!(AEDECOD == '') & !(AEBODSYS %in% names(SOCcnts[SOCcnts>=15])))

repfun::ru_list(dsetin=df,
        columns=c('AEBODSYS','AEDECOD','tt_01','tt_02','tt_03','tt_99'),
        nowidowvar='AEBODSYS',
        widths=c(8.0,2,2,2,2),
        skipvars=c('AEBODSYS'),
        sharecolvars=c('AEBODSYS','AEDECOD'),
        centrevars=c('tt_01','tt_02','tt_03','tt_99'),
        labels=list('AEDECOD'='New AEDECOD Label', 'AEBODSYS'='New AEBODSYS Label'),
        lpp=28,
        dddatasetlabel=paste0('DD Dataframe for AE Table ',repfun:::rfenv$G_DSPLYNUM))

Select Page(s) of Table 9 (1)

Table 9 (pg 1) Image
Table 9 (pg 1) Image

DDDATA for Table 9 (First few obs)

t9 <- readRDS(repfun:::rfenv$G_DDDATA) %>% dplyr::filter(gsub("\\s+", "", STACKVAR) != '') %>% dplyr::filter(row_number()<=10)
lbls <- sapply(t9,function(x){attr(x,"label")})
names(t9) <- paste(names(lbls),lbls,sep=": ")
datatable(
  t9, extensions = 'FixedColumns',
  options = list(
  dom = 't',
  pageLength=1000,
  scrollY = 300,
  scrollX = TRUE,
  scrollCollapse = TRUE
))

Table 9 RTF

Download

Table 9 PDF

View

Generate Table 10: Summary of Adverse Events [Keywords: NoWidows, SkipVars, ShareColVars, Two PageByVars, ReOrder Pages]

setup(10)

df <- readRDS(file=tbl1dd) %>%
  dplyr::select(-PAGEVAR) %>%
  dplyr::filter(!(AEDECOD == '') & !(AEBODSYS %in% names(SOCcnts[SOCcnts>=15])))

dfpg <- rbind(df %>% dplyr::mutate(MYPAGEVAR1='1:XYZ',MYPAGEVAR2='1:JKL'),
              df %>% dplyr::mutate(MYPAGEVAR1='1:XYZ',MYPAGEVAR2='2:GHI'),
              df %>% dplyr::mutate(MYPAGEVAR1='2:UVW',MYPAGEVAR2='3:DEF'),
              df %>% dplyr::mutate(MYPAGEVAR1='2:UVW',MYPAGEVAR2='4:ABC')) %>%
  repfun::ru_labels(varlabels=list('MYPAGEVAR1'='My Page Variable 1',
                           'MYPAGEVAR2'='My Page Variable 2'))

repfun::ru_list(dsetin=dfpg,
        columns=c('AEBODSYS','AEDECOD','tt_01','tt_02','tt_03','tt_99'),
        nowidowvar='AEBODSYS',
        sharecolvars=c('AEBODSYS','AEDECOD'),
        widths=c(8,2,2,2,2),
        skipvars=c('AEBODSYS'),
        centrevars=c('tt_01','tt_02','tt_03','tt_99'),
        pagevars=c('MYPAGEVAR1','MYPAGEVAR2'),
        lpp=27,
        computebeforepagelines="paste0('This is page value 1: ',
                                sub('[0-9]:','',MYPAGEVAR1),
                                ' and this is page value 2: ',
                                sub('[0-9]:','',MYPAGEVAR2))",
        dddatasetlabel=paste0('DD Dataframe for AE Table ',repfun:::rfenv$G_DSPLYNUM))

Select Page(s) of Table 10 (1)

Table 10 (pg 1) Image
Table 10 (pg 1) Image

DDDATA for Table 10 (First few obs)

t10 <- readRDS(repfun:::rfenv$G_DDDATA) %>% dplyr::filter(gsub("\\s+", "", STACKVAR) != '') %>% dplyr::filter(row_number()<=10)
lbls <- sapply(t10,function(x){attr(x,"label")})
names(t10) <- paste(names(lbls),lbls,sep=": ")
datatable(
  t10, extensions = 'FixedColumns',
  options = list(
  dom = 't',
  pageLength=1000,
  scrollY = 300,
  scrollX = TRUE,
  scrollCollapse = TRUE
))

