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feat: added "fraction" statistic to the "analyze_var_count" method gr…
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…oup (#1309)


Signed-off-by: Konrad Pagacz <[email protected]>
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@kpagacz
kpagacz authored Sep 17, 2024
1 parent e4ee976 commit d76a95c
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Showing 6 changed files with 167 additions and 18 deletions.
1 change: 1 addition & 0 deletions NEWS.md
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Expand Up @@ -6,6 +6,7 @@
* Added the `riskdiff` argument to `tabulate_rsp_subgroups` and `tabulate_survival_subgroups` to allow users to add a risk difference table column, and function `control_riskdiff` to specify settings for the risk difference column.
* Added warning to `tabulate_rsp_subgroups` when `pval` statistic is selected but `df` has not been correctly generated to add p-values to the output table.
* Added `n_rate` statistic as a non-default option to `estimate_incidence_rate` which returns both number of events observed and estimated incidence rate.
* Added `fraction` statistic to the `analyze_var_count` method group.

### Bug Fixes
* Fixed a bug in `a_surv_time` that threw an error when split only has `"is_event"`.
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4 changes: 4 additions & 0 deletions R/analyze_variables.R
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Expand Up @@ -310,6 +310,10 @@ s_summary.factor <- function(x,
c(x, ifelse(dn > 0, x / dn, 0))
}
)
y$fraction <- lapply(
y$count,
function(count) c("num" = count, "denom" = dn)
)

y$n_blq <- sum(grepl("BLQ|LTR|<[1-9]|<PCLLOQ", x))

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2 changes: 1 addition & 1 deletion R/utils_default_stats_formats_labels.R
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Expand Up @@ -368,7 +368,7 @@ tern_default_stats <- list(
abnormal_by_worst_grade = c("count_fraction", "count_fraction_fixed_dp"),
abnormal_by_worst_grade_worsen = c("fraction"),
analyze_patients_exposure_in_cols = c("n_patients", "sum_exposure"),
analyze_vars_counts = c("n", "count", "count_fraction", "count_fraction_fixed_dp", "n_blq"),
analyze_vars_counts = c("n", "count", "count_fraction", "count_fraction_fixed_dp", "fraction", "n_blq"),
analyze_vars_numeric = c(
"n", "sum", "mean", "sd", "se", "mean_sd", "mean_se", "mean_ci", "mean_sei", "mean_sdi", "mean_pval",
"median", "mad", "median_ci", "quantiles", "iqr", "range", "min", "max", "median_range", "cv",
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152 changes: 140 additions & 12 deletions tests/testthat/_snaps/analyze_variables.md
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Expand Up @@ -628,6 +628,20 @@
[1] 4.0000000 0.4444444
$fraction
$fraction$Female
num denom
2 9
$fraction$Male
num denom
3 9
$fraction$Unknown
num denom
4 9
$n_blq
[1] 0
Expand Down Expand Up @@ -668,6 +682,24 @@
[1] 1.0000000 0.1428571
$fraction
$fraction$Female
num denom
2 7
$fraction$Male
num denom
2 7
$fraction$Unknown
num denom
2 7
$fraction$`NA`
num denom
1 7
$n_blq
[1] 0
Expand Down Expand Up @@ -702,6 +734,20 @@
[1] 4.0000000 0.4444444
$fraction
$fraction$Female
num denom
2 9
$fraction$Male
num denom
3 9
$fraction$Unknown
num denom
4 9
$n_blq
[1] 0
Expand Down Expand Up @@ -736,6 +782,20 @@
[1] 0 0
$fraction
$fraction$a
num denom
0 0
$fraction$b
num denom
0 0
$fraction$c
num denom
0 0
$n_blq
[1] 0
Expand Down Expand Up @@ -770,6 +830,20 @@
[1] 4.0 0.2
$fraction
$fraction$Female
num denom
2 20
$fraction$Male
num denom
3 20
$fraction$Unknown
num denom
4 20
$n_blq
[1] 0
Expand Down Expand Up @@ -804,6 +878,20 @@
[1] 4.0000000 0.1333333
$fraction
$fraction$Female
num denom
2 30
$fraction$Male
num denom
3 30
$fraction$Unknown
num denom
4 30
$n_blq
[1] 0
Expand Down Expand Up @@ -844,6 +932,24 @@
[1] 1.0 0.1
$fraction
$fraction$Female
num denom
2 10
$fraction$Male
num denom
3 10
$fraction$Unknown
num denom
4 10
$fraction$`NA`
num denom
1 10
$n_blq
[1] 0
Expand Down Expand Up @@ -971,7 +1077,10 @@
8 a 3 (60.0%) 0 a
9 b 1 (20.0%) 0 b
10 c 1 (20.0%) 0 c
11 n_blq 0 0 n_blq
11 a 3/5 (60.0%) 0 a
12 b 1/5 (20.0%) 0 b
13 c 1/5 (20.0%) 0 c
14 n_blq 0 0 n_blq

