Tplyr
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Published
20 hours ago •
atorus-research
atorus-research
Add set_numeric_where functionality
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set_numeric_where
This new function adds a filter step after the numeric_data is created to filter out rows that don't meet the cutoff. Columns, stat, and cutoffs can all be set
Examples
mtcars %>%
tplyr_table(gear) %>%
add_layer(
group_count(cyl) %>%
set_numeric_where(10, "n") %>%
add_total_row() %>%
set_order_count_method("bycount")
) %>% build()
# A tibble: 2 × 6
row_label1 var1_3 var1_4 var1_5 ord_layer_index ord_layer_1
<chr> <chr> <chr> <chr> <int> <dbl>
1 8 12 ( 80.0%) " 0 ( 0.0%)" " 2 ( 40.0%)" 1 0
2 Total 15 (100.0%) "12 (100.0%)" " 5 (100.0%)" 1 12
load(test_path("adae.Rdata"))
adae %>%
tplyr_table(TRTA) %>%
add_layer(
group_count(vars(AEBODSYS, AEDECOD)) %>%
set_numeric_where(3, "n", "Placebo") %>%
add_total_row()
) %>%
build()
# A tibble: 13 × 8
row_label1 row_label2 var1_Placebo `var1_Xanomeli…` `var1_Xanomeli…` ord_layer_index ord_layer_1 ord_layer_2
<chr> <chr> <chr> <chr> <chr> <int> <dbl> <dbl>
1 CARDIAC DISORDERS "CARDIAC DIS… " 5 ( 10.6%… " 6 ( 7.8%)" " 6 ( 7.9%)" 1 1 Inf
2 GASTROINTESTINAL DISORDERS "GASTROINTES… " 6 ( 12.8%… " 6 ( 7.8%)" " 3 ( 3.9%)" 1 2 Inf
3 GASTROINTESTINAL DISORDERS " DIARRHOE… " 3 ( 6.4%… " 1 ( 1.3%)" " 2 ( 2.6%)" 1 2 1
4 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS "GENERAL DIS… "11 ( 23.4%… "21 ( 27.3%)" "21 ( 27.6%)" 1 3 Inf
5 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS " APPLICAT… " 4 ( 8.5%… " 7 ( 9.1%)" " 5 ( 6.6%)" 1 3 1
6 INFECTIONS AND INFESTATIONS "INFECTIONS … " 5 ( 10.6%… " 4 ( 5.2%)" " 3 ( 3.9%)" 1 4 Inf
7 INFECTIONS AND INFESTATIONS " UPPER RE… " 4 ( 8.5%… " 1 ( 1.3%)" " 1 ( 1.3%)" 1 4 1
8 INVESTIGATIONS "INVESTIGATI… " 3 ( 6.4%… " 1 ( 1.3%)" " 1 ( 1.3%)" 1 5 Inf
9 PSYCHIATRIC DISORDERS "PSYCHIATRIC… " 3 ( 6.4%… " 2 ( 2.6%)" " 3 ( 3.9%)" 1 6 Inf
10 SKIN AND SUBCUTANEOUS TISSUE DISORDERS "SKIN AND SU… " 7 ( 14.9%… "21 ( 27.3%)" "26 ( 34.2%)" 1 7 Inf
11 SKIN AND SUBCUTANEOUS TISSUE DISORDERS " ERYTHEMA" " 4 ( 8.5%… " 3 ( 3.9%)" " 2 ( 2.6%)" 1 7 1
12 SKIN AND SUBCUTANEOUS TISSUE DISORDERS " PRURITUS" " 3 ( 6.4%… " 8 ( 10.4%)" " 7 ( 9.2%)" 1 7 2
13 Total "Total" "47 (100.0%… "77 (100.0%)" "76 (100.0%)" 1 8 Inf
@elimillera looking at this output, note row 1:
# A tibble: 13 × 8
row_label1 row_label2 var1_Placebo `var1_Xanomeli…` `var1_Xanomeli…` ord_layer_index ord_layer_1 ord_layer_2
<chr> <chr> <chr> <chr> <chr> <int> <dbl> <dbl>
