reffn_at_path<- for postprocessing

[gmbecker]

as discussed with @anajens

[gmbecker]

@anajens I've added the fnotes_at_path<- function which allows for row and cell referntial footnotes to be added to an existing table. If we construct a table without any referential footnotes

race_levels <- c("WHITE",
                     "BLACK OR AFRICAN AMERICAN",
                     "ASIAN",
                     "AMERICAN INDIAN OR ALASKA NATIVE",
                     "MULTIPLE")
l1 <- basic_table() %>% split_cols_by("ARM") %>%
        split_rows_by("RACE", split_fun = keep_split_levels(race_levels)) %>%
        summarize_row_groups() %>%
        analyze("AGE", mean)


 tb1 <- build_table(l1, DM)
 tb1
                                      A: Drug X          B: Placebo       C: Combination 
-----------------------------------------------------------------------------------------
WHITE                                 14 (11.6%)         14 (13.2%)          18 (14%)    
  mean                             39.3571428571429   36.9285714285714   35.1111111111111
BLACK OR AFRICAN AMERICAN             28 (23.1%)         24 (22.6%)         27 (20.9%)   
  mean                             34.6785714285714   31.7083333333333          34       
ASIAN                                 79 (65.3%)         68 (64.2%)         84 (65.1%)   
  mean                             34.2025316455696   32.6764705882353   34.6309523809524
AMERICAN INDIAN OR ALASKA NATIVE        0 (0%)             0 (0%)             0 (0%)     
  mean                                    NA                 NA                 NA       
MULTIPLE                                0 (0%)             0 (0%)             0 (0%)     
  mean                                    NA                 NA                 NA       

We can then add them

fnotes_at_path(tb1, rowpath = c("RACE", "WHITE", "AGE", "mean"),
                   colpath = c("ARM", "B: Placebo")) <- "white arm b mean"

    fnotes_at_path(tb1, rowpath = c("RACE", "ASIAN", "@content", "ASIAN"),
                   colpath = c("ARM", "C: Combination")) <- "asian arm c content"

    fnotes_at_path(tb1, rowpath = c("RACE", "MULTIPLE", "@content", "MULTIPLE"),
                   colpath = NULL) <-  c("race multiple row fn 1", "race multiple row fn 2")
fnotes_at_path(tb1, rowpath = c("RACE", "WHITE", "AGE", "mean"),

tb1
                                      A: Drug X            B: Placebo         C: Combination 
---------------------------------------------------------------------------------------------
WHITE                                 14 (11.6%)           14 (13.2%)            18 (14%)    
  mean                             39.3571428571429   36.9285714285714 {1}   35.1111111111111
BLACK OR AFRICAN AMERICAN             28 (23.1%)           24 (22.6%)           27 (20.9%)   
  mean                             34.6785714285714     31.7083333333333            34       
ASIAN                                 79 (65.3%)           68 (64.2%)         84 (65.1%) {2} 
  mean                             34.2025316455696     32.6764705882353     34.6309523809524
AMERICAN INDIAN OR ALASKA NATIVE        0 (0%)               0 (0%)               0 (0%)     
  mean                                    NA                   NA                   NA       
MULTIPLE {3, 4}                         0 (0%)               0 (0%)               0 (0%)     
  mean                                    NA                   NA                   NA       
---------------------------------------------------------------------------------------------

{1} - white arm b mean
{2} - asian arm c content
{3} - race multiple row fn 1
{4} - race multiple row fn 2
`

[anajens]

Thanks so much @gmbecker, this looks great!

One question - does this also work for column footnotes? I tried the code below but I'm getting an error:

> fnotes_at_path(tb1, rowpath = NULL, colpath = c("ARM", "C: Combination")) <-  c("test col footer")
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘fnotes_at_path<-’ for signature ‘"TableTree", "NULL"’

I'm trying to make a table that looks like this:

                                      A: Drug X            B: Placebo         C: Combination {1}
---------------------------------------------------------------------------------------------
WHITE                                 14 (11.6%)           14 (13.2%)            18 (14%)    
...
---------------------------------------------------------------------------------------------

{1} - test col footer

[gmbecker]

Hi Jana. Column references are not yet supported but they will be and when they are, that is how you will create them. They're listed under a separate issue that is still open

…

On Thu, Aug 12, 2021 at 6:28 AM Jana Stoilova ***@***.***> wrote: Thanks so much @gmbecker <https://github.com/gmbecker>, this looks great! One question - does this also work for column footnotes? I tried the code below but I'm getting an error: > fnotes_at_path(tb1, rowpath = NULL, colpath = c("ARM", "C: Combination")) <- c("test col footer") Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘fnotes_at_path<-’ for signature ‘"TableTree", "NULL"’ I'm trying to make a table that looks like this: A: Drug X B: Placebo C: Combination {1} --------------------------------------------------------------------------------------------- WHITE 14 (11.6%) 14 (13.2%) 18 (14%) ... --------------------------------------------------------------------------------------------- {1} - test col footer — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#219 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAG53MMMIJCPV5I6YUO5SLTT4PEBNANCNFSM5AWERBZA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email> .

[anajens]

According to the docs, rowpath does take NULL. I guess it's just a placeholder for now?

https://github.com/Roche/rtables/blob/78f8c7a3b89b74f55e0db38deb67b576a9a2192f/R/tree_accessors.R#L2265

[gmbecker]

Yes, correct. I'm working on implementing that now. That is a placeholder for what will work, so I didn't forget to to change the docs later. Sorry about the confusion.

…

On Thu, Aug 12, 2021 at 1:44 PM Jana Stoilova ***@***.***> wrote: According to the docs, rowpath does take NULL. I guess it's just a placeholder for now? https://github.com/Roche/rtables/blob/78f8c7a3b89b74f55e0db38deb67b576a9a2192f/R/tree_accessors.R#L2265 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#219 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAG53MJZ5JLSVV7EWMNV76DT4QXCFANCNFSM5AWERBZA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email> .