Introduction to Chevron
Adrian Waddell
2022-10-21
chevron.RmdIntroduction
The chevron R package provides functions to produce
standard tables, listings and graphs (TLGs) used to analyze and report
clinical trials data. The ensemble of function used to produce a
particular output are stored in an S4 object of virtual
class chevron_tlg. Each type of output are associated with
a specific class: chevron_t for tables,
chevron_l for listings and chevron_g for
graphs.
Each standard output is associated with one
chevron_tlg object. They contain the following
objects in separate slots:
- A
mainfunction also refereed to as TLG-function. - A
preprocessfunction. - A
postprocessfunction - A
adam_datasetscharacter vector of the name of theAdAMdatasets required to create the output.
TLG-functions
The TLG-functions in chevron use other packages
to produce the final outputs, for example rtables and
tern are used to create tables, ggplot2,
lattice, and grid are used to create graphs,
rlistings to create listings.
TLG-functions in chevron such as
dmt01_main, aet02_main,
aet02_main have the following properties:
- they produce a narrow defined output (currently standards in Roche
GDS). Note, that the naming convention<gds template id>_mainindicates that a RocheGDSdefined standard may have different implementations. Or, alternatively, aGDStemplate id can be regarded as a guideline and the function name inchevronas a standard. - have, if possible, few arguments to modify the standard. Generally, arguments may change the structure of the table (arm variable, which variables are summarized) and also parameterize the cell content (i.e. alpha-level for p-value).
- have always the first argument
adam_dbwhich is the collection ofADaMdatasets (ADSL,ADAE,ADRS, etc.). Please read the Theadam_dbArgument vignette in this package for more details.
preprocessing
The preprocess functions in chevron use
base, dplyr and dunlin packages
to process input data object and turn them into a suitable input for
TLG-functions.
preprocess in chevron such as dmt01_pre,
aet02_pre, aet02_pre have the following
properties:
- they return a
listofdata.frameobject amenable to processing by a TLG-functions. message. - have very few arguments to modify the standard.
- have always the first argument
adam_dbwhich is the collection ofADaMdatasets (ADSL,ADAE,ADRS, etc.). Please read the Theadam_dbArgument vignette in this package for more details.
Please note that the ultimate responsible person of the preprocessing
functions is the end user. The provided preprocessing function is only a
template and users could modify depending on their need/data. This
preprocessing function will be printed to allow modification in script
generated in citril.
Example AET02
For example, the GDS template aet02 is
implemented in chevron with the chevropn_tlg
objects that have the name aet02.
We first load the data as a list of
data.frame, where each table represents a domain.
library(chevron)
#> Registered S3 method overwritten by 'tern':
#> method from
#> tidy.glm broom
data(syn_data, package = "chevron")A the aet02 output is then created as follows:
run(aet02, syn_data)
#> MedDRA System Organ Class A: Drug X B: Placebo C: Combination
#> MedDRA Preferred Term (N=134) (N=134) (N=132)
#> ———————————————————————————————————————————————————————————————————————————————————————————————————————
#> Total number of patients with at least one adverse event 122 (91.0%) 123 (91.8%) 120 (90.9%)
#> Overall total number of events 609 622 703
#> cl A.1
#> Total number of patients with at least one adverse event 78 (58.2%) 75 (56.0%) 89 (67.4%)
#> Total number of events 132 130 160
#> dcd A.1.1.1.1 50 (37.3%) 45 (33.6%) 63 (47.7%)
#> dcd A.1.1.1.2 48 (35.8%) 48 (35.8%) 50 (37.9%)
#> cl B.2
#> Total number of patients with at least one adverse event 79 (59.0%) 74 (55.2%) 85 (64.4%)
#> Total number of events 129 138 143
#> dcd B.2.2.3.1 48 (35.8%) 54 (40.3%) 51 (38.6%)
#> dcd B.2.1.2.1 49 (36.6%) 44 (32.8%) 52 (39.4%)
#> cl D.1
#> Total number of patients with at least one adverse event 79 (59.0%) 67 (50.0%) 80 (60.6%)
#> Total number of events 127 106 135
#> dcd D.1.1.1.1 50 (37.3%) 42 (31.3%) 51 (38.6%)
#> dcd D.1.1.4.2 48 (35.8%) 42 (31.3%) 50 (37.9%)
#> cl D.2
#> Total number of patients with at least one adverse event 47 (35.1%) 58 (43.3%) 57 (43.2%)
#> Total number of events 62 72 74
#> dcd D.2.1.5.3 47 (35.1%) 58 (43.3%) 57 (43.2%)
#> cl B.1
#> Total number of patients with at least one adverse event 47 (35.1%) 49 (36.6%) 43 (32.6%)
#> Total number of events 56 60 62
#> dcd B.1.1.1.1 47 (35.1%) 49 (36.6%) 43 (32.6%)
#> cl C.2
#> Total number of patients with at least one adverse event 35 (26.1%) 48 (35.8%) 55 (41.7%)
#> Total number of events 48 53 65
#> dcd C.2.1.2.1 35 (26.1%) 48 (35.8%) 55 (41.7%)
#> cl C.1
#> Total number of patients with at least one adverse event 43 (32.1%) 46 (34.3%) 43 (32.6%)
#> Total number of events 55 63 64
#> dcd C.1.1.1.3 43 (32.1%) 46 (34.3%) 43 (32.6%)The function associated with a particular slot can be retrieved with
the corresponding method: main, lyt,
preprocess postprocess and
datasets.
