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Get Started

Overview of TLG Programming

tidytlg provides a framework of creating TLG outputs for clinical study report. The TLG programming workflow includes the following steps:

We will illustrate the above steps by creating a demographic table first, and then follow by examples of creating listing and graph.

Prep environment

To set up the R environment, you can set the path objects of the input folder and output folder consistently for all TLG programs. The analysis datasets and other required inputs such as the titles file and column metadata file are placed in the input folder, while the output folder will be used to store the output files. The envsetup package can be used to set up the R environment for TLG programming.

titles and footnotes

The information for titles and footnotes for each TLG can be stored in an excel file called titles.xls (see below snapshot), which will be used later to create the outputs.

column metadata

Column metadata provides the column structure of the table layout and includes the following variables:

Please see below for a snapshot of column_metadata.xlsx.

Different types of column layouts identified by different tbltype can be stored in an excel file called column_metadata.xlsx. Within each tbltype, the coldef variable defines the order of the column based on the column variable used for creating the output (typically the numeric treatment variable, TRT01PN, is used as the column variable). For example, there are 3 columns for tbltype = “type1” in the above snapshot and the column layout is defined as follows: the first column of summary statistics represents the treatment group of TRT01PN = 0 with the column header of Placebo defined by decode, the second and third columns represent the Low Dose and High Dose groups respectively with the spanning header of Xanomeline defined by the span1 variable.

Users can also include the column that is derived from combination of individual columns. For example, the tbltype of type3 include the 4th column of combined Low Dose and High Dose as well as the 5th column of total group. Please see below for the snapshot of column headers defined by type3.

We will use the adsl data from the PHUSE Test Data Factory to illustrate the creation of a demographic table.

# Prep Environment -------------------------------------------------------------------------------------
library(dplyr)
library(haven)
library(tidytlg)

# read adsl from PhUSE test data factory
testdata <- "https://github.com/phuse-org/TestDataFactory/raw/main/Updated/TDF_ADaM/"
adsl <- read_xpt(url(paste0(testdata,"adsl.xpt")))

Process data

Before generating analysis summary, the analysis data need to be processed first as shown in the code below.

# Process Data -----------------------------------------------------------------------------------------
adsl <- adsl %>%
  filter(ITTFL == "Y") %>%
  mutate(SEX = factor(SEX, levels = c("M", "F", "U"), labels = c("Male", "Female", "Unknown"))) %>%
  tlgsetup(var = "TRT01PN",
           column_metadata_file = system.file("extdata/column_metadata.xlsx", package = "tidytlg"),
           tbltype = "type3")

The above code perform the tasks below:

If you need multiple analysis datasets for creating TLG, tlgsetup will need to be applied to each dataset. Therefore, you will have a consistent column variable of colnbr for creating analysis summary.

Generate results

tidytlg provides 3 functions, univar, freq, and nested_freq, to generate analysis summary of descriptive statistics (univariate statistics and count (percentages)). For more details, please see the frequency analysis vignette("freq") and the univariate statistical analysis vignette("univar").

# Generate Results -------------------------------------------------------------------------------------

## Analysis set row
t1 <- adsl %>%
  freq(colvar = "colnbr",
       rowvar = "ITTFL",
       statlist = statlist("n"),
       subset = ITTFL == "Y",
       rowtext = "Analysis set: ITT")

## Univariate summary for AGE
t2 <- adsl %>%
  univar(colvar = "colnbr",
         rowvar = "AGE",
         statlist = statlist(c("N", "MEANSD", "MEDIAN", "RANGE", "IQRANGE")),
         decimal = 0,
         row_header = "Age, years")

## Count (percentages) for SEX
t3 <- adsl %>%
  freq(colvar = "colnbr",
       rowvar = "SEX",
       statlist = statlist(c("N","n (x.x%)")),
       row_header = "Gender")

The above function calls generate the requested analysis rows for the table output sequentially and store the results in individual objects (i.e. t1, t2, t3). The next step is to combine analysis results into a single tbl dataframe through the bind_table function call.