Table 10 RTF

Download

Table 10 PDF

View

Generate Table 11: Summary of Adverse Events [Keywords: SkipVars, ShareColVars]

setup(11)

df <- readRDS(file=tbl1dd) %>%
  dplyr::select(-PAGEVAR) %>% dplyr::filter(!(AEDECOD == '')) 
repfun::ru_list(dsetin=df,
        columns=c('AEBODSYS','AEDECOD','tt_01','tt_02','tt_03','tt_99'),
        sharecolvars=c('AEBODSYS','AEDECOD'),
        skipvars=c('AEBODSYS'),
        widths=c(8.0,2,2,2,2),
        centrevars=c('tt_01','tt_02','tt_03','tt_99'),
        dddatasetlabel=paste0('DD Dataframe for AE Table ',repfun:::rfenv$G_DSPLYNUM))

Select Page(s) of Table 11 (1)

Table 11 (pg 1) Image
Table 11 (pg 1) Image

DDDATA for Table 11 (First few obs)

t11 <- readRDS(repfun:::rfenv$G_DDDATA) %>% dplyr::filter(gsub("\\s+", "", STACKVAR) != '') %>% dplyr::filter(row_number()<=10)
lbls <- sapply(t11,function(x){attr(x,"label")})
names(t11) <- paste(names(lbls),lbls,sep=": ")
datatable(
  t11, extensions = 'FixedColumns',
  options = list(
  dom = 't',
  pageLength=1000,
  scrollY = 300,
  scrollX = TRUE,
  scrollCollapse = TRUE
))

Table 11 RTF

Download

Table 11 PDF

View

Generate Table 12: Summary of Adverse Events [Keywords: SkipVars]

setup(12)

df <- readRDS(file=tbl1dd) %>%
  dplyr::select(-PAGEVAR) %>% dplyr::filter(!(AEDECOD == '')) 
repfun::ru_list(dsetin=df,
        columns=c('AEBODSYS','AEDECOD','tt_01','tt_02','tt_03','tt_99'),
        skipvars=c('AEBODSYS'),
        ordervars=c('AEBODSYS','AEDECOD'),
        orderdata=TRUE,
        widths=c(6,4,2,2,2,2),
        centrevars=c('tt_01','tt_02','tt_03','tt_99'),
        dddatasetlabel=paste0('DD Dataframe for AE Table ',repfun:::rfenv$G_DSPLYNUM))

Select Page(s) of Table 12 (1)

Table 12 (pg 1) Image
Table 12 (pg 1) Image

DDDATA for Table 12 (First few obs)

t12 <- readRDS(repfun:::rfenv$G_DDDATA) %>% dplyr::filter(AEDECOD != '') %>% dplyr::filter(row_number()<=10)
lbls <- sapply(t12,function(x){attr(x,"label")})
names(t12) <- paste(names(lbls),lbls,sep=": ")
datatable(
  t12, extensions = 'FixedColumns',
  options = list(
  dom = 't',
  pageLength=1000,
  scrollY = 300,
  scrollX = TRUE,
  scrollCollapse = TRUE
))

Table 12 RTF

Download

Table 12 PDF

View

Generate Table 13: Summary of Adverse Events [Keywords: SkipVars, NoWidowVars, ByVar, PageVar, No Column Sharing]

setup(13)

df <- readRDS(file=tbl1dd) %>%
  dplyr::select(-PAGEVAR) %>%
  dplyr::filter(!(AEDECOD == '') & !(AEBODSYS %in% names(SOCcnts[SOCcnts>=15])))

dfpg <- rbind(df %>% dplyr::mutate(MYPAGEVAR1=1,MYPAGEVAR2=1),
              df %>% dplyr::mutate(MYPAGEVAR1=1,MYPAGEVAR2=2),
              df %>% dplyr::mutate(MYPAGEVAR1=2,MYPAGEVAR2=3),
              df %>% dplyr::mutate(MYPAGEVAR1=2,MYPAGEVAR2=4))

