Criteria functions (and constructors thereof) for trimming and pruning tables.
Usage
all_zero_or_na(tr)
all_zero(tr)
content_all_zeros_nas(tt, criteria = all_zero_or_na)
prune_empty_level(tt)
prune_zeros_only(tt)
low_obs_pruner(min, type = c("sum", "mean"))Arguments
- tr
TableRow(or related class). ATableRowobject representing a single row within a populated table.- tt
TableTree(or related class). ATableTreeobject representing a populated table.- criteria
function. Function which takes a
TableRowobject and returnsTRUEif that row should be removed. Defaults toall_zero_or_na- min
numeric(1). (
low_obs_pruneronly). Minimum aggregate count value. Subtables whose combined/average count are below this threshold will be pruned- type
character(1). How count values should be aggregated. Must be
"sum"(the default) or"mean"
Value
A logical value indicating whether tr should be included
(TRUE) or pruned (FALSE) during pruning.
Details
all_zero_or_na returns TRUE (and thus indicates
trimming/pruning) for any non-LabelRow TableRow which contain
only any mix of NA (including NaN), 0, Inf and
-Inf values.
all_zero returns TRUE for any non-Label row which
contains only (non-missing) zero values.
content_all_zeros_nas Prunes a subtable if a) it has a
content table with exactly one row in it, and b) all_zero_or_na
returns TRUE for that single content row. In practice, when the
default summary/content function is used, this represents pruning any
subtable which corresponds to an empty set of the input data (e.g., because
a factor variable was used in split_rows_by but not all
levels were present in the data).
prune_empty_level combines all_zero_or_na behavior for
TableRow objects, content_all_zeros_nas on
content_table(tt) for TableTree objects, and an additional
check that returns TRUE if the tt has no children.
prune_zeros_only behaves as prune_empty_level does,
except that like all_zero it prunes only in the case of all
non-missing zero values.
low_obs_pruner is a constructor function which, when
called, returns a pruning criteria function which will prune on content
rows by comparing sum or mean (dictated by type) of the count
portions of the cell values (defined as the first value per cell regardless
of how many values per cell there are) against min.
Examples
adsl <- ex_adsl
levels(adsl$SEX) <- c(levels(ex_adsl$SEX), "OTHER")
adsl$AGE[adsl$SEX == "UNDIFFERENTIATED"] <- 0
adsl$BMRKR1 <- 0
tbl_to_prune <- basic_table() %>%
analyze("BMRKR1") %>%
split_cols_by("ARM") %>%
split_rows_by("SEX") %>%
summarize_row_groups() %>%
split_rows_by("STRATA1") %>%