# Format Results ---------------------------------------------------------------------------------------

tbl <- bind_table(t1, t2, t3,
       column_metadata_file = system.file("extdata/column_metadata.xlsx", package = "tidytlg"),
       tbltype = "type3")

The above bind_table function call performs the following tasks:

Output results

The tbl data frame is the main input to the gentlg function for creating the RTF/HTML outputs.

The basic structure of tbl includes label, col1, col2, …, coln, where

All other columns contain formatting instructions to create the RTF/HTML outputs. For tweaking the formatting variables to customize the table layout, please see the vignette("tbl_manipulation") for more details.

knitr::kable(tbl)
label col1 col2 col3 col4 col5 row_type anbr indentme roworder newrows newpage
Analysis set: ITT 86 84 84 168 254 HEADER 1 0 1 0 0
Age, years HEADER 2 0 1 1 0
N 86 84 84 168 254 N 2 1 2 0 0
Mean (SD) 75.2 (8.59) 75.7 (8.29) 74.4 (7.89) 75.0 (8.09) 75.1 (8.25) VALUE 2 2 3 0 0
Median 76.0 77.5 76.0 77.0 77.0 VALUE 2 2 4 0 0
Range (52; 89) (51; 88) (56; 88) (51; 88) (51; 89) VALUE 2 2 5 0 0
IQ range (69.0; 82.0) (71.0; 82.0) (70.5; 80.0) (71.0; 81.0) (70.0; 81.0) VALUE 2 2 6 0 0
Gender HEADER 3 0 1 1 0
N 86 84 84 168 254 N 3 1 2 0 0
Male 33 (38.4%) 34 (40.5%) 44 (52.4%) 78 (46.4%) 111 (43.7%) VALUE 3 2 3 0 0
Female 53 (61.6%) 50 (59.5%) 40 (47.6%) 90 (53.6%) 143 (56.3%) VALUE 3 2 4 0 0
Unknown 0 0 0 0 0 VALUE 3 2 5 0 0

The gentlg function call below will create the rtf output using the tblid as the file name in the folder defined by the opath argument. Please ensure that the titles.xls file contains the records of titles and footnotes for the specified tblid.

tblid <- "Table01"

gentlg(huxme       = tbl,
       opath       = file.path(working_dir),
       file        = tblid,
       orientation = "landscape",
       title_file = system.file("extdata/titles.xls", package = "tidytlg"))

To create the html output, users need to specify the format argument as “HTML” and print.hux argument as FALSE in the gentlg call.

