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tests/testthat/_snaps/count_patients_with_flags.md
In tern: Create Common TLGs Used in Clinical Trials
s_count_patients_with_flags handles NA
Code
res
Output
$n
$n$TRTEMFL
[1] 2
$count
$count$TRTEMFL
[1] 2
$count_fraction
$count_fraction$TRTEMFL
[1] 2 1
$n_blq
$n_blq[[1]]
[1] 0
s_count_patients_with_flags handles multiple columns
Code
res
Output
$n
$n$TRTEMFL
[1] 3
$n$AEOUTFL
[1] 3
$count
$count$TRTEMFL
[1] 3
$count$AEOUTFL
[1] 1
$count_fraction
$count_fraction$TRTEMFL
[1] 3 1
$count_fraction$AEOUTFL
[1] 1.0000000 0.3333333
$n_blq
$n_blq$TRTEMFL
[1] 0
$n_blq$AEOUTFL
[1] 0
s_count_patients_with_flags custom variable label behaviour works
Code
res
Output
$n
$n$SER
[1] 164
$n$REL
[1] 164
$n$CTC35
[1] 164
$n$CTC45
[1] 164
$count
$count$SER
[1] 128
$count$REL
[1] 137
$count$CTC35
[1] 134
$count$CTC45
[1] 104
$count_fraction
$count_fraction$SER
[1] 128.0000000 0.7804878
$count_fraction$REL
[1] 137.0000000 0.8353659
$count_fraction$CTC35
[1] 134.0000000 0.8170732
$count_fraction$CTC45
[1] 104.0000000 0.6341463
$n_blq
$n_blq$SER
[1] 0
$n_blq$REL
[1] 0
$n_blq$CTC35
[1] 0
$n_blq$CTC45
[1] 0
Code
res
Output
$n
$n$`Serious AE`
[1] 164
$n$`Related AE`
[1] 164
$n$`Grade 3-5 AE`
[1] 164
$n$`Grade 4/5 AE`
[1] 164
$count
$count$`Serious AE`
[1] 128
$count$`Related AE`
[1] 137
$count$`Grade 3-5 AE`
[1] 134
$count$`Grade 4/5 AE`
[1] 104
$count_fraction
$count_fraction$`Serious AE`
[1] 128.0000000 0.7804878
$count_fraction$`Related AE`
[1] 137.0000000 0.8353659
$count_fraction$`Grade 3-5 AE`
[1] 134.0000000 0.8170732
$count_fraction$`Grade 4/5 AE`
[1] 104.0000000 0.6341463
$n_blq
$n_blq$`Serious AE`
[1] 0
$n_blq$`Related AE`
[1] 0
$n_blq$`Grade 3-5 AE`
[1] 0
$n_blq$`Grade 4/5 AE`
[1] 0
Code
res
Output
$n
$n$`Category 1`
[1] 164
$n$`Category 2`
[1] 164
$n$`Category 3`
[1] 164
$n$`Category 4`
[1] 164
$count
$count$`Category 1`
[1] 128
$count$`Category 2`
[1] 137
$count$`Category 3`
[1] 134
$count$`Category 4`
[1] 104
$count_fraction
$count_fraction$`Category 1`
[1] 128.0000000 0.7804878
$count_fraction$`Category 2`
[1] 137.0000000 0.8353659
$count_fraction$`Category 3`
[1] 134.0000000 0.8170732
$count_fraction$`Category 4`
[1] 104.0000000 0.6341463
$n_blq
$n_blq$`Category 1`
[1] 0
$n_blq$`Category 2`
[1] 0
$n_blq$`Category 3`
[1] 0
$n_blq$`Category 4`
[1] 0
Code
res
Output
$n
$n$`Serious AE`
[1] 164
$n$`Related AE`
[1] 164
$n$`Grade 3-5 AE`
[1] 164
$n$`Grade 4/5 AE`
[1] 164
$count
$count$`Serious AE`
[1] 128
$count$`Related AE`
[1] 137
$count$`Grade 3-5 AE`
[1] 134
$count$`Grade 4/5 AE`
[1] 104
$count_fraction
$count_fraction$`Serious AE`
[1] 128.0000000 0.7804878
$count_fraction$`Related AE`
[1] 137.0000000 0.8353659
$count_fraction$`Grade 3-5 AE`
[1] 134.0000000 0.8170732
$count_fraction$`Grade 4/5 AE`