1 CARDIAC DISORDERS "CARDIAC DIS… " 5 ( 10.6%… " 6 ( 7.8%)" " 6 ( 7.9%)" 1 1 Inf
2 GASTROINTESTINAL DISORDERS "GASTROINTES… " 6 ( 12.8%… " 6 ( 7.8%)" " 3 ( 3.9%)" 1 2 Inf
3 GASTROINTESTINAL DISORDERS " DIARRHOE… " 3 ( 6.4%… " 1 ( 1.3%)" " 2 ( 2.6%)" 1 2 1
4 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS "GENERAL DIS… "11 ( 23.4%… "21 ( 27.3%)" "21 ( 27.6%)" 1 3 Inf
5 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS " APPLICAT… " 4 ( 8.5%… " 7 ( 9.1%)" " 5 ( 6.6%)" 1 3 1
6 INFECTIONS AND INFESTATIONS "INFECTIONS … " 5 ( 10.6%… " 4 ( 5.2%)" " 3 ( 3.9%)" 1 4 Inf
7 INFECTIONS AND INFESTATIONS " UPPER RE… " 4 ( 8.5%… " 1 ( 1.3%)" " 1 ( 1.3%)" 1 4 1
8 INVESTIGATIONS "INVESTIGATI… " 3 ( 6.4%… " 1 ( 1.3%)" " 1 ( 1.3%)" 1 5 Inf
9 PSYCHIATRIC DISORDERS "PSYCHIATRIC… " 3 ( 6.4%… " 2 ( 2.6%)" " 3 ( 3.9%)" 1 6 Inf
10 SKIN AND SUBCUTANEOUS TISSUE DISORDERS "SKIN AND SU… " 7 ( 14.9%… "21 ( 27.3%)" "26 ( 34.2%)" 1 7 Inf
11 SKIN AND SUBCUTANEOUS TISSUE DISORDERS " ERYTHEMA" " 4 ( 8.5%… " 3 ( 3.9%)" " 2 ( 2.6%)" 1 7 1
12 SKIN AND SUBCUTANEOUS TISSUE DISORDERS " PRURITUS" " 3 ( 6.4%… " 8 ( 10.4%)" " 7 ( 9.2%)" 1 7 2
13 Total "Total" "47 (100.0%… "77 (100.0%)" "76 (100.0%)" 1 8 Inf
If there aren't any inner layer values, the outer layer should be suppressed.
Hey @mstackhouse
That is updated. Here is the new functionality:
load(test_path("adae.Rdata"))
tmo <- adae %>%
tplyr_table(TRTA) %>%
add_layer(
group_count(vars(AEBODSYS, AEDECOD)) %>%
set_numeric_where(3, "n", "Placebo") %>%
add_total_row()
) %>%
build()
# A tibble: 10 × 8
row_label1 row_label2 var1_Placebo `var1_Xanomeli…` `var1_Xanomeli…` ord_layer_index ord_layer_1
<chr> <chr> <chr> <chr> <chr> <int> <dbl>
1 GASTROINTESTINAL D… "GASTROIN… " 6 ( 12.8%… " 6 ( 7.8%)" " 3 ( 3.9%)" 1 1
2 GASTROINTESTINAL D… " DIARR… " 3 ( 6.4%… " 1 ( 1.3%)" " 2 ( 2.6%)" 1 1
3 GENERAL DISORDERS … "GENERAL … "11 ( 23.4%… "21 ( 27.3%)" "21 ( 27.6%)" 1 2
4 GENERAL DISORDERS … " APPLI… " 4 ( 8.5%… " 7 ( 9.1%)" " 5 ( 6.6%)" 1 2
5 INFECTIONS AND INF… "INFECTIO… " 5 ( 10.6%… " 4 ( 5.2%)" " 3 ( 3.9%)" 1 3
6 INFECTIONS AND INF… " UPPER… " 4 ( 8.5%… " 1 ( 1.3%)" " 1 ( 1.3%)" 1 3
7 SKIN AND SUBCUTANE… "SKIN AND… " 7 ( 14.9%… "21 ( 27.3%)" "26 ( 34.2%)" 1 4
8 SKIN AND SUBCUTANE… " ERYTH… " 4 ( 8.5%… " 3 ( 3.9%)" " 2 ( 2.6%)" 1 4
9 SKIN AND SUBCUTANE… " PRURI… " 3 ( 6.4%… " 8 ( 10.4%)" " 7 ( 9.2%)" 1 4
10 Total "Total" "47 (100.0%… "77 (100.0%)" "76 (100.0%)" 1 5
# … with 1 more variable: ord_layer_2 <dbl>
@elimillera The functionality looks right now - but I have a suggestion for the API so I'm curious of your thoughts on that.