[Bug]: Possible bug with risk_diff (rtables/tern)?
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aassuied-ps commented
What happened?
I'm not sure about the calculation that is done without using risk_diff (when the option is available).
Here's an example:
library(falcon)
library(dplyr)
packageVersion("falcon")
adsl <- random.cdisc.data::cadsl
adae <- random.cdisc.data::cadae
# Output Table
risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") # optional
make_table_06(adae = adae, alt_counts_df = adsl, risk_diff = risk_diff)
make_table_06(adae = adae, alt_counts_df = adsl)
The output without using risk_diff does not seem to be right (to me). Got 104 SAE over 134 participants in A: group: i don't think the percentage shoult be 85.2%. When using risk_diff, the percentage is 77.6% (seems correct).
The output is displayed below.
Did I miss something? If it's a bug I could help to find the cause.
sessionInfo()
No response
Relevant log output
> library(falcon)
> library(dplyr)
> packageVersion("falcon")
[1] ‘0.1.0.9053’
>
> adsl <- random.cdisc.data::cadsl
> adae <- random.cdisc.data::cadae
> # Output Table
> risk_diff <- list(arm_x = "B: Placebo", arm_y = "A: Drug X") # optional
> make_table_06(adae = adae, alt_counts_df = adsl, risk_diff = risk_diff)
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
Event (N=134) (N=134) (N=132) (N=268)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
SAE 104 (77.6%) 101 (75.4%) 99 (75.0%) -2.2 (-12.4 - 7.9)
SAEs with fatal outcome 76 (56.7%) 70 (52.2%) 75 (56.8%) -4.5 (-16.4 - 7.4)
Life-threatening SAEs 9 (6.7%) 13 (9.7%) 19 (14.4%) 3.0 (-3.6 - 9.5)
SAEs requiring hospitalization 24 (17.9%) 28 (20.9%) 30 (22.7%) 3.0 (-6.5 - 12.4)
SAEs resulting in substantial disruption of normal life functions 28 (20.9%) 21 (15.7%) 23 (17.4%) -5.2 (-14.5 - 4.0)
Congenital anomaly or birth defect 26 (19.4%) 27 (20.1%) 20 (15.2%) 0.7 (-8.8 - 10.3)
Other 30 (22.4%) 37 (27.6%) 32 (24.2%) 5.2 (-5.1 - 15.6)
AE leading to permanent discontinuation of study drug 27 (20.1%) 26 (19.4%) 30 (22.7%) -0.7 (-10.3 - 8.8)
AE leading to dose modification of study drug 71 (53.0%) 86 (64.2%) 83 (62.9%) 11.2 (-0.5 - 22.9)
AE leading to interruption of study drug 4 (3.0%) 4 (3.0%) 3 (2.3%) 0.0 (-4.1 - 4.1)
AE leading to reduction of study drug 46 (34.3%) 46 (34.3%) 51 (38.6%) 0.0 (-11.4 - 11.4)
AE leading to dose delay of study drug 20 (14.9%) 28 (20.9%) 30 (22.7%) 6.0 (-3.2 - 15.1)
Other 34 (25.4%) 48 (35.8%) 46 (34.8%) 10.4 (-0.5 - 21.4)
Any AE 122 (91.0%) 123 (91.8%) 120 (90.9%) 0.7 (-6.0 - 7.5)
MILD 7 (5.2%) 9 (6.7%) 4 (3.0%) 1.5 (-4.2 - 7.2)
MODERATE 24 (17.9%) 24 (17.9%) 23 (17.4%) 0.0 (-9.2 - 9.2)
SEVERE 91 (67.9%) 90 (67.2%) 93 (70.5%) -0.7 (-12.0 - 10.5)
> make_table_06(adae = adae, alt_counts_df = adsl)
A: Drug X B: Placebo C: Combination
Event (N=134) (N=134) (N=132)
————————————————————————————————————————————————————————————————————————————————————————————————————————————————
SAE 104 (85.2%) 101 (82.1%) 99 (82.5%)
SAEs with fatal outcome 76 (62.3%) 70 (56.9%) 75 (62.5%)
Life-threatening SAEs 9 (7.4%) 13 (10.6%) 19 (15.8%)
SAEs requiring hospitalization 24 (19.7%) 28 (22.8%) 30 (25.0%)
SAEs resulting in substantial disruption of normal life functions 28 (23.0%) 21 (17.1%) 23 (19.2%)
Congenital anomaly or birth defect 26 (21.3%) 27 (22.0%) 20 (16.7%)
Other 30 (24.6%) 37 (30.1%) 32 (26.7%)
AE leading to permanent discontinuation of study drug 27 (22.1%) 26 (21.1%) 30 (25.0%)
AE leading to dose modification of study drug 71 (58.2%) 86 (69.9%) 83 (69.2%)
AE leading to interruption of study drug 4 (3.3%) 4 (3.3%) 3 (2.5%)
AE leading to reduction of study drug 46 (37.7%) 46 (37.4%) 51 (42.5%)
AE leading to dose delay of study drug 20 (16.4%) 28 (22.8%) 30 (25.0%)
Other 34 (27.9%) 48 (39.0%) 46 (38.3%)
Any AE 122 (91.0%) 123 (91.8%) 120 (90.9%)
MILD 7 (5.2%) 9 (6.7%) 4 (3.0%)
MODERATE 24 (17.9%) 24 (17.9%) 23 (17.4%)
SEVERE 91 (67.9%) 90 (67.2%) 93 (70.5%)