Melkiades
commented
1 month ago It seems to be a legitimate bug. @gmbecker, could you take a look? It may be coming from the colcounts update
Open hafen opened 1 month ago
Melkiades
commented
1 month ago It seems to be a legitimate bug. @gmbecker, could you take a look? It may be coming from the colcounts update
gmbecker
commented
1 month ago @Melkiades This isn't coming from the colcounts method, its been there for a long time (see end of message, those versions of rtables and formatters are cran versions from 2023).
What is happening has to do with the structure generated by adding an overall column that way inserts a root table that the arm substructure and overall substructure are siblings within:
> coltree_structure(tbl)
[root] (no pos)
[ARM] (no pos)
[A: Drug X] (ARM: A: Drug X)
[B: Placebo] (ARM: B: Placebo)
[C: Combination] (ARM: C: Combination)
[overall] (no pos)
[overall] (overall: overall)Also (this is back to using the cran versions), we do have working pathing because the brackets work, so the issue is mroe specifically with the column footnote machinery.
> tbl[, c("ARM", "B: Placebo")]
Note: method with signature ‘VTableTree#missing#ANY’ chosen for function ‘[’,
target signature ‘TableTree#missing#character’.
"VTableTree#ANY#character" would also be valid
B: Placebo
——————————————————————
Asian 66 (55.5%)
AGE
Mean 36.68
STRATA1
A 24
B 22
C 20
Black 28 (23.5%)
AGE
Mean 34.93
STRATA1
A 11
B 7
C 10
White 25 (21.0%)
AGE
Mean 33.12
STRATA1
A 6
B 12
C 7
> tbl[, c("overall", "overall")]
overall
———————————————————————
Asian 203 (56.2%)
AGE
Mean 35.43
STRATA1
A 63
B 67
C 73
Black 86 (23.8%)
AGE
Mean 34.30
STRATA1
A 28
B 26
C 32
White 72 (19.9%)
AGE
Mean 33.88
STRATA1
A 22
B 28
C 22 note the more technically correct paths also work within the pathing machinery that the bracket is hitting:
> tbl[, c("root", "overall", "overall")]
overall
———————————————————————
Asian 203 (56.2%)
AGE
Mean 35.43
STRATA1
A 63
B 67
C 73
Black 86 (23.8%)
AGE
Mean 34.30
STRATA1
A 28
B 26
C 32
White 72 (19.9%)
AGE
Mean 33.88
STRATA1
A 22
B 28
C 22 The culprit looks to be col_fnotes_at_path which has custom pathing machinery which looks like it never successfully handled the nested=FALSE column splitting case correctly.
Sesssion info for error
> library(formatters)
> library(rtables)
> library(dplyr)
> .simpleCap <- function(x) {
+ if (length(x) > 1) {
+ return(sapply(x, .simpleCap))
+ }
+ s <- strsplit(tolower(x), " ")[[1]]
+ paste(toupper(substring(s, 1, 1)), substring(s, 2), sep = "", collapse = " ")
+ }
> adsl2 <- ex_adsl |>
+ filter(SEX %in% c("M", "F") & RACE %in% (levels(RACE)[1:3])) |>
+ mutate(ethnicity = .simpleCap(gsub("(.*)OR.*", "\\1", RACE)), RACE = factor(RACE))
> lyt2 <- basic_table() |>
+ split_cols_by("ARM") |>
+ split_rows_by("RACE", labels_var = "ethnicity", split_fun = drop_split_levels) |>
+ summarize_row_groups() |>
+ analyze(c("AGE", "STRATA1"))
> lyt3 <- lyt2 |> add_overall_col("overall")
> tbl <- build_table(lyt3, adsl2)
> fnotes_at_path(tbl, rowpath = NULL, c("ARM", "B: Placebo")) <- c("this is a placebo")
Error in col_fnotes_at_path(coltree(ttrp), colpath, fnotes = value) :
Path appears invalid at step: ARM
> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Los_Angeles
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_1.1.4 rtables_0.6.3 magrittr_2.0.3 formatters_0.5.2
loaded via a namespace (and not attached):
[1] digest_0.6.34 backports_1.4.1 utf8_1.2.4 R6_2.5.1 fastmap_1.1.1 tidyselect_1.2.0
[7] glue_1.7.0 tibble_3.2.1 pkgconfig_2.0.3 htmltools_0.5.8.1 generics_0.1.3 lifecycle_1.0.4
[13] cli_3.6.2 fansi_1.0.6 grid_4.3.3 vctrs_0.6.5 compiler_4.3.3 tools_4.3.3
[19] checkmate_2.3.1 pillar_1.9.0 rlang_1.1.3 @hafen this is a legitimate bug. In the meantime, the workaround is to use add_overall_level as a split function (or more accurately a split function factory):
lyt4 <- basic_table() |>
split_cols_by("ARM", split_fun = add_overall_level("overall", first = FALSE)) |>
split_rows_by("RACE", labels_var = "ethnicity", split_fun = drop_split_levels) |>
summarize_row_groups() |>
analyze(c("AGE", "STRATA1"))> tbl2 <- build_table(lyt4, adsl2)
> fnotes_at_path(tbl2, rowpath = NULL, c("ARM", "B: Placebo")) <- c("this is a placebo")
> tbl2
A: Drug X B: Placebo {1} C: Combination overall
——————————————————————————————————————————————————————————————————————
Asian 66 (54.1%) 66 (55.5%) 71 (59.2%) 203 (56.2%)
AGE
Mean 32.50 36.68 36.99 35.43
STRATA1
A 21 24 18 63
B 20 22 25 67
C 25 20 28 73
Black 30 (24.6%) 28 (23.5%) 28 (23.3%) 86 (23.8%)
AGE
Mean 34.27 34.93 33.71 34.30
STRATA1
A 7 11 10 28
B 11 7 8 26
C 12 10 10 32
White 26 (21.3%) 25 (21.0%) 21 (17.5%) 72 (19.9%)
AGE
Mean 36.15 33.12 31.95 33.88
STRATA1
A 8 6 8 22
B 9 12 7 28
C 9 7 6 22
——————————————————————————————————————————————————————————————————————
{1} - this is a placebo
——————————————————————————————————————————————————————————————————————The difference here is that we are adding an "overall" facet that is a direct sibling to the arm facets, rather than one that derives from a separate top-level branch like add_overall_col does.
> coltree_structure(tbl2)
[ARM] (no pos)
[A: Drug X] (ARM: A: Drug X)
[B: Placebo] (ARM: B: Placebo)
[C: Combination] (ARM: C: Combination)
[overall] (ARM: overall)
Using the example found here (minus the secondary column splitting
split_cols_by("SEX")):Adding a column footnote works for this, for example:
However, if we add an overall column, this no longer works:
Also, possibly related, note that the actual example found here has its footnote numbered as
NAin the output found in the article.I encounter this using rtables 0.6.9 installed from CRAN as well as v0.6.9.9005 installed from GitHub.