what's the use of the cextra_args element, can we remove it by default?

[shajoezhu]

Original issue reported by Elisabeth_Gruendl at https://overflow.roche.com/t/error-invalid-class-instantiatedcolumninfo-object-invalid-object-for-slot-cextra-args-in-class-instantiatedcolumninfo-got-class-numeric-should-be-or-extend-class-list/10903

library(rtables)
library(dplyr)

df <- tibble(visit = factor(rep(c("24", "52", "76", "104", "116"), times = 2), levels = c("24", "52", "76", "104", "116")),
group = factor(rep(c("Placebo", "Active"), each = 5), levels = c("Placebo", "Active")),
est = c(1, 1.2, 1.4, 1.6, 1.8, 0.9, 1, 1.1, 1.2, 1.3),
est_se = c(.3, .4, .5, .4, .3, .2, .1, .3, .4, .2),
p_value = c(NA, NA, NA, NA, NA, .8758390, .726295, .5397435, .3175389, .1563281),
header_p_value = rep("p-value of difference"))

dummy <- character()

# create first table with information by treatment
s_rbmi_trt <- function(df, .in_ref_col) {
list(
zeile1 = df$est,
zeile2 = df$est_se
)
}

a_rbmi_trt <- make_afun(
s_rbmi_trt,
.labels = c(
zeile1 = "Change from Baseline",
zeile2 = "at Week"
),
.formats = c(
zeile1 = sprintf_format("%.3f "),
zeile2 = "xx.xxx"
),
.indent_mods = c(
zeile1 = 1L,
zeile2 = 1L
)
)

summarize_rbmi_trt <- function(lyt,
...,
table_names = "rbmi_summary",
.stats = NULL,
.formats = NULL,
.indent_mods = NULL,
.labels = NULL) {
afun <- make_afun(
a_rbmi_trt,
.stats = .stats,
.formats = .formats,
.indent_mods = .indent_mods,
.labels = .labels
)
analyze(
lyt = lyt,
vars = "est",
afun = afun,
table_names = table_names,
extra_args = list(...)
)
}

rbmi_trt <- basic_table() %>%
split_cols_by("group", ref_group = levels(df$group)[1]) %>%
split_rows_by("visit", split_label = "Visit", label_pos = "topleft") %>%
summarize_rbmi_trt() %>%
build_table(df)

###############################################

########################

s_rbmi_pval <- function(df) {
list(
zeile1 = df$p_value,
zeile2 = dummy
)
}

a_rbmi_pval <- make_afun(
s_rbmi_pval,
.labels = c(
zeile1 = "Change from Baseline",
zeile2 = "at Week"
),
.formats = c(
zeile1 = "x.xxxx | (<0.0001)"
),
.indent_mods = c(
zeile1 = 1L,
zeile2 = 1L
)
)

summarize_rbmi_pval <- function(lyt,
...,
table_names = "rbmi_summary",
.stats = NULL,
.formats = NULL,
.indent_mods = NULL,
.labels = NULL) {
afun <- make_afun(
a_rbmi_pval,
.stats = .stats,
.formats = .formats,
.indent_mods = .indent_mods,
.labels = .labels
)
analyze(
lyt = lyt,
vars = "est",
afun = afun,
table_names = table_names,
extra_args = list(...)
)
}

rbmi_pval <- basic_table() %>%
split_cols_by("header_p_value") %>%
split_rows_by("visit", split_label = " ", label_pos = "topleft") %>%
summarize_rbmi_pval() %>%
build_table(df %>% filter(group == "Active"))

top_left(rbmi_trt) <- "Visit"
top_left(rbmi_pval) <- "Visit"

rbmi_landscape <- cbind_rtables(rbmi_trt, rbmi_pval)

work around provided by Liming

rbmi_trt1 <- rbmi_trt
rbmi_trt1@col_info@cextra_args <- list()
cbind_rtables(rbmi_trt1, rbmi_pval)

This will remove the cextra_args in that object, so it works.