gentlg(huxme       = tbl,
       format      = "HTML",
       print.hux = FALSE,
       file        = tblid,
       orientation = "landscape",
       title_file = system.file("extdata/titles.xls", package = "tidytlg"))
#> [[1]]
#>    <div style='border-top :1pt solid; border-bottom :1pt solid; '>             
#>    <div style = "text-indent: -36px; padding-left: 36px;"> Table01:            
#>    &emsp; Demographic and Baseline Characteristics; Intent-to-treat            
#>    Analysis Set</div>                                                          
#>                                                                <div            
#>                                                         style='border-bott     
#>                                                           om:1pt solid'>       
#>                                                             Xanomeline         
#>                                               <div        <div        <div     
#>                                             style='bo   style='bo   style='bo  
#>                                             rder-bott   rder-bott   rder-bott  
#>                                              om:1pt      om:1pt      om:1pt    
#>                                              solid'>     solid'>     solid'>   
#>                                              Placebo    Low Dose    High Dose  
#>    <div style='text-indent: -17.76px;          86          84          84      
#>    padding-left: 17.76px'> Analysis set:                                       
#>    ITT                                                                         
#>    <div style='text-indent: -17.76px;                                          
#>    padding-left: 17.76px'>                                                     
#>    <div style='text-indent: -17.76px;                                          
#>    padding-left: 17.76px'> Age, years                                          
#>    <div style='text-indent: -17.76px;          86          84          84      
#>    padding-left: 35.52px'> N                                                   
#>    <div style='text-indent: -17.76px;         75.2        75.7        74.4     
#>    padding-left: 53.28px'> Mean (SD)         (8.59)      (8.29)      (7.89)    
#>    <div style='text-indent: -17.76px;         76.0        77.5        76.0     
#>    padding-left: 53.28px'> Median                                              
#>    <div style='text-indent: -17.76px;       (52; 89)    (51; 88)    (56; 88)   
#>    padding-left: 53.28px'> Range                                               
#>    <div style='text-indent: -17.76px;        (69.0;      (71.0;      (70.5;    
#>    padding-left: 53.28px'> IQ range           82.0)       82.0)       80.0)    
#>    <div style='text-indent: -17.76px;                                          
#>    padding-left: 17.76px'>                                                     
#>    <div style='text-indent: -17.76px;                                          
#>    padding-left: 17.76px'> Gender                                              
#>    <div style='text-indent: -17.76px;          86          84          84      
#>    padding-left: 35.52px'> N                                                   
#>    <div style='text-indent: -17.76px;          33          34          44      
#>    padding-left: 53.28px'> Male              (38.4%)     (40.5%)     (52.4%)   
#>    <div style='text-indent: -17.76px;          53          50          40      
#>    padding-left: 53.28px'> Female            (61.6%)     (59.5%)     (47.6%)   
#>    <div style='text-indent: -17.76px;           0           0           0      
#>    padding-left: 53.28px'> Unknown                                             
#>    <div style='border-top:1pt solid;'> <br />Key: IQ = interquartile           
#>    Note: N reflects non-missing values                                         
#>    <div style='border-bottom:1pt solid'> [table01.html][] 14JUN2024,           
#>                                                                18:46           
#> 
#> Column names: label, col1, col2, col3, col4, col5
#> 
#> 4/6 columns shown.

Users can also include superscripts, subscripts, or line breaks via unicode. Please see the vignette("symbols") for more details. Besides using univar, freq, and nested_freq functions to create the tbl dataframe, users can use other R packages to create analysis results and perform data wrangling to fit the tbl structure, which can be passed into the gentlg function call for generating the desired outputs.

Listing programming

The above workflow can also be used to create listings. Users need to prepare the data and assign it to tbl. In the gentlg function, users need to pay attention to:

# Prep Environment ---------------------------------------------------------------------------------------
library(dplyr)
library(haven)
library(tidytlg)

adsl <- cdisc_adsl
adae <- cdisc_adae

# Process Data --------------------------------------------------------------------------------------------
adsl <- adsl %>%
  filter(SAFFL == "Y") %>%
  select(USUBJID, SAFFL, TRT01AN, TRT01A)

adae <- adae %>%
  filter(SAFFL == "Y" & TRTEMFL == "Y") %>%
  mutate(BSPT  = paste(AEBODSYS, "[", AEDECOD, "]"),
         SAEFL = if_else(AESER == "Y", "Yes", "No"),
         DTHFL = if_else(AEOUT == "FATAL", "Yes", "No")) %>%
   select(USUBJID, ASTDY, TRTA, BSPT, AETERM, SAEFL, DTHFL)

tbl <- inner_join(adsl, adae, by = "USUBJID") %>%
  arrange(TRT01AN, USUBJID, ASTDY) %>%
  select(TRT01A, USUBJID, ASTDY, TRTA, BSPT, AETERM, SAEFL, DTHFL) %>%
  filter(USUBJID %in% c("01-701-1015", "01-701-1023"))

