Referential Footnotes
Emily de la Rua
2023-12-06
Source:vignettes/ref_footnotes.Rmd
ref_footnotes.RmdIntroduction
There is currently no formal method for adding referential footnotes
to a listing object. This vignette demonstrates how referential
footnotes can be added to a listing_df object via a
workaround applied during pre-processing.
To learn more about how listings are constructed using the
rlistings package, see the Getting
Started vignette.
Referential Footnotes Workaround
When creating a listing with the rlistings package, you
may want to add referential footnotes, similar to how referential
footnotes can be added to rtable objects. Since there is no
formal method in rlistings for applying referential
footnotes to a listing_df object, we will demonstrate how a
workaround can be applied to add a set of pseudo-referential footnotes
to your listing.
To demonstrate, we will create a basic listing below.
We begin by loading in the rlistings package.
For this example, we will use the dummy ADAE dataset provided within
the formatters package as our data frame, which consists of
48 columns of adverse event patient data, and one or more rows per
patient. For the purpose of this example, we will subset the data and
only use the first 30 records of the dataset.
adae <- ex_adae[1:30, ]Now we will create a basic listing.
lsting <- as_listing(
df = adae,
key_cols = c("ARM", "USUBJID", "ASEQ", "ASTDY"),
disp_cols = c("BMRKR1", "AESEV"),
)
#> sorting incoming data by key columns
lsting
#> Description of Planned Arm Unique Subject Identifier Analysis Sequence Number Analysis Start Relative Day Continous Level Biomarker 1 Severity/Intensity
#> ——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
#> A: Drug X AB12345-BRA-1-id-134 1 251 6.46299057842479 MODERATE
#> 2 304 6.46299057842479 MODERATE
#> 3 497 6.46299057842479 MODERATE
#> 4 608 6.46299057842479 MODERATE
#> AB12345-BRA-1-id-42 1 39 2.26753940777848 MODERATE
#> 2 65 2.26753940777848 SEVERE
#> 3 95 2.26753940777848 MODERATE
#> 4 160 2.26753940777848 MODERATE
#> 5 292 2.26753940777848 MILD
#> 6 460 2.26753940777848 MODERATE
#> 7 470 2.26753940777848 SEVERE
#> 8 476 2.26753940777848 MODERATE
#> 9 497 2.26753940777848 SEVERE
#> 10 642 2.26753940777848 SEVERE
#> B: Placebo AB12345-BRA-1-id-236 1 22 7.66300121077566 SEVERE
#> 2 181 7.66300121077566 SEVERE
#> 3 702 7.66300121077566 SEVERE
#> AB12345-BRA-1-id-65 1 145 7.34091885189189 MODERATE
#> 2 191 7.34091885189189 MILD
#> 3 233 7.34091885189189 SEVERE
#> C: Combination AB12345-BRA-1-id-141 1 259 7.51607612428241 MODERATE
#> 2 303 7.51607612428241 MILD
#> 3 493 7.51607612428241 MILD
#> 4 600 7.51607612428241 MODERATE
#> 5 635 7.51607612428241 MILD
#> 6 730 7.51607612428241 SEVERE
#> AB12345-BRA-1-id-265 1 48 10.323346349886 MODERATE
#> 2 200 10.323346349886 MODERATE
#> 3 392 10.323346349886 SEVERE
#> 4 403 10.323346349886 SEVEREFor this example, we will add 4 referential footnotes.
- In the
ARMcolumn, for all records withARM = "A: Drug X"andASEQequal to 1 or 2. - In the
ASTDYcolumn, for imputed dates, where imputed dates are indicated by theASTDTFvariable. - In the
AESEVcolumn, for all records withAETOXGRequal to 5. - In the
USUBJIDcolumn header.
Footnote text can be supplied either as a vector, where each element
is a new footnote, or as a single string with footnotes separated by the
new line (\n) character. For example, see the following
list of referential footnotes:
ref_fns <- "* ASEQ 1 or 2\n** Analysis start date is imputed\n*** Records with ATOXGR = 5\n**** ID column"We start with our first footnote in the ARM column for
records with arm “A: Drug X” which also have analysis sequence number 1
or 2. Referential footnotes can be added to any variable by converting
the variable to a factor, editing the variable values, and adding a
corresponding footnote below the listing. We will add our first
referential footnote in the ARM column. To ensure that
levels are correctly ordered, be sure to specify the new level order
when mutating your variable.
