Tplyr Metadata

Generating the Metadata

Consider the following example:

t <- tplyr_table(tplyr_adsl, TRT01P, where = SAFFL == "Y") %>% 
  add_layer(
    group_count(RACE)
  ) %>% 
  add_layer(
    group_desc(AGE, where = EFFFL == "Y")
  )

dat <- t %>% build(metadata=TRUE)

kable(dat)

To trigger the creation of metadata, the build() function has a new argument metadata. By specifying TRUE, the underlying metadata within Tplyr are prepared in an extractable format. This is the only action a user needs to specify for this action to take place.

When the metadata argument is used, a new column will be produced in the output dataframe called row_id. The row_id variable provides a persistent reference to a row of interest, even if the output dataframe is sorted. If you review vignette("styled-table"), note that we expect a certain amount of post processing and styling of the built data frame from Tplyr, to let you use whatever other packages you prefer. As such, this reference ID is necessary.

Extracting The Input Source

So, let’s cut to the chase. The most likely way you would use this metadata is to pull out the source data that created a cell. For this, we’ve provided the function get_meta_subset(). The only information that you need is the row_id and column name of the result cell of interest. For example, looking at the result above, what if we want to know who the 8 subjects in the Placebo group who where Black or African American:

get_meta_subset(t, 'c2_1', 'var1_Placebo') %>% 
  kable()

By using the row_id and column, the dataframe is pulled right out for us. Notice that USUBJID was included by default, even though Tplyr there’s no reference anywhere in the tplyr_table() to the variable USUBJID. This is because get_meta_subset() has an additional argument add_cols that allows you to specify additional columns you want included in the resulting dataframe, and has a default of USUBJID. So let’s say we want additionally include the variable SEX.

get_meta_subset(t, 'c2_1', 'var1_Placebo', add_cols = vars(USUBJID, SEX)) %>% 
  kable()

Variables should be provided using dplyr::vars(), just like the cols argument on tplyr_table() and the by arguments in each layer type.

As mentioned, the input source data can be extracted for any result cell created by Tplyr. So let’s say we want to know the subjects relevant for the descriptive statistics around age in the Xanomeline High Dose group:

get_meta_subset(t, 'd1_2', 'var1_Xanomeline High Dose') %>% 
  head(10) %>% 
  kable()

Note: Trimmed for space

Notice how the columns returned are different. First off, within the summary above, we pulled results from the descriptive statistics layer. The target variable for this layer was AGE, and as such AGE is returned in the resulting output. Additionally, a layer level where argument was used to subset to EFFFL == "Y", which leads to EFFFL being included in the output as well.

Extracting a Result Cell’s Metadata

To extract the dataframe in get_meta_subset(), the metadata of the result cell needs to first be extracted. This metadata can be directly accessed using the function get_meta_result(). Using the last example of get_meta_subset() above:

get_meta_result(t, 'd1_2', 'var1_Xanomeline High Dose')
#> tplyr_meta: 4 names, 3 filters
#> Names:
#>      TRT01P, EFFFL, SAFFL, AGE 
#> Filters:
#>      TRT01P == c("Xanomeline High Dose"), EFFFL == "Y", SAFFL == "Y"

The resulting output is a new object Tplyr called tplyr_meta(). This is a container of a relevent metadata for a specific result. The object itself is a list with two elements: names and filters.

The names element contains quosures for each variable relevant to a specific result. This will include the target variable, the by variables used on the layer, the cols variables used on the table, and all variables included in any filter condition relevant to create the result.

The filters element contains each filter condition (provided as calls) necessary to create a particular cell. This will include the table level where argument, the layer level where argument, the filter condition for the specific value of any by variable or cols variable necessary to create the cell, and similarly the filter for the treatment group of interest.

The results are provided this was so that they can be unpacked directly into dplyr syntax when necessary, which is exactly what happens in get_meta_subset(). For example:

m <- get_meta_result(t, 'd1_2', 'var1_Xanomeline High Dose')

tplyr_adsl %>% 
  filter(!!!m$filters) %>% 
  select(!!!m$names) %>% 
  head(10) %>% 
  kable()

Note: Trimmed for space

But - who says you can’t let your imagination run wild?

cat(c("tplyr_adsl %>%\n",
  "   filter(\n      ",
  paste(purrr::map_chr(m$filters, ~ rlang::as_label(.)), collpase=",\n      "),
  ") %>%\n",
  paste("   select(", paste(purrr::map_chr(m$names, rlang::as_label), collapse=", "), ")", sep="")
))

t <- tplyr_table(tplyr_adae, TRTA) %>%
  set_pop_data(tplyr_adsl) %>%
  set_pop_treat_var(TRT01A) %>%
  add_layer(
    group_count(vars(AEBODSYS, AEDECOD)) %>%
      set_distinct_by(USUBJID) %>%
      add_missing_subjects_row(f_str("xx (XX.x%)", distinct_n, distinct_pct), sort_value = Inf)
  )

x <- build(t, metadata=TRUE)

tail(x) %>% 
  select(starts_with('row'), var1_Placebo) %>% 
  kable()

m <- get_meta_result(t, 'c23_1', 'var1_Placebo')
m
#> tplyr_meta: 3 names, 4 filters
#> Names:
#>      TRTA, AEBODSYS, AEDECOD 
#> Filters:
#>      TRTA == c("Placebo"), AEBODSYS == c("SKIN AND SUBCUTANEOUS TISSUE DISORDERS"), TRUE, TRUE 
#> Anti-join:
#>     Join Meta:
#>         tplyr_meta: 1 names, 3 filters
#>         Names:
#>              TRT01A 
#>         Filters:
#>              TRT01A == c("Placebo"), TRUE, TRUE 
#>     On:
#>         USUBJID

head(get_meta_subset(t, 'c23_1', 'var1_Placebo'))
#> # A tibble: 6 × 2
#>   USUBJID     TRT01A 
#>   <chr>       <chr>  
#> 1 01-701-1015 Placebo
#> 2 01-701-1047 Placebo
#> 3 01-701-1118 Placebo
#> 4 01-701-1153 Placebo
#> 5 01-701-1203 Placebo
#> 6 01-701-1234 Placebo

head(get_meta_subset(t$metadata, 'c23_1', 'var1_Placebo', 
                     target=t$target, pop_data=t$pop_data))
#> # A tibble: 6 × 2
#>   USUBJID     TRT01A 
#>   <chr>       <chr>  
#> 1 01-701-1015 Placebo
#> 2 01-701-1047 Placebo
#> 3 01-701-1118 Placebo
#> 4 01-701-1153 Placebo
#> 5 01-701-1203 Placebo
#> 6 01-701-1234 Placebo

tplyr_adsl %>%
    filter(
       TRTA == c("Placebo") ,
       AEBODSYS == c("SKIN AND SUBCUTANEOUS TISSUE DISORDERS") ,
       TRUE ,
       TRUE ,
       ) %>%
    select(TRTA, AEBODSYS, AEDECOD)

So, What Does This Get Me?

So we get get metadata around a result cell, and we can get the exact results from a result cell. You just need a row ID and a column name. But - what does that get you? You can query your tables - and that’s great. But how do you use that.

The idea behind this is really to support Shiny. Consider this minimal application. Click any of the result cells within the table and see what happens.

Source code available here

That’s what this is all about. The persistent row_id and column selection enables you to use something like Shiny to automatically query a cell based on its position in a table. Using click events and a package like reactable, you can pick up the row and column selected and pass that information into get_meta_result(). Once you get the resulting data frame, it’s up to you what you do with it, and you have the world of Shiny at the tip of your fingers.