---

Expand All @@ -991,7 +1100,10 @@
8 A 2 (50.0%) 0 A
9 B 1 (25.0%) 0 B
10 C 1 (25.0%) 0 C
11 n_blq 0 0 n_blq
11 A 2/4 (50.0%) 0 A
12 B 1/4 (25.0%) 0 B
13 C 1/4 (25.0%) 0 C
14 n_blq 0 0 n_blq

---

Expand All @@ -1005,7 +1117,8 @@
2 count 3 0 count
3 count_fraction 3 (60%) 0 count_fraction
4 count_fraction 3 (60.0%) 0 count_fraction
5 n_blq 0 0 n_blq
5 fraction 0 fraction
6 n_blq 0 0 n_blq

# a_summary works with custom input.

Expand Down Expand Up @@ -1039,7 +1152,11 @@
11 b 1 (20.0%) 0 b
12 c 1 (20.0%) 0 c
13 NA 1 (20.0%) 0 NA
14 n_blq 0 0 n_blq
14 a 2/5 (40.0%) 0 a
15 b 1/5 (20.0%) 0 b
16 c 1/5 (20.0%) 0 c
17 NA 1/5 (20.0%) 0 NA
18 n_blq 0 0 n_blq

# a_summary works with healthy input when compare = TRUE.

Expand Down Expand Up @@ -1093,8 +1210,11 @@
8 a 3 (60.0%) 0 a
9 b 1 (20.0%) 0 b
10 c 1 (20.0%) 0 c
11 n_blq 0 0 n_blq
12 p-value (chi-squared test) 0.9560 0 p-value (chi-squared test)
11 a 3/5 (60.0%) 0 a
12 b 1/5 (20.0%) 0 b
13 c 1/5 (20.0%) 0 c
14 n_blq 0 0 n_blq
15 p-value (chi-squared test) 0.9560 0 p-value (chi-squared test)

---

Expand All @@ -1114,8 +1234,11 @@
8 A 2 (50.0%) 0 A
9 B 1 (25.0%) 0 B
10 C 1 (25.0%) 0 C
11 n_blq 0 0 n_blq
12 p-value (chi-squared test) 0.9074 0 p-value (chi-squared test)
11 A 2/4 (50.0%) 0 A
12 B 1/4 (25.0%) 0 B
13 C 1/4 (25.0%) 0 C
14 n_blq 0 0 n_blq
15 p-value (chi-squared test) 0.9074 0 p-value (chi-squared test)

---

Expand All @@ -1129,8 +1252,9 @@
2 count 3 0 count
3 count_fraction 3 (60%) 0 count_fraction
4 count_fraction 3 (60.0%) 0 count_fraction
5 n_blq 0 0 n_blq
6 p-value (chi-squared test) 0.8091 0 p-value (chi-squared test)
5 fraction 0 fraction
6 n_blq 0 0 n_blq
7 p-value (chi-squared test) 0.8091 0 p-value (chi-squared test)

# a_summary works with custom input when compare = TRUE.

Expand Down Expand Up @@ -1164,8 +1288,12 @@
11 b 1 (20.0%) 0 b
12 c 1 (20.0%) 0 c
13 NA 1 (20.0%) 0 NA
14 n_blq 0 0 n_blq
15 p-value (chi-squared test) 0.8254 0 p-value (chi-squared test)
14 a 2/5 (40.0%) 0 a
15 b 1/5 (20.0%) 0 b
16 c 1/5 (20.0%) 0 c
17 NA 1/5 (20.0%) 0 NA
18 n_blq 0 0 n_blq
19 p-value (chi-squared test) 0.8254 0 p-value (chi-squared test)

# `analyze_vars` works with healthy input, default `na.rm = TRUE`.

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18 changes: 16 additions & 2 deletions tests/testthat/_snaps/compare_variables.md
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Expand Up @@ -21,8 +21,8 @@
Code
res
Output
[1] "n" "count" "count_fraction" "n_blq"
[5] "pval_counts"
[1] "n" "count" "count_fraction" "fraction"
[5] "n_blq" "pval_counts"

---

Expand Down Expand Up @@ -75,6 +75,20 @@
[1] 1.0 0.2
$fraction
$fraction$a
num denom
3 5
$fraction$b
num denom
1 5
$fraction$c
num denom
1 5
$n_blq
[1] 0
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8 changes: 5 additions & 3 deletions tests/testthat/_snaps/utils_default_stats_formats_labels.md
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Expand Up @@ -20,7 +20,7 @@
Output
[1] "n" "count"
[3] "count_fraction" "count_fraction_fixed_dp"
[5] "n_blq"
[5] "fraction" "n_blq"

---

Expand Down Expand Up @@ -138,6 +138,8 @@
"n" "count"
count_fraction count_fraction_fixed_dp
"count_fraction" "count_fraction"
n_blq pval_counts
"n_blq" "p-value (chi-squared test)"
fraction n_blq
"fraction" "n_blq"
pval_counts
"p-value (chi-squared test)"

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