# Save variable labels for your data to add back in after mutating dataset
df_lbls <- var_labels(adae)
# Mutate variable where referential footnotes are to be added according to your conditions
# Specify order of levels with new referential footnotes added
adae <- adae %>% dplyr::mutate(
ARM = factor(
ifelse(ARM == "A: Drug X" & ASEQ %in% 1:2, paste0(ARM, "*"), as.character(ARM)),
levels = c(sapply(levels(adae$ARM), paste0, c("", "*")))
)
)
# Add data variable labels back in
var_labels(adae) <- df_lbls
# Generate listing
lsting <- as_listing(
df = adae,
key_cols = c("ARM", "USUBJID", "ASEQ", "ASTDY"),
disp_cols = c("BMRKR1", "AESEV"),
)
#> sorting incoming data by key columns
lsting
#> Description of Planned Arm Unique Subject Identifier Analysis Sequence Number Analysis Start Relative Day Continous Level Biomarker 1 Severity/Intensity
#> ——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
#> A: Drug X AB12345-BRA-1-id-134 3 497 6.46299057842479 MODERATE
#> 4 608 6.46299057842479 MODERATE
#> AB12345-BRA-1-id-42 3 95 2.26753940777848 MODERATE
#> 4 160 2.26753940777848 MODERATE
#> 5 292 2.26753940777848 MILD
#> 6 460 2.26753940777848 MODERATE
#> 7 470 2.26753940777848 SEVERE
#> 8 476 2.26753940777848 MODERATE
#> 9 497 2.26753940777848 SEVERE
#> 10 642 2.26753940777848 SEVERE
#> A: Drug X* AB12345-BRA-1-id-134 1 251 6.46299057842479 MODERATE
#> 2 304 6.46299057842479 MODERATE
#> AB12345-BRA-1-id-42 1 39 2.26753940777848 MODERATE
#> 2 65 2.26753940777848 SEVERE
#> B: Placebo AB12345-BRA-1-id-236 1 22 7.66300121077566 SEVERE
#> 2 181 7.66300121077566 SEVERE
#> 3 702 7.66300121077566 SEVERE
#> AB12345-BRA-1-id-65 1 145 7.34091885189189 MODERATE
#> 2 191 7.34091885189189 MILD
#> 3 233 7.34091885189189 SEVERE
#> C: Combination AB12345-BRA-1-id-141 1 259 7.51607612428241 MODERATE
#> 2 303 7.51607612428241 MILD
#> 3 493 7.51607612428241 MILD
#> 4 600 7.51607612428241 MODERATE
#> 5 635 7.51607612428241 MILD
#> 6 730 7.51607612428241 SEVERE
#> AB12345-BRA-1-id-265 1 48 10.323346349886 MODERATE
#> 2 200 10.323346349886 MODERATE
#> 3 392 10.323346349886 SEVERE
#> 4 403 10.323346349886 SEVEREAdditional referential footnotes can be added to the data be repeating the above steps.
For example, we can add the second referential footnote to the
ASTDY column for imputed analysis start days. We use dummy
variable ASTDTF to indicate imputed analysis start dates.
When adding referential footnotes to numeric variables, the variables
must be converted to factors.
set.seed(1)
# Save variable labels for your data to add back in after mutating dataset
df_lbls <- var_labels(adae)
# Mutate variable where referential footnotes are to be added according to your conditions
# Specify order of levels with new referential footnotes added
adae <- adae %>%
dplyr::mutate(ASTDTF = sample(c("Y", NA), nrow(.), replace = TRUE, prob = c(0.25, 0.75))) %>%
dplyr::mutate(ASTDY = factor(
ifelse(!is.na(ASTDTF), paste0(as.character(ASTDY), "**"), as.character(ASTDY)),
levels = c(sapply(sort(unique(adae$ASTDY)), paste0, c("", "**")))
)) %>%
dplyr::select(-ASTDTF)
# Add data variable labels back in
var_labels(adae) <- df_lbls
# Generate listing
lsting <- as_listing(
df = adae,
key_cols = c("ARM", "USUBJID", "ASEQ", "ASTDY"),
disp_cols = c("BMRKR1", "AESEV"),
)
#> sorting incoming data by key columns
lsting
#> Description of Planned Arm Unique Subject Identifier Analysis Sequence Number Analysis Start Relative Day Continous Level Biomarker 1 Severity/Intensity
#> ——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
#> A: Drug X AB12345-BRA-1-id-134 3 497 6.46299057842479 MODERATE
#> 4 608** 6.46299057842479 MODERATE
#> AB12345-BRA-1-id-42 3 95** 2.26753940777848 MODERATE
#> 4 160** 2.26753940777848 MODERATE
#> 5 292 2.26753940777848 MILD
#> 6 460 2.26753940777848 MODERATE
#> 7 470 2.26753940777848 SEVERE
#> 8 476 2.26753940777848 MODERATE
#> 9 497 2.26753940777848 SEVERE
#> 10 642 2.26753940777848 SEVERE
#> A: Drug X* AB12345-BRA-1-id-134 1 251 6.46299057842479 MODERATE
#> 2 304 6.46299057842479 MODERATE
#> AB12345-BRA-1-id-42 1 39** 2.26753940777848 MODERATE
#> 2 65 2.26753940777848 SEVERE
#> B: Placebo AB12345-BRA-1-id-236 1 22 7.66300121077566 SEVERE
#> 2 181 7.66300121077566 SEVERE
#> 3 702 7.66300121077566 SEVERE
#> AB12345-BRA-1-id-65 1 145 7.34091885189189 MODERATE
#> 2 191** 7.34091885189189 MILD
#> 3 233 7.34091885189189 SEVERE
#> C: Combination AB12345-BRA-1-id-141 1 259 7.51607612428241 MODERATE
#> 2 303** 7.51607612428241 MILD
#> 3 493** 7.51607612428241 MILD
#> 4 600 7.51607612428241 MODERATE
#> 5 635 7.51607612428241 MILD
#> 6 730 7.51607612428241 SEVERE
#> AB12345-BRA-1-id-265 1 48 10.323346349886 MODERATE
#> 2 200** 10.323346349886 MODERATE
#> 3 392 10.323346349886 SEVERE
#> 4 403 10.323346349886 SEVERENext we can add our third referential footnote to the
AESEV column for records with analysis toxicity grade
5.