repfun::ru_list(dsetin=dfpg,
        columns=c('AEBODSYS','AEDECOD','tt_01','tt_02','tt_03','tt_99'),
        nowidowvar='AEBODSYS',
        skipvars='AEBODSYS',
        centrevars=c('tt_01','tt_02','tt_03','tt_99'),
        byvars=c('MYPAGEVAR2'),
        pagevars=c('MYPAGEVAR1'),
        widths=c(6,4,2,2,2,2),
        lpp=23,
        computebeforepagelines="paste0('This is page value 1: ',MYPAGEVAR1,' and this is page value 2: ',MYPAGEVAR2)",
        dddatasetlabel=paste0('DD Dataframe for AE Table ',repfun:::rfenv$G_DSPLYNUM))

Select Page(s) of Table 13 (1)

Table 13 (pg 1) Image
Table 13 (pg 1) Image

DDDATA for Table 13 (First few obs)

t13 <- readRDS(repfun:::rfenv$G_DDDATA) %>% dplyr::filter(AEDECOD != '') %>% dplyr::filter(row_number()<=10)
lbls <- sapply(t13,function(x){attr(x,"label")})
names(t13) <- paste(names(lbls),lbls,sep=": ")
datatable(
  t13, extensions = 'FixedColumns',
  options = list(
  dom = 't',
  pageLength=1000,
  scrollY = 300,
  scrollX = TRUE,
  scrollCollapse = TRUE
))

Table 13 RTF

Download

Table 13 PDF

View

Generate Table 14: Summary of Adverse Events [Keywords: SkipVars, NoWidowVars, ByVar, PageVar, No Column Sharing]

setup(14)

df <- readRDS(file=tbl1dd) %>%
  dplyr::select(-PAGEVAR) %>%
  dplyr::filter(!(AEDECOD == ''))

dfpg <- rbind(df %>% dplyr::mutate(MYPAGEVAR1=1,MYPAGEVAR2=1),
              df %>% dplyr::mutate(MYPAGEVAR1=1,MYPAGEVAR2=2),
              df %>% dplyr::mutate(MYPAGEVAR1=2,MYPAGEVAR2=3),
              df %>% dplyr::mutate(MYPAGEVAR1=2,MYPAGEVAR2=4))

repfun::ru_list(dsetin=dfpg,
        columns=c('AEBODSYS','AEDECOD','tt_01','tt_02','tt_03','tt_99'),
        skipvars='AEBODSYS',
        ordervars=c('AEBODSYS','AEDECOD'),
        orderdata=TRUE,
        centrevars=c('tt_01','tt_02','tt_03','tt_99'),
        widths=c(6,4,2,2,2,2),
        byvars=c('MYPAGEVAR2'),
        pagevars=c('MYPAGEVAR1'),
        computebeforepagelines="paste0('This is page value 1: ',MYPAGEVAR1,' and this is page value 2: ',MYPAGEVAR2)",
        dddatasetlabel=paste0('DD Dataframe for AE Table ',repfun:::rfenv$G_DSPLYNUM))

Select Page(s) of Table 14 (1)

Table 14 (pg 1) Image
Table 14 (pg 1) Image

DDDATA for Table 14 (First few obs)

t14 <- readRDS(repfun:::rfenv$G_DDDATA) %>% dplyr::filter(AEDECOD != '') %>% dplyr::filter(row_number()<=10)
lbls <- sapply(t14,function(x){attr(x,"label")})
names(t14) <- paste(names(lbls),lbls,sep=": ")
datatable(
  t14, extensions = 'FixedColumns',
  options = list(
  dom = 't',
  pageLength=1000,
  scrollY = 300,
  scrollX = TRUE,
  scrollCollapse = TRUE
))

Table 14 RTF

Download

Table 14 PDF

View

Clean up Temporary Files

unlink(tmpdr, recursive = TRUE)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.