# Output Results ------------------------------------------------------------------------------------------
gentlg(huxme       = tbl,
       tlf         = "l",
       format      = "HTML",
       print.hux = FALSE,
       orientation = "landscape",
       file        = "Listing01",
       title       = "Listing of Adverse Events",
       idvars      = c("TRT01A", "USUBJID"),
       wcol        = 0.15,
       colheader   = c("Treatment Group",
                       "Subject ID",
                       "Study Day of AE",
                       "Treatment Period",
                       "Body System [Preferred Term]",
                       "Verbatim Term",
                       "Serious",
                       "Fatal"))
#> [[1]]
#>   <div style='border-top :1pt solid; border-bottom :1pt                        
#>   solid; '> <div style = "text-indent: -36px; padding-left:                    
#>   36px;"> Listing01: &emsp; Listing of Adverse                                 
#>   Events</div>                                                                 
#>   <div          <div       <div       <div       <div       <div       <div    
#>   style='bo   style='b   style='b   style='b   style='b   style='b   style='b  
#>   rder-bott   order-bo   order-bo   order-bo   order-bo   order-bo   order-bo  
#>   om:1pt      ttom:1pt   ttom:1pt   ttom:1pt   ttom:1pt   ttom:1pt   ttom:1pt  
#>   solid'>     solid'>    solid'>    solid'>    solid'>    solid'>    solid'>   
#>   Treatment   Subject     Study     Treatmen     Body     Verbatim   Serious   
#>   Group          ID       Day of    t Period    System      Term               
#>                             AE                 [Preferr                        
#>                                                ed Term]                        
#>   Placebo     01-701-1      2       Placebo    GENERAL    APPLICAT      No     
#>                 015                            DISORDER   ION SITE             
#>                                                 S AND     ERYTHEMA             
#>                                                ADMINIST                        
#>                                                 RATION                         
#>                                                  SITE                          
#>                                                CONDITIO                        
#>                                                  NS [                          
#>                                                APPLICAT                        
#>                                                ION SITE                        
#>                                                ERYTHEMA                        
#>                                                   ]                            
#>                             2       Placebo    GENERAL    APPLICAT      No     
#>                                                DISORDER   ION SITE             
#>                                                 S AND     PRURITUS             
#>                                                ADMINIST                        
#>                                                 RATION                         
#>                                                  SITE                          
#>                                                CONDITIO                        
#>                                                  NS [                          
#>                                                APPLICAT                        
#>                                                ION SITE                        
#>                                                PRURITUS                        
#>                                                   ]                            
#>                             8       Placebo    GASTROIN   DIARRHOE      No     
#>                                                TESTINAL      A                 
#>                                                DISORDER                        
#>                                                  S [                           
#>                                                DIARRHOE                        
#>                                                  A ]                           
#>               01-701-1      3       Placebo    SKIN AND   ERYTHEMA      No     
#>                 023                            SUBCUTAN                        
#>                                                  EOUS                          
#>                                                 TISSUE                         
#>                                                DISORDER                        
#>                                                  S [                           
#>                                                ERYTHEMA                        
#>                                                   ]                            
#>                             3       Placebo    SKIN AND   ERYTHEMA      No     
#>                                                SUBCUTAN                        
#>                                                  EOUS                          
#>                                                 TISSUE                         
#>                                                DISORDER                        
#>                                                  S [                           
#>                                                ERYTHEMA                        
#>                                                   ]                            
#>                             3       Placebo    SKIN AND   ERYTHEMA      No     
#>                                                SUBCUTAN                        
#>                                                  EOUS                          
#>                                                 TISSUE                         
#>                                                DISORDER                        
#>                                                  S [                           
#>                                                ERYTHEMA                        
#>                                                   ]                            
#>                             22      Placebo    CARDIAC    ATRIOVEN      No     
#>                                                DISORDER   TRICULAR             
#>                                                  S [       BLOCK               
#>                                                ATRIOVEN    SECOND              
#>                                                TRICULAR    DEGREE              
#>                                                 BLOCK                          
#>                                                 SECOND                         
#>                                                DEGREE ]                        
#>    <div style='border-bottom:1pt solid'> [listing01.html][]                    
#>                                            14JUN2024, 18:46                    
#> 
#> Column names: TRT01A, USUBJID, ASTDY, TRTA, BSPT, AETERM, SAEFL, DTHFL
#> 
#> 7/8 columns shown.

Graph programming

To create the graph output, tidytlg provides a framework of integrating the png file with titles and footnotes for producing the rtf or html output.

