Many tables call for column counts to be displayed in the header material of a table (i.e., interspersed with the column labels).
Historically, rtables supported this only for so-called leaf or individual columns.
Display of column counts (off by default) was primarily achieved via passing show_colcounts = TRUE to basic_table , e.g.
library(dplyr)
#
# Attaching package: 'dplyr'
# The following objects are masked from 'package:stats':
#
# filter, lag
# The following objects are masked from 'package:base':
#
# intersect, setdiff, setequal, union
library(rtables)
# Loading required package: formatters
#
# Attaching package: 'formatters'
# The following object is masked from 'package:base':
#
# %||%
# Loading required package: magrittr
#
# Attaching package: 'rtables'
# The following object is masked from 'package:utils':
#
# str
lyt <- basic_table(show_colcounts = TRUE) %>%
split_cols_by("ARM") %>%
split_cols_by("SEX", split_fun = keep_split_levels(c("F", "M"))) %>%
analyze("AGE")
tbl <- build_table(lyt, ex_adsl)
tbl
# A: Drug X B: Placebo C: Combination
# F M F M F M
# (N=79) (N=51) (N=77) (N=55) (N=66) (N=60)
# ————————————————————————————————————————————————————————————
# Mean 32.76 35.57 34.12 37.44 35.20 35.38The format of the counts could also be controlled by the colcount_format argument to basic_table.
We had no way of displaying (or, in fact, even easily calculating) the ARM facet counts.
(Leaf-)column counts could be altered after the fact via the col_counts<- getter:
col_counts(tbl) <- c(17, 18, 19, 17, 18, 19)
tbl
# A: Drug X B: Placebo C: Combination
# F M F M F M
# (N=17) (N=18) (N=19) (N=17) (N=18) (N=19)
# ————————————————————————————————————————————————————————————
# Mean 32.76 35.57 34.12 37.44 35.20 35.38NB doing this has never updated percentages that appear within the table as they are calculated at table-creation time, so this can lead to misleading results when not used with care.
Hiding countsWe did not provide a user-visible way to toggle column count display after table creation, though we did support showing a blank space for particular counts by setting them to NA:
col_counts(tbl) <- c(17, 18, NA, 17, 18, 19)
tbl
# A: Drug X B: Placebo C: Combination
# F M F M F M
# (N=17) (N=18) (N=17) (N=18) (N=19)
# ———————————————————————————————————————————————————————————
# Mean 32.76 35.57 34.12 37.44 35.20 35.38These mechanisms will all continue to work for the forseeable future, though new code is advised use the new API discussed below.
Higher Level Column CountsStarting in rtables version 6.8.0, the concept of column counts is modeled and handled with much more granularity than previously. Each facet in column space now has a column count (whether or not it is displayed), which will appear directly under the corresponding column label (spanning the same number of rows) when set to be visible.
The primary way for users to create tables which displays these “high-level” column counts is to create a layout that specifies they should be visible.
We do this with the new show_colcounts argument now accepted by all split_cols_by* layout functions.
As before, these column counts are calculated at table creation time, using alt_counts_df if it is provided (or simply df otherwise).
Column formats are set at layout time via the colcount_format argument of the specific split_cols_by call.
Manipulation of column counts (beyond the old setters provided for backwards compatibility) is path based. In other words, when we set a column count (e.g., to NA so it displays as a blank) or set the visibilty of a set of column counts, we do so by indicating them via column paths. The ability to alter column count formats on an existing table is currently not offered by any exported functions.
Column paths can be obtained via col_paths for the leaf columns, or via make_col_df(tbl, visible_only = FALSE)$path for all addressable facets.
The facet_colcount getter and setter queries and sets the column count for a facet in column space (note it needs not be a leaf facet). E.g.,
facet_colcount(tbl3, c("ARM", "C: Combination")) <- 75
tbl3
# A: Drug X B: Placebo C: Combination
# (N=134) (N=134) (N=75)
# F M F M F M
# ————————————————————————————————————————————————————————
# Mean 32.76 35.57 34.12 37.44 35.20 35.38For convenience (primarily because it was needed internally), we also provide rm_all_colcounts which sets all column counts for a particular table to NA at all levels of nesting. We do not expect this to be particularly useful to end-users.
Typically we do not set column count visibility individually. *This is due to a constraint where direct leaf siblings (e.g. F and M under one of the arms in our layout) must have the same visibility for their column counts in order for the rendering machinery to work.
Instead, we can reset the column count visibility of groups of siblings via the facet_colcounts_visible (note the ‘s’) setter. This function accepts a path which ends in the name associated with a splitting instruction in the layout (e.g., c("ARM"), c("ARM", "B: Placebo", "SEX"), etc) and resets the visibility of all direct children of that path.
facet_colcounts_visible(tbl3, c("ARM", "A: Drug X", "SEX")) <- TRUE
tbl3
# A: Drug X
# (N=134) B: Placebo C: Combination
# F M (N=134) (N=75)
# (N=79) (N=51) F M F M
# ——————————————————————————————————————————————————————————
# Mean 32.76 35.57 34.12 37.44 35.20 35.38NOTE as we can see here, the visibility of column counts can have an “unbalanced design”, provided the direct-siblings agreeing constraint is met. This leads to things not lining up directly as one might expect (it does not generate any blank spaces the way setting a visible column count to NA does).
Currently paths with "*" in them do not work within facet_colcounts_visible, but that capability is likely to be added in future releases.
colcount_visible getters and setters do also exist which retrieve and set individual column counts’ visibilities, but these are largely an internal detail and in virtually all cases end users should avoid calling them directly.
## BEWARE, the following is expected to show error
tbl4 <- tbl3
colcount_visible(tbl4, c("ARM", "A: Drug X", "SEX", "F")) <- FALSE
tbl4
# Expected Error message
# Error in h(simpleError(msg, call)) :
# error in evaluating the argument 'x' in selecting a method for function 'toString':
# Detected different colcount visibility among sibling facets (those arising from the
# same split_cols_by* layout instruction). This is not supported.
# Set count values to NA if you want a blank space to appear as the displayed count for particular facets.
# First disagreement occured at paths:
# ARM[A: Drug X]->SEX[F]
# ARM[A: Drug X]->SEX[M]Note currently this restriction is currently only enforced for leaf columns due to technical implementation details but how a table renders should be considered undefined behavior when it contains a group of sibling column facets arising from the same layout instruction whose column count visibilities disagree. That may become an error in future versions without warning.
Advanced SettingsBy using make_col_df() we can see the full path to any column count. One example application is to add a NA value that would print to the default value is "", that will show nothing. To change (for now uniformly only) the output string in case of missing values in the column counts you can use colcount_na_str:
coldf <- make_col_df(tbl3)
facet_colcount(tbl3, coldf$path[[1]][c(1, 2)]) <- NA_integer_
print(tbl3) # Keeps the missing space
# A: Drug X
# B: Placebo C: Combination
# F M (N=134) (N=75)
# (N=79) (N=51) F M F M
# ——————————————————————————————————————————————————————————
# Mean 32.76 35.57 34.12 37.44 35.20 35.38
colcount_na_str(tbl3) <- "NaN"
tbl3 # Shows NaN
# A: Drug X
# NaN B: Placebo C: Combination
# F M (N=134) (N=75)
# (N=79) (N=51) F M F M
# ——————————————————————————————————————————————————————————
# Mean 32.76 35.57 34.12 37.44 35.20 35.38RetroSearch is an open source project built by @garambo | Open a GitHub Issue
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