main(aet02)
#> function (adam_db, arm_var = "ACTARM", row_split_var = "AEBODSYS",
#> lbl_overall = NULL, ...)
#> {
#> assert_all_tablenames(adam_db, "adsl", "adae")
#> checkmate::assert_character(row_split_var, null.ok = TRUE)
#> checkmate::assert_string(lbl_overall, null.ok = TRUE)
#> checkmate::assert_string(arm_var)
#> assert_valid_variable(adam_db$adsl, c("USUBJID", arm_var),
#> types = list(c("character", "factor")))
#> assert_valid_variable(adam_db$adae, c(arm_var, row_split_var,
#> "AEDECOD"), types = list(c("character", "factor")))
#> assert_valid_variable(adam_db$adae, "USUBJID", empty_ok = TRUE,
#> types = list(c("character", "factor")))
#> assert_valid_var_pair(adam_db$adsl, adam_db$adae, arm_var)
#> lbl_row_split <- var_labels_for(adam_db$adae, row_split_var)
#> lbl_aedecod <- var_labels_for(adam_db$adae, "AEDECOD")
#> lyt <- aet02_lyt(arm_var = arm_var, lbl_overall = lbl_overall,
#> row_split_var = row_split_var, lbl_row_split = lbl_row_split,
#> lbl_aedecod = lbl_aedecod)
#> tbl <- build_table(lyt, adam_db$adae, alt_counts_df = adam_db$adsl)
#> tbl
#> }
#> <bytecode: 0x55baf6250b80>
#> <environment: namespace:chevron>These are standard functions that can be used on their own.
res <- preprocess(aet02)(syn_data)
# or
foo <- aet02@preprocess
res <- foo(syn_data)
str(res, max.level = 0)
#> List of 19
chevron_tlg object customization
In some instances it is useful to customize the
chevron_tlg object, for example by changing the pre
processing functions in script generated. Please modify the code
directly inside the pre_fun, and make sure the function
returns a named list of data frames. Please be careful about the
argument names. The default argument of pre functions will
be override by the argument in spec.
Custom chevron_tlg object creation
In some cases, you may want to create a new chevron_tlg
template. To create a chevron_tlg object from scratch, use
the provided constructors corresponding to the desired output:
-
chevron_t()for tables. -
chevron_l()for listings. -
chevron_g()for graphs.
library(rtables)
library(tern)
my_template <- chevron_t(
main = "<your main function to build the table>",
preprocess = "<your pre function to process the data>",
postprocess = "<your post function to add custom sorting>",
adam_datasets = c("adsl")
)
run(my_template, syn_data)Note that to ensure the correct execution of the run
function, the name of the first argument of the main
function must be adam_db; the input list of
data.frame object to pre-process. The name of the first
argument of the preprocess function must be
adam_db; the input dm object to create
TLG output and finally, the name of the first argument of
the postprocess function must be tlg, the
input TableTree object to post-process. Validation criteria
enforce these rules upon creation of a chevron_tlg
object.