update cumulative table (#238)

* update branch 207 (#222)

* 201 new figure figure 14 (#209)

* First draft

First draft (not fully working)

* New push

Now the results are correct. Colors in the table are missing and the order of the group is not correct.

* Delete width= in geom_errorbar

To avoid warning `position_dodge()` requires non-overlapping x intervals

* Update

Put example in comments @examples

* Update fda-fig_14 and argument convention

* tests

Update setup.R to add ggplot2

* quarto page

* _quarto.yml and NEWS.md

* typo

* Put PARAMCD in code mode

* Remove id_var, add visit_var, reverse order of table rows

* [skip actions] Restyle files

* Add to index

* [skip actions] Restyle files

* Empty commit

* Fix unrelated broken template

* [skip actions] Roxygen Man Pages Auto Update

* Empty commit

* Fix lint

* Fix imports/exports

* Update template

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* 196-new-table-38 (#204)

* 1st commitment for all documents

* [skip actions] Restyle files

* [skip actions] Roxygen Man Pages Auto Update

* Fix table 35 title

* Update index

* Update label indentation

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* 195 new table table 36 (#208)

* Add make_table_36

* Add tests for make_table_36

* Addd quarto page for make_table_36

* [skip actions] Restyle files

* Update NEWS file

* Remove scda from table 22

* Solve lintr marks for table 22

* empty commit

* Update WORDLIST

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* 105 table 09 tplyr (#192)

* Prepare first raw tplyr table including risk difference columns

* Table 9 Tplyr: Update header string in case risk difference columns are expected

* Table 9 Tplyr: Add parameter for overall column

* Tab 9 Tplyr: Introduce soc_var parameter

* Add show_colcounts and prune functionality

* Clean comments

* Replace remaining hard-coded variable names by parameters

* Add option to return a gt_table object

* Add checkmate checks

* Allow for both, character and factor, since tplyr seems to prefer character

* Update roxygen documentation

* Add make_table_09_tplyr() to web page

* Establish first test cases

* Add test for correct column header assignment (make_table_09_tplyr)

* Add column ordering based on arm order for make_table_09_tplyr

* Add final tests and clean

* [skip actions] Restyle files

* Solve lintr markers

* Update after devtools::check()

* [skip actions] Restyle files

* [skip actions] Roxygen Man Pages Auto Update

* Restart github check by code modification

* Update example data frpm scda to random.cdisc.data

* [skip actions] Restyle files

* [skip actions] Roxygen Man Pages Auto Update

* Set RoxygenNote to 7.3.0 as required by GitHub action

* Fix make_table_09_tplyr() row order

* Add scda to 'Suggests' since table 22 still includes it in the example and tests

* Move scda from Suggests to Imports since table 22 quarto page relies on it as well...

* Replace scda w/ random.cdisc.data for table 22 examples and tests

* [skip actions] Roxygen Man Pages Auto Update

* Restrict Tplyr version to <= 1.1.0 until newly introduced incompatibilities w/ higher versions are solved

* Restrict to Tplyr version 1.1.0

* Remove version restriction for Tplyr

* Deactivate risk difference feature until {Tplyr} issue is solved

* Re-document

* [skip style] [skip vbump] Restyle files

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* Update boehringer company logo on website (#214)

* [skip actions] Bump version to 0.1.0.9054

* 211 new table table 33 with gtsummary (#212)

Closes #211

* [skip actions] Bump version to 0.1.0.9055

* 205_BUG_fix _make_table_34 Issue (#215)

* Calculate counts for FMQ levels.
Updated test file and Qualt file accordingly.

* [skip style] [skip vbump] Restyle files

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* lint R check

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* with fda-fig_03 added

* [skip style] [skip vbump] Restyle files

* switch from {survminer} to {ggsurvfit}

* [skip style] [skip vbump] Restyle files

* Clean up aesthetics

* Import ggsurvfit

* Update tests

* Refresh template table

* Fix lint

* Fix spelling

* Load data in template

* Use DCSREAS instead of DCTREAS in figure 3 (and table 4)

* Fix R CMD Check note

* Fix remaining documentation

* update cumulative table

* Update test snapshots

---------

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Author: 9 people

R/fda-fig_03.R

@@ -152,7 +152,7 @@ make_fig_03 <- function(df,
       scale_x_continuous(breaks = xtick_lbls, limits = c(min(xlims, xtick_lbls), max(xlims, xtick_lbls)))
 
     for (i in seq_len(nrow(tbl_n_cum))) {
-      tbl_n_cum$n[i] <- sum(df$ARM == tbl_n_cum$arm[i] & df$TRTDUR >= tbl_n_cum$x[i])
+      tbl_n_cum$n[i] <- sum(df$ARM == tbl_n_cum$arm[i] & df$TRTDUR <= tbl_n_cum$x[i] & df$STATUS == 1)
       colors <- ifelse(tbl_n_cum$arm[i] == levels(df[[arm_var]])[1], "blue", "darkgrey")
       g_tbl_cum <- g_tbl_cum +
         annotate("text", label = as.character(tbl_n_cum$n[i]), x = tbl_n_cum$x[i], y = tbl_n_cum$arm[i], color = colors)