In the gentlg function, users need to:

The code below will create the rtf output of the plot.

# Prep Environment ---------------------------------------------------------------------------------------
library(dplyr)
library(haven)
library(ggplot2)
#> 
#> Attaching package: 'ggplot2'
#> The following object is masked from 'package:huxtable':
#> 
#>     theme_grey
library(tidytlg)

# read adsl from PhUSE test data factory
testdata <- "https://github.com/phuse-org/TestDataFactory/raw/main/Updated/TDF_ADaM/"
adsl <- read_xpt(url(paste0(testdata,"adsl.xpt")))

tblid <- "Graph01"

# Process Data --------------------------------------------------------------------------------------------
adsl <- adsl  %>%
  filter(ITTFL == "Y") %>%
  select(USUBJID, ITTFL, TRT01PN, TRT01P, AGE, SEX, HEIGHTBL, WEIGHTBL) %>%
  mutate(SEX = factor(SEX, levels = c("M", "F"), labels = c("Male", "Female")))

# Generate Results ----------------------------------------------------------------------------------------

plot <- ggplot(data = adsl, aes(x = HEIGHTBL, y = WEIGHTBL)) +
  geom_point() +
  labs(x = "Baseline Height (cm)",
       y = "Baseline Weight (kg)") +
  facet_wrap(~SEX, nrow=1)

# create png file
png(file.path(working_dir, paste0(tblid,".png")), width=2800, height=1300, res=300, type = "cairo")
#> Warning in grSoftVersion(): unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
#>   dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 0x0006): Library not loaded: /opt/X11/lib/libSM.6.dylib
#>   Referenced from: <7A10C056-E1B5-3B12-A4C4-BC4C6FE72F15> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/modules/R_X11.so
#>   Reason: tried: '/opt/X11/lib/libSM.6.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/X11/lib/libSM.6.dylib' (no such file), '/opt/X11/lib/libSM.6.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libSM.6.dylib' (no such file), '/Users/kpagacz/.sdkman/candidates/java/current/lib/server/libSM.6.dylib' (no such file)
#> Warning in cairoVersion(): unable to load shared object '/Library/Frameworks/R.framework/Resources/library/grDevices/libs//cairo.so':
#>   dlopen(/Library/Frameworks/R.framework/Resources/library/grDevices/libs//cairo.so, 0x0006): Library not loaded: /opt/X11/lib/libXrender.1.dylib
#>   Referenced from: <6A49BDEB-1475-3762-8723-97B6A3A47DB9> /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/grDevices/libs/cairo.so
#>   Reason: tried: '/opt/X11/lib/libXrender.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/X11/lib/libXrender.1.dylib' (no such file), '/opt/X11/lib/libXrender.1.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libXrender.1.dylib' (no such file), '/Users/kpagacz/.sdkman/candidates/java/current/lib/server/libXrender.1.dylib' (no such file)
#> Warning in png(file.path(working_dir, paste0(tblid, ".png")), width = 2800, :
#> failed to load cairo DLL

plot
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_point()`).


dev.off()
#> null device 
#>           1

# Output Results ------------------------------------------------------------------------------------------

gentlg(tlf = "g",
       plotnames = file.path(system.file("extdata", package = "tidytlg"), paste0(tblid,".png")),
       plotwidth = 10,
       plotheight = 5,
       orientation = "landscape",
       opath       = file.path(working_dir),,
       file = tblid,
       title_file = system.file("extdata/titles.xls", package = "tidytlg"))

Metadata method

Besides building the table section-by-section as shown above, we can use the table metadata approach as an efficient alternative for generating outputs. Table metadata is a data frame describing the data, functions and arguments needed to produce your table results. The table metadata shown below can be used to create the same table output as above. Each row in the table metadata describes how a tbl chunk will be created by the function defined in the func column. The rest of the columns defines the arguments (i.e. df, colvar, rowvar, statlist, rowtext, row_header) that will be passed into the function.

