Dev (#147)

* feat: prepare dev book version and its URL * Modify wording of notice (#142) * fix #144 fnotes_at_path issue (#145) * add latest minutes * re-add aliasing of RefFootnote function so it works with 0.6.6 CRAN release * fix silly typo in realias * add definition of RefFootnote where it is missing so CRAN version works * remove second line of flextable columnheader formatting in 04-04 --------- Co-authored-by: Joseph Rickert <[email protected]> Co-authored-by: Joseph Rickert <[email protected]> Co-authored-by: joseph-rickert <[email protected]> * JBR April Minutes * JBR: May minutes * fix: update rtables codes it seems summarize_vars is replaced by analyze_vars * JBR: small change * JBR: small chane --------- Co-authored-by: David Gohel <[email protected]> Co-authored-by: Richard Iannone <[email protected]> Co-authored-by: Gabe Becker <[email protected]> Co-authored-by: Joseph Rickert <[email protected]> Co-authored-by: Joseph Rickert <[email protected]>
RConsortium · Jun 6, 2024 · 597708c · 597708c
1 parent 8859922
commit 597708c
Show file tree

Hide file tree

Showing 9 changed files with 966 additions and 16 deletions.
diff --git a/Minutes/2024-04-04_RTRS_Min.html b/Minutes/2024-04-04_RTRS_Min.html
diff --git a/Minutes/2024-04-04_RTRS_Min.md b/Minutes/2024-04-04_RTRS_Min.md
@@ -0,0 +1,34 @@
+## Minutes RTRS WG Meeting April 4, 2024
+
+Minutes by Joseph Rickert
+
+### Attendees
+* Gabe Becker
+* David Gohel
+* Alexandra Lauer
+* Himanshu Panya - Arcus
+* Joseph B Rickert - ProCogia
+* Adrian Waddell = Genentech
+* S. W. Wang
+
+Those present agreed that there is still work to be done on: 
+
+* Value Formatting
+* Listings
+
+There was no consensus, however, on whether the working group should take the next step beyond showing how to build tables and produce table shells. It was agreed than this task would require agreement on the details from a number of pharma companies and perhaps require FDA buy in.
+
+Alex suggested writing a position paper on what would be required to do this work.
+
+There was also some discussion as to whether activity initiated by the new European agreement might make Health Technology Assessment an area of interest for this working group.
+
+Alex informed the group that she has change employment and will no longer be attending group meeting.
+
+We all wish to than Alex for her many, varied contributions to the working group and the document. We will miss her analytical approach and wry wit in group discussions.
+
+**Actions:**
+
+* Adrian and David will fix the problem with the link for the dev version of the document
+* Gabe will complete the section outlining value formatting.
+
+The May meeting of the working group will be on Thursday May 2, 2024 at 9AM PST.
diff --git a/Minutes/2024-05-02_RTRS_Min.html b/Minutes/2024-05-02_RTRS_Min.html
diff --git a/Minutes/2024-05-02_RTRS_Min.md b/Minutes/2024-05-02_RTRS_Min.md
@@ -0,0 +1,23 @@
+## Minutes RTRS WG Meeting May 2, 2024
+
+Minutes by Joseph Rickert
+
+### Attendees
+
+* Joseph B Rickert
+* David Gohel 
+* Adrian Waddell - Genentech
+
+It is apparent from the light attendance at the last few meetings that enthusiasm for the the working group is waning. This is not surprising. The publication of version 1 of *Tables in Clinical Trials with R* was a significant accomplishment which involved the sustained commitment of several contributors for more than three years. This kind of sustained effort is difficult to maintain.
+
+Because attrition and job changes, the working group no longer enjoys the participation of enough members working directly in clinical environments. The successful continuation of the group will require recruiting new members.
+
+There is general agreement that a second version of the document would address the topics of table value formatting and listings. 
+
+There is also a recognition that the whole issue of the workflows required to produce tables in an R environment is largely un-addressed and presents several challenges. Table productions for a clinical trial submission spans several departments including Biostatistics, Safety, and Medical Writing. Every pharma has their own workflows and protocols and agreement on a common standard would require collaboration from a large number of organizations.
+
+In the upcoming June meeting we will discuss the future of the working group. In preparation for this meeting Adrian has agreed to develop a short statement of what an effort to investigate Table related workflows would involve.
+
+The next meeting of the working group will be held at 9AM Pacific Time on Thursday June 6, 2024.
+
+
diff --git a/tables-book/04-01-demographics.Rmd b/tables-book/04-01-demographics.Rmd
@@ -47,7 +47,7 @@ lyt <- basic_table(title = "x.x: Study Subject Data",
                                 "Table x.x.x.x: Demographic Characteristics - Full Analysis Set"),
                    prov_footer = "Source: ADSL DDMMYYYY hh:mm; Listing x.xx; SDTM package: DDMMYYYY") |>
   split_cols_by("ARM") |>
-  summarize_vars(c("AGE", "SEX", "COUNTRY"))
+  analyze_vars(c("AGE", "SEX", "COUNTRY"))
 