# Save variable labels for your data to add back in after mutating dataset
df_lbls <- var_labels(adae)
# Mutate variable where referential footnotes are to be added according to your conditions
# Specify order of levels with new referential footnotes added
adae <- adae %>% dplyr::mutate(
AESEV = factor(
ifelse(AETOXGR == 5, paste0(AESEV, "***"), as.character(AESEV)),
levels = c(sapply(levels(adae$AESEV), paste0, c("", "***")))
)
)
# Add data variable labels back in
var_labels(adae) <- df_lbls
# Generate listing
lsting <- as_listing(
df = adae,
key_cols = c("ARM", "USUBJID", "ASEQ", "ASTDY"),
disp_cols = c("BMRKR1", "AESEV"),
)
#> sorting incoming data by key columns
lsting
#> Description of Planned Arm Unique Subject Identifier Analysis Sequence Number Analysis Start Relative Day Continous Level Biomarker 1 Severity/Intensity
#> ——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
#> A: Drug X AB12345-BRA-1-id-134 3 497 6.46299057842479 MODERATE
#> 4 608** 6.46299057842479 MODERATE
#> AB12345-BRA-1-id-42 3 95** 2.26753940777848 MODERATE
#> 4 160** 2.26753940777848 MODERATE
#> 5 292 2.26753940777848 MILD
#> 6 460 2.26753940777848 MODERATE
#> 7 470 2.26753940777848 SEVERE***
#> 8 476 2.26753940777848 MODERATE
#> 9 497 2.26753940777848 SEVERE
#> 10 642 2.26753940777848 SEVERE***
#> A: Drug X* AB12345-BRA-1-id-134 1 251 6.46299057842479 MODERATE
#> 2 304 6.46299057842479 MODERATE
#> AB12345-BRA-1-id-42 1 39** 2.26753940777848 MODERATE
#> 2 65 2.26753940777848 SEVERE***
#> B: Placebo AB12345-BRA-1-id-236 1 22 7.66300121077566 SEVERE***
#> 2 181 7.66300121077566 SEVERE***
#> 3 702 7.66300121077566 SEVERE***
#> AB12345-BRA-1-id-65 1 145 7.34091885189189 MODERATE
#> 2 191** 7.34091885189189 MILD
#> 3 233 7.34091885189189 SEVERE***
#> C: Combination AB12345-BRA-1-id-141 1 259 7.51607612428241 MODERATE
#> 2 303** 7.51607612428241 MILD
#> 3 493** 7.51607612428241 MILD
#> 4 600 7.51607612428241 MODERATE
#> 5 635 7.51607612428241 MILD
#> 6 730 7.51607612428241 SEVERE***
#> AB12345-BRA-1-id-265 1 48 10.323346349886 MODERATE
#> 2 200** 10.323346349886 MODERATE
#> 3 392 10.323346349886 SEVERE***
#> 4 403 10.323346349886 SEVEREReferential footnotes can also be added to column header labels.