Once table metadata is defined, users just need to call the generate_results function with the column metadata define in the column_metadata_file and tbltype arguments to create the tbl dataframe. In the processing data step, users don’t need to call tlgsetp, since tlgsetup is embedded within the generate_results function. That’s why we need to specify the column metadata in the generate_results call.

library(dplyr)
library(haven)
library(tidytlg)

# read adsl from PhUSE test data factory
testdata <- "https://github.com/phuse-org/TestDataFactory/raw/main/Updated/TDF_ADaM/"
adsl <- read_xpt(url(paste0(testdata,"adsl.xpt")))

# Process data
adsl <- adsl %>%
  filter(ITTFL == "Y") %>%
  mutate(SEX = factor(SEX, levels = c("M", "F", "U"), labels = c("Male", "Female", "Unknown")))

# define table metadata
table_metadata <- tibble::tribble(
  ~func,     ~df,   ~rowvar, ~decimal, ~rowtext,     ~row_header, ~statlist,         ~subset,
  "freq",  "adsl",  "ITTFL",     NA, "Analysis set: ITT",     NA, statlist("n"),  "ITTFL == 'Y'",
  "univar", "adsl",   "AGE",      0,         NA, "Age (Years)",           NA,              NA,
  "freq",  "adsl",    "SEX",     NA,         NA, "Gender", statlist(c("N", "n (x.x%)")),   NA
) %>%
  mutate(colvar  = "TRT01PN")

# Generate results
tbl <- generate_results(table_metadata,
                        column_metadata_file = system.file("extdata/column_metadata.xlsx", package = "tidytlg"),
                        tbltype = "type3")

# Output results
tblid <- "Table01"

gentlg(huxme       = tbl,
       format      = "HTML",
       print.hux = FALSE,
       file        = tblid,
       orientation = "landscape",
       title_file = system.file("extdata/titles.xls", package = "tidytlg"))
#> [[1]]
#>    <div style='border-top :1pt solid; border-bottom :1pt solid; '>             
#>    <div style = "text-indent: -36px; padding-left: 36px;"> Table01:            
#>    &emsp; Demographic and Baseline Characteristics; Intent-to-treat            
#>    Analysis Set</div>                                                          
#>                                                                <div            
#>                                                         style='border-bott     
#>                                                           om:1pt solid'>       
#>                                                             Xanomeline         
#>                                               <div        <div        <div     
#>                                             style='bo   style='bo   style='bo  
#>                                             rder-bott   rder-bott   rder-bott  
#>                                              om:1pt      om:1pt      om:1pt    
#>                                              solid'>     solid'>     solid'>   
#>                                              Placebo    Low Dose    High Dose  
#>    <div style='text-indent: -17.76px;          86          84          84      
#>    padding-left: 17.76px'> Analysis set:                                       
#>    ITT                                                                         
#>    <div style='text-indent: -17.76px;                                          
#>    padding-left: 17.76px'>                                                     
#>    <div style='text-indent: -17.76px;                                          
#>    padding-left: 17.76px'> Age (Years)                                         
#>    <div style='text-indent: -17.76px;          86          84          84      
#>    padding-left: 35.52px'> N                                                   
#>    <div style='text-indent: -17.76px;         75.2        75.7        74.4     
#>    padding-left: 53.28px'> Mean (SD)         (8.59)      (8.29)      (7.89)    
#>    <div style='text-indent: -17.76px;         76.0        77.5        76.0     
#>    padding-left: 53.28px'> Median                                              
#>    <div style='text-indent: -17.76px;       (52; 89)    (51; 88)    (56; 88)   
#>    padding-left: 53.28px'> Range                                               
#>    <div style='text-indent: -17.76px;        (69.0;      (71.0;      (70.5;    
#>    padding-left: 53.28px'> IQ range           82.0)       82.0)       80.0)    
#>    <div style='text-indent: -17.76px;                                          
#>    padding-left: 17.76px'>                                                     
#>    <div style='text-indent: -17.76px;                                          
#>    padding-left: 17.76px'> Gender                                              
#>    <div style='text-indent: -17.76px;          86          84          84      
#>    padding-left: 35.52px'> N                                                   
#>    <div style='text-indent: -17.76px;          33          34          44      
#>    padding-left: 53.28px'> Male              (38.4%)     (40.5%)     (52.4%)   
#>    <div style='text-indent: -17.76px;          53          50          40      
#>    padding-left: 53.28px'> Female            (61.6%)     (59.5%)     (47.6%)   
#>    <div style='text-indent: -17.76px;           0           0           0      
#>    padding-left: 53.28px'> Unknown                                             
#>    <div style='border-top:1pt solid;'> <br />Key: IQ = interquartile           
#>    Note: N reflects non-missing values                                         
#>    <div style='border-bottom:1pt solid'> [table01.html][] 14JUN2024,           
#>                                                                18:46           
#> 
#> Column names: label, col1, col2, col3, col4, col5
#> 
#> 4/6 columns shown.