 build_table(lyt, ex_adsl)
 ```

diff --git a/tables-book/04-03-kaplan-meier.Rmd b/tables-book/04-03-kaplan-meier.Rmd
@@ -54,7 +54,8 @@ stitle_txt <- c("x.x.x: Time to First Serious Adverse Event",
 resetSession(.kmState)
 library(rtables)
 
-## this will be properly exported in the next release of rtables
+## this is exported in development version of rtables, and will be so in the
+## next CRAN release
 RefFootnote <- rtables:::RefFootnote
 
 cnsr_counter <- function(df, .var, .N_col) {
@@ -101,7 +102,8 @@ a_tte <- function(df, .var,  kp_table) {
             "Min Max" = mm_val_str,
             .formats = c("xx.xx",
                          "xx.xx - xx.xx",
-                         "xx"), .cell_footnotes = list(NULL, NULL, list(RefFootnote("Denotes censoring", index = 0L, symbol = "*"))))
+                         "xx"),
+            .cell_footnotes = list(NULL, NULL, list(RefFootnote("Denotes censoring", index = 0L, symbol = "*"))))
 }
             
 
@@ -135,7 +137,7 @@ particulate, its implementation of the Cox pairwise analysis does not
 implement the one-tailed p-value strategy used in the rest of this
 chapter.
 
-We will first showcaes the pure *tern* solution, which has different
+We will first showcase the pure *tern* solution, which has different
 p-values for this reason, and then implement a hybrid *tern* +
 explicit *rtables* solution which fully recreates the exact table
 generated by other systems.
@@ -144,9 +146,11 @@ generated by other systems.
 resetSession(.kmState)
 library(tern)
 
-## this will be properly exported in the next release of rtables
+## this is exported in development version of rtables, and will be so in the
+## next CRAN release
 RefFootnote <- rtables:::RefFootnote
 
+
 adtte3 <- adtte
 adtte3$is_event <- adtte$CNSR == 0
 adtte3$CNSDTDSC[adtte$CNSDTDSC == ""] <- NA
@@ -201,7 +205,7 @@ fnote <- RefFootnote("Censored.", index = 0L, symbol = "^")
 
 for(pth in col_paths(tbl_tte_tern)) {
     fnotes_at_path(tbl_tte_tern,
-                   rowpath = c("ma_STUDYID_CNSDTDSC_coxph_AVAL", "AVAL", "range"),
+                   rowpath = c("ma_STUDYID_CNSDTDSC_coxph_AVAL", "AVAL", "Min Max"),
                    colpath = pth) <- fnote
 }
 tbl_tte_tern
@@ -213,6 +217,9 @@ rest of the table structure.
 
 ```{r}
 
+## this is exported in development version of rtables, and will be so in the
+## next CRAN release
+RefFootnote <- rtables:::RefFootnote
 
 a_cph <- function(df, .var, .in_ref_col, .ref_full, full_cox_fit) {
   if(.in_ref_col) {
@@ -274,7 +281,7 @@ fnote <- RefFootnote("Denotes censoring.", index = 0L, symbol = "*")
 
 for(pth in col_paths(tbl_tte_tern2)) {
     fnotes_at_path(tbl_tte_tern2,
-                   rowpath = c("ma_STUDYID_CNSDTDSC_ARM_AVAL", "AVAL", "range"),
+                   rowpath = c("ma_STUDYID_CNSDTDSC_ARM_AVAL", "AVAL", "Min Max"),
                    colpath = pth) <- fnote
 }
 tbl_tte_tern2

diff --git a/tables-book/04-04-concomitant-medications.Rmd b/tables-book/04-04-concomitant-medications.Rmd
@@ -77,9 +77,7 @@ tt_to_flextable(build_table(lyt, cadcm, alt_counts_df = cadsl)) |>
   set_table_properties(layout = "fixed") |> 
   autofit() |> 
   mk_par(i = 1, j = 1, part = "header",
-         as_paragraph(as_chunk("Conmed Example", props = fp_text_default(font.size = 14)))) |> 
-  mk_par(i = 2, j = 1, part = "header",
-         as_paragraph("Uses the adcm dataset from ", as_b("random.cdisc.data")))
+         as_paragraph(as_chunk("Conmed Example", props = fp_text_default(font.size = 14))))
 ```
 
 ### gt

diff --git a/tables-book/04-05-disposition.Rmd b/tables-book/04-05-disposition.Rmd
@@ -63,12 +63,12 @@ lyt <- basic_table(show_colcounts = TRUE) |>
                .labels = c(count_fraction = "Ongoing Study")) |>
   split_rows_by("EOSSTT",
                 split_fun = keep_split_levels("DISCONTINUED")) |>
-  summarize_vars("DCSREAS",
+  analyze_vars("DCSREAS",
                  .stats = "count_fraction",
                  denom = "N_col") |>
   split_rows_by("DCSREAS",
                 split_fun = keep_split_levels("DEATH")) |>
-  summarize_vars("DTHCAUS",
+  analyze_vars("DTHCAUS",
                  .stats = "count_fraction",
                  denom = "N_col")
 

diff --git a/tables-book/index.Rmd b/tables-book/index.Rmd
@@ -14,15 +14,18 @@ github-repo: "RConsortium/rtrs-wg"
 editor_options:
   chunk_output_type: console
 params:
-  version: "1.0"
+  version: "1.1.001"
 ---
 
 # About
 
-You are currently reading version `r params$version` of the book whose URL is https://rconsortium.github.io/rtrs-wg/. 
+<!---You are currently reading version `r params$version` of the book whose URL is https://rconsortium.github.io/rtrs-wg/. 
 
-The future version named *dev* version, currently being prepared, is 
-available at the URL https://rconsortium.github.io/rtrs-wg/dev/.
+The future version (named the *dev* version, which is currently being prepared) is 
+available at the URL https://rconsortium.github.io/rtrs-wg/dev/.--->
+
+You are currently reading the development version (`r params$version`) 
+of the book whose URL is https://rconsortium.github.io/rtrs-wg/dev. 
 
 ## Introduction