summarize_row_groups() %>%
analyze("AGE") %>%
build_table(adsl)
tbl_to_prune %>% prune_table(all_zero_or_na)
#> A: Drug X B: Placebo C: Combination
#> ———————————————————————————————————————————————————
#> F 79 (59.0%) 77 (57.5%) 66 (50.0%)
#> A 21 (15.7%) 24 (17.9%) 18 (13.6%)
#> Mean 31.14 32.08 34.22
#> B 25 (18.7%) 27 (20.1%) 21 (15.9%)
#> Mean 32.84 35.33 36.57
#> C 33 (24.6%) 26 (19.4%) 27 (20.5%)
#> Mean 33.73 34.73 34.78
#> M 51 (38.1%) 55 (41.0%) 60 (45.5%)
#> A 16 (11.9%) 19 (14.2%) 20 (15.2%)
#> Mean 35.62 39.37 33.55
#> B 21 (15.7%) 17 (12.7%) 21 (15.9%)
#> Mean 35.33 37.12 36.05
#> C 14 (10.4%) 19 (14.2%) 19 (14.4%)
#> Mean 35.86 35.79 36.58
#> U 3 (2.2%) 2 (1.5%) 4 (3.0%)
#> A 1 (0.7%) 1 (0.7%) 1 (0.8%)
#> Mean 33.00 27.00 38.00
#> B 1 (0.7%) 1 (0.7%) 1 (0.8%)
#> Mean 28.00 35.00 37.00
#> C 1 (0.7%) 0 (0.0%) 2 (1.5%)
#> Mean 34.00 NA 33.00
tbl_to_prune %>% prune_table(all_zero)
#> A: Drug X B: Placebo C: Combination
#> ———————————————————————————————————————————————————————————
#> F 79 (59.0%) 77 (57.5%) 66 (50.0%)
#> A 21 (15.7%) 24 (17.9%) 18 (13.6%)
#> Mean 31.14 32.08 34.22
#> B 25 (18.7%) 27 (20.1%) 21 (15.9%)
#> Mean 32.84 35.33 36.57
#> C 33 (24.6%) 26 (19.4%) 27 (20.5%)
#> Mean 33.73 34.73 34.78
#> M 51 (38.1%) 55 (41.0%) 60 (45.5%)
#> A 16 (11.9%) 19 (14.2%) 20 (15.2%)
#> Mean 35.62 39.37 33.55
#> B 21 (15.7%) 17 (12.7%) 21 (15.9%)
#> Mean 35.33 37.12 36.05
#> C 14 (10.4%) 19 (14.2%) 19 (14.4%)
#> Mean 35.86 35.79 36.58
#> U 3 (2.2%) 2 (1.5%) 4 (3.0%)
#> A 1 (0.7%) 1 (0.7%) 1 (0.8%)
#> Mean 33.00 27.00 38.00
#> B 1 (0.7%) 1 (0.7%) 1 (0.8%)
#> Mean 28.00 35.00 37.00
#> C 1 (0.7%) 0 (0.0%) 2 (1.5%)
#> Mean 34.00 NA 33.00
#> UNDIFFERENTIATED 1 (0.7%) 0 (0.0%) 2 (1.5%)
#> A 0 (0.0%) 0 (0.0%) 1 (0.8%)
#> Mean NA NA 0.00
#> B 0 (0.0%) 0 (0.0%) 0 (0.0%)
#> Mean NA NA NA
#> C 1 (0.7%) 0 (0.0%) 1 (0.8%)
#> Mean 0.00 NA 0.00
#> OTHER 0 (0.0%) 0 (0.0%) 0 (0.0%)
#> A 0 (0.0%) 0 (0.0%) 0 (0.0%)
#> Mean NA NA NA
#> B 0 (0.0%) 0 (0.0%) 0 (0.0%)
#> Mean NA NA NA
#> C 0 (0.0%) 0 (0.0%) 0 (0.0%)
#> Mean NA NA NA
tbl_to_prune %>% prune_table(content_all_zeros_nas)
#> A: Drug X B: Placebo C: Combination
#> ———————————————————————————————————————————————————————————
#> Mean 0.00 0.00 0.00
#> F 79 (59.0%) 77 (57.5%) 66 (50.0%)
#> A 21 (15.7%) 24 (17.9%) 18 (13.6%)
#> Mean 31.14 32.08 34.22
#> B 25 (18.7%) 27 (20.1%) 21 (15.9%)
#> Mean 32.84 35.33 36.57
#> C 33 (24.6%) 26 (19.4%) 27 (20.5%)
#> Mean 33.73 34.73 34.78
#> M 51 (38.1%) 55 (41.0%) 60 (45.5%)
#> A 16 (11.9%) 19 (14.2%) 20 (15.2%)
#> Mean 35.62 39.37 33.55
#> B 21 (15.7%) 17 (12.7%) 21 (15.9%)