By processing

There are two types of by-processing that tidytlg functions can provide:

The code below provides an example of summarizing age and race by gender using tablebyvar.

library(dplyr)
library(haven)
library(tidytlg)

# read adsl from PhUSE test data factory
testdata <- "https://github.com/phuse-org/TestDataFactory/raw/main/Updated/TDF_ADaM/"
adsl <- read_xpt(url(paste0(testdata,"adsl.xpt")))

# Process data
adsl <- adsl %>%
  filter(ITTFL == "Y") %>%
  mutate(SEX = factor(SEX, levels = c("M", "F"), labels = c("Male", "Female")))

# define table metadata
table_metadata <- tibble::tribble(
  ~func,     ~df,   ~rowvar, ~decimal, ~rowtext,     ~row_header, ~statlist,         ~subset, ~tablebyvar,
  "univar", "adsl",   "AGE",      0,         NA, "Age (Years)",           NA,              NA, "SEX",
  "freq",  "adsl",    "RACE",     NA,         NA, "Race", statlist(c("N", "n (x.x%)")),   NA, "SEX"
) %>%
  mutate(colvar  = "TRT01PN")

# Generate results
tbl <- generate_results(table_metadata,
                        column_metadata_file = system.file("extdata/column_metadata.xlsx", package = "tidytlg"),
                        tbltype = "type3")