Suppose we want to add our fourth referential footnote to the
USUBJID column label. We can do so by editing the
USUBJID variable label and adding the footnote text as
follows:
# Modify data variable label
adae <- adae %>% var_relabel(
USUBJID = paste0(var_labels(adae)[["USUBJID"]], "****")
)
# Generate listing
lsting <- as_listing(
df = adae,
key_cols = c("ARM", "USUBJID", "ASTDY", "ASEQ"),
disp_cols = c("BMRKR1", "AESEV")
)
#> sorting incoming data by key columns
lsting
#> Description of Planned Arm Unique Subject Identifier**** Analysis Start Relative Day Analysis Sequence Number Continous Level Biomarker 1 Severity/Intensity
#> ——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
#> A: Drug X AB12345-BRA-1-id-134 497 3 6.46299057842479 MODERATE
#> 608** 4 6.46299057842479 MODERATE
#> AB12345-BRA-1-id-42 95** 3 2.26753940777848 MODERATE
#> 160** 4 2.26753940777848 MODERATE
#> 292 5 2.26753940777848 MILD
#> 460 6 2.26753940777848 MODERATE
#> 470 7 2.26753940777848 SEVERE***
#> 476 8 2.26753940777848 MODERATE
#> 497 9 2.26753940777848 SEVERE
#> 642 10 2.26753940777848 SEVERE***
#> A: Drug X* AB12345-BRA-1-id-134 251 1 6.46299057842479 MODERATE
#> 304 2 6.46299057842479 MODERATE
#> AB12345-BRA-1-id-42 39** 1 2.26753940777848 MODERATE
#> 65 2 2.26753940777848 SEVERE***
#> B: Placebo AB12345-BRA-1-id-236 22 1 7.66300121077566 SEVERE***
#> 181 2 7.66300121077566 SEVERE***
#> 702 3 7.66300121077566 SEVERE***
#> AB12345-BRA-1-id-65 145 1 7.34091885189189 MODERATE
#> 191** 2 7.34091885189189 MILD
#> 233 3 7.34091885189189 SEVERE***
#> C: Combination AB12345-BRA-1-id-141 259 1 7.51607612428241 MODERATE
#> 303** 2 7.51607612428241 MILD
#> 493** 3 7.51607612428241 MILD
#> 600 4 7.51607612428241 MODERATE
#> 635 5 7.51607612428241 MILD
#> 730 6 7.51607612428241 SEVERE***
#> AB12345-BRA-1-id-265 48 1 10.323346349886 MODERATE
#> 200** 2 10.323346349886 MODERATE
#> 392 3 10.323346349886 SEVERE***
#> 403 4 10.323346349886 SEVEREFinally, we add in the referential footnote text below the listing as follows.
# Generate listing
lsting <- as_listing(
df = adae,
key_cols = c("ARM", "USUBJID", "ASTDY", "ASEQ"),
disp_cols = c("BMRKR1", "AESEV")
)
#> sorting incoming data by key columns
main_footer(lsting) <- c(main_footer(lsting), ref_fns)
lsting
#> Description of Planned Arm Unique Subject Identifier**** Analysis Start Relative Day Analysis Sequence Number Continous Level Biomarker 1 Severity/Intensity
#> ——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
#> A: Drug X AB12345-BRA-1-id-134 497 3 6.46299057842479 MODERATE
#> 608** 4 6.46299057842479 MODERATE
#> AB12345-BRA-1-id-42 95** 3 2.26753940777848 MODERATE
#> 160** 4 2.26753940777848 MODERATE
#> 292 5 2.26753940777848 MILD
#> 460 6 2.26753940777848 MODERATE
#> 470 7 2.26753940777848 SEVERE***
#> 476 8 2.26753940777848 MODERATE
#> 497 9 2.26753940777848 SEVERE
#> 642 10 2.26753940777848 SEVERE***
#> A: Drug X* AB12345-BRA-1-id-134 251 1 6.46299057842479 MODERATE
#> 304 2 6.46299057842479 MODERATE
#> AB12345-BRA-1-id-42 39** 1 2.26753940777848 MODERATE
#> 65 2 2.26753940777848 SEVERE***
#> B: Placebo AB12345-BRA-1-id-236 22 1 7.66300121077566 SEVERE***
#> 181 2 7.66300121077566 SEVERE***
#> 702 3 7.66300121077566 SEVERE***
#> AB12345-BRA-1-id-65 145 1 7.34091885189189 MODERATE
#> 191** 2 7.34091885189189 MILD
#> 233 3 7.34091885189189 SEVERE***
#> C: Combination AB12345-BRA-1-id-141 259 1 7.51607612428241 MODERATE
#> 303** 2 7.51607612428241 MILD
#> 493** 3 7.51607612428241 MILD
#> 600 4 7.51607612428241 MODERATE
#> 635 5 7.51607612428241 MILD
#> 730 6 7.51607612428241 SEVERE***
#> AB12345-BRA-1-id-265 48 1 10.323346349886 MODERATE
#> 200** 2 10.323346349886 MODERATE
#> 392 3 10.323346349886 SEVERE***
#> 403 4 10.323346349886 SEVERE
#> ——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
#>
#> * ASEQ 1 or 2
#> ** Analysis start date is imputed
#> *** Records with ATOXGR = 5
#> **** ID columnNow our listing is complete, with all four referential footnotes denoted within the listing and described in the footnotes section below.
Summary
In this vignette, you have learned how a pre-processing workaround can be applied to add referential footnotes to listings.
For more information please explore the rlistings website.