#> Mean 35.33 37.12 36.05
#> C 14 (10.4%) 19 (14.2%) 19 (14.4%)
#> Mean 35.86 35.79 36.58
#> U 3 (2.2%) 2 (1.5%) 4 (3.0%)
#> A 1 (0.7%) 1 (0.7%) 1 (0.8%)
#> Mean 33.00 27.00 38.00
#> B 1 (0.7%) 1 (0.7%) 1 (0.8%)
#> Mean 28.00 35.00 37.00
#> C 1 (0.7%) 0 (0.0%) 2 (1.5%)
#> Mean 34.00 NA 33.00
#> UNDIFFERENTIATED 1 (0.7%) 0 (0.0%) 2 (1.5%)
#> A 0 (0.0%) 0 (0.0%) 1 (0.8%)
#> Mean NA NA 0.00
#> C 1 (0.7%) 0 (0.0%) 1 (0.8%)
#> Mean 0.00 NA 0.00
tbl_to_prune %>% prune_table(prune_empty_level)
#> A: Drug X B: Placebo C: Combination
#> ———————————————————————————————————————————————————
#> F 79 (59.0%) 77 (57.5%) 66 (50.0%)
#> A 21 (15.7%) 24 (17.9%) 18 (13.6%)
#> Mean 31.14 32.08 34.22
#> B 25 (18.7%) 27 (20.1%) 21 (15.9%)
#> Mean 32.84 35.33 36.57
#> C 33 (24.6%) 26 (19.4%) 27 (20.5%)
#> Mean 33.73 34.73 34.78
#> M 51 (38.1%) 55 (41.0%) 60 (45.5%)
#> A 16 (11.9%) 19 (14.2%) 20 (15.2%)
#> Mean 35.62 39.37 33.55
#> B 21 (15.7%) 17 (12.7%) 21 (15.9%)
#> Mean 35.33 37.12 36.05
#> C 14 (10.4%) 19 (14.2%) 19 (14.4%)
#> Mean 35.86 35.79 36.58
#> U 3 (2.2%) 2 (1.5%) 4 (3.0%)
#> A 1 (0.7%) 1 (0.7%) 1 (0.8%)
#> Mean 33.00 27.00 38.00
#> B 1 (0.7%) 1 (0.7%) 1 (0.8%)
#> Mean 28.00 35.00 37.00
#> C 1 (0.7%) 0 (0.0%) 2 (1.5%)
#> Mean 34.00 NA 33.00
tbl_to_prune %>% prune_table(prune_zeros_only)
#> A: Drug X B: Placebo C: Combination
#> ———————————————————————————————————————————————————————————
#> F 79 (59.0%) 77 (57.5%) 66 (50.0%)
#> A 21 (15.7%) 24 (17.9%) 18 (13.6%)
#> Mean 31.14 32.08 34.22
#> B 25 (18.7%) 27 (20.1%) 21 (15.9%)
#> Mean 32.84 35.33 36.57
#> C 33 (24.6%) 26 (19.4%) 27 (20.5%)
#> Mean 33.73 34.73 34.78
#> M 51 (38.1%) 55 (41.0%) 60 (45.5%)
#> A 16 (11.9%) 19 (14.2%) 20 (15.2%)
#> Mean 35.62 39.37 33.55
#> B 21 (15.7%) 17 (12.7%) 21 (15.9%)
#> Mean 35.33 37.12 36.05
#> C 14 (10.4%) 19 (14.2%) 19 (14.4%)
#> Mean 35.86 35.79 36.58
#> U 3 (2.2%) 2 (1.5%) 4 (3.0%)
#> A 1 (0.7%) 1 (0.7%) 1 (0.8%)
#> Mean 33.00 27.00 38.00
#> B 1 (0.7%) 1 (0.7%) 1 (0.8%)
#> Mean 28.00 35.00 37.00
#> C 1 (0.7%) 0 (0.0%) 2 (1.5%)
#> Mean 34.00 NA 33.00
#> UNDIFFERENTIATED 1 (0.7%) 0 (0.0%) 2 (1.5%)
#> A 0 (0.0%) 0 (0.0%) 1 (0.8%)
#> Mean NA NA 0.00
#> C 1 (0.7%) 0 (0.0%) 1 (0.8%)
#> Mean 0.00 NA 0.00
min_prune <- low_obs_pruner(70, "sum")
tbl_to_prune %>% prune_table(min_prune)
#> A: Drug X B: Placebo C: Combination
#> ———————————————————————————————————————————————————
#> Mean 0.00 0.00 0.00
#> F 79 (59.0%) 77 (57.5%) 66 (50.0%)
#> B 25 (18.7%) 27 (20.1%) 21 (15.9%)
#> Mean 32.84 35.33 36.57
#> C 33 (24.6%) 26 (19.4%) 27 (20.5%)
#> Mean 33.73 34.73 34.78