# Output results
tblid <- "Table01"

gentlg(huxme       = tbl,
       format      = "HTML",
       print.hux = FALSE,
       file        = tblid,
       orientation = "landscape",
       title_file = system.file("extdata/titles.xls", package = "tidytlg"))
#> [[1]]
#>    <div style='border-top :1pt solid; border-bottom :1pt solid; '>             
#>    <div style = "text-indent: -36px; padding-left: 36px;"> Table01:            
#>    &emsp; Demographic and Baseline Characteristics; Intent-to-treat            
#>    Analysis Set</div>                                                          
#>                                                                <div            
#>                                                         style='border-bott     
#>                                                           om:1pt solid'>       
#>                                                             Xanomeline         
#>                                               <div        <div        <div     
#>                                             style='bo   style='bo   style='bo  
#>                                             rder-bott   rder-bott   rder-bott  
#>                                              om:1pt      om:1pt      om:1pt    
#>                                              solid'>     solid'>     solid'>   
#>                                              Placebo    Low Dose    High Dose  
#>    <div style='text-indent: -17.76px;                                          
#>    padding-left: 17.76px'> Male                                                
#>    <div style='text-indent: -17.76px;                                          
#>    padding-left: 17.76px'>                                                     
#>    <div style='text-indent: -17.76px;                                          
#>    padding-left: 35.52px'> Age (Years)                                         
#>    <div style='text-indent: -17.76px;          33          34          44      
#>    padding-left: 53.28px'> N                                                   
#>    <div style='text-indent: -17.76px;         73.4        75.6        74.1     
#>    padding-left: 71.04px'> Mean (SD)         (8.15)      (8.69)      (8.16)    
#>    <div style='text-indent: -17.76px;         74.0        77.5        77.0     
#>    padding-left: 71.04px'> Median                                              
#>    <div style='text-indent: -17.76px;       (52; 85)    (51; 88)    (56; 86)   
#>    padding-left: 71.04px'> Range                                               
#>    <div style='text-indent: -17.76px;        (69.0;      (68.0;      (69.0;    
#>    padding-left: 71.04px'> IQ range           80.0)       82.0)       80.5)    
#>    <div style='text-indent: -17.76px;                                          
#>    padding-left: 17.76px'>                                                     
#>    <div style='text-indent: -17.76px;                                          
#>    padding-left: 35.52px'> Race                                                
#>    <div style='text-indent: -17.76px;          33          34          44      
#>    padding-left: 53.28px'> N                                                   
#>    <div style='text-indent: -17.76px;           0           0       1 (2.3%)   
#>    padding-left: 71.04px'> AMERICAN                                            
#>    INDIAN OR ALASKA NATIVE                                                     
#>    <div style='text-indent: -17.76px;       3 (9.1%)        0       3 (6.8%)   
#>    padding-left: 71.04px'> BLACK OR                                            
#>    AFRICAN AMERICAN                                                            
#>    <div style='text-indent: -17.76px;          30          34          40      
#>    padding-left: 71.04px'> WHITE             (90.9%)    (100.0%)     (90.9%)   
#>    <div style='text-indent: -17.76px;                                          
#>    padding-left: 17.76px'> Female                                              
#>    <div style='text-indent: -17.76px;                                          
#>    padding-left: 17.76px'>                                                     
#>    <div style='text-indent: -17.76px;                                          
#>    padding-left: 35.52px'> Age (Years)                                         
#>    <div style='text-indent: -17.76px;          53          50          40      
#>    padding-left: 53.28px'> N                                                   
#>    <div style='text-indent: -17.76px;         76.4        75.7        74.7     
#>    padding-left: 71.04px'> Mean (SD)         (8.73)      (8.09)      (7.67)    
#>    <div style='text-indent: -17.76px;         78.0        77.5        76.0     
#>    padding-left: 71.04px'> Median                                              
#>    <div style='text-indent: -17.76px;       (59; 89)    (54; 87)    (56; 88)   
#>    padding-left: 71.04px'> Range                                               
#>    <div style='text-indent: -17.76px;        (70.0;      (72.0;      (72.0;    
#>    padding-left: 71.04px'> IQ range           84.0)       81.0)       79.0)    
#>    <div style='text-indent: -17.76px;                                          
#>    padding-left: 17.76px'>                                                     
#>    <div style='text-indent: -17.76px;                                          
#>    padding-left: 35.52px'> Race                                                
#>    <div style='text-indent: -17.76px;          53          50          40      
#>    padding-left: 53.28px'> N                                                   
#>    <div style='text-indent: -17.76px;           0           0           0      
#>    padding-left: 71.04px'> AMERICAN                                            
#>    INDIAN OR ALASKA NATIVE                                                     
#>    <div style='text-indent: -17.76px;       5 (9.4%)    6 (12.0%)   6 (15.0%)  
#>    padding-left: 71.04px'> BLACK OR                                            
#>    AFRICAN AMERICAN                                                            
#>    <div style='text-indent: -17.76px;          48          44          34      
#>    padding-left: 71.04px'> WHITE             (90.6%)     (88.0%)     (85.0%)   
#>    <div style='border-top:1pt solid;'> <br />Key: IQ = interquartile           
#>    Note: N reflects non-missing values                                         
#>    <div style='border-bottom:1pt solid'> [table01.html][] 14JUN2024,           
#>                                                                18:46           
#> 
#> Column names: label, col1, col2, col3, col4, col5
#> 
#> 4/6 columns shown.

In summary, rowbyvar is used to create the by-variable summary for one rowvar in a single function call. To perform sub-group analysis, users need to specify tablebyvar in every function calls except the analysis population row.

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.
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