[1] 104.0000000 0.6341463
$n_blq
$n_blq$`Serious AE`
[1] 0
$n_blq$`Related AE`
[1] 0
$n_blq$`Grade 3-5 AE`
[1] 0
$n_blq$`Grade 4/5 AE`
[1] 0
count_patients_with_flags works as expected
Code
res
Output
A B
(N=6) (N=4)
————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one adverse event 1 (16.7%) 1 (25.0%)
Total number of patients with fatal AEs 0 1 (25.0%)
count_patients_with_flags works as expected when specifying table_names
Code
res
Output
A B
(N=6) (N=4)
————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one adverse event 1 (16.7%) 1 (25.0%)
Total number of patients with fatal AEs 0 1 (25.0%)
Total number of patients with at least one adverse event 1 (16.7%) 1 (25.0%)
Total number of patients with fatal AEs 0 1 (25.0%)
count_patients_with_flags works with label row specified
Code
res
Output
A: Drug X B: Placebo C: Combination
(N=69) (N=73) (N=58)
———————————————————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one adverse event 59 (85.5%) 57 (78.1%) 48 (82.8%)
Total number of patients with at least one
Serious AE 45 (65.2%) 46 (63.0%) 37 (63.8%)
Related AE 49 (71.0%) 48 (65.8%) 40 (69.0%)
Grade 3-5 AE 47 (68.1%) 46 (63.0%) 41 (70.7%)
Grade 4/5 AE 34 (49.3%) 38 (52.1%) 32 (55.2%)
count_patients_with_flags custom variable label behaviour works with var_labels specified
Code
res
Output
A: Drug X B: Placebo C: Combination
—————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one
SER 45 (65.2%) 46 (63.0%) 37 (63.8%)
REL 49 (71.0%) 48 (65.8%) 40 (69.0%)
CTC35 47 (68.1%) 46 (63.0%) 41 (70.7%)
CTC45 34 (49.3%) 38 (52.1%) 32 (55.2%)
Code
res
Output
A: Drug X B: Placebo C: Combination
—————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one
Serious AE 45 (65.2%) 46 (63.0%) 37 (63.8%)
Related AE 49 (71.0%) 48 (65.8%) 40 (69.0%)
Grade 3-5 AE 47 (68.1%) 46 (63.0%) 41 (70.7%)
Grade 4/5 AE 34 (49.3%) 38 (52.1%) 32 (55.2%)
Code
res
Output
A: Drug X B: Placebo C: Combination
—————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one
Category 1 45 (65.2%) 46 (63.0%) 37 (63.8%)
Category 2 49 (71.0%) 48 (65.8%) 40 (69.0%)
Category 3 47 (68.1%) 46 (63.0%) 41 (70.7%)
Category 4 34 (49.3%) 38 (52.1%) 32 (55.2%)
Code
res
Output
A: Drug X B: Placebo C: Combination
—————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one
Serious AE 45 (65.2%) 46 (63.0%) 37 (63.8%)
Related AE 49 (71.0%) 48 (65.8%) 40 (69.0%)
Grade 3-5 AE 47 (68.1%) 46 (63.0%) 41 (70.7%)
Grade 4/5 AE 34 (49.3%) 38 (52.1%) 32 (55.2%)
count_patients_with_flags works as expected with risk difference column
Code
res
Output
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=69) (N=73) (N=58) (N=142)
————————————————————————————————————————————————————————————————————————————————————————————————
SAE 53 (76.8%) 49 (67.1%) 39 (67.2%) 9.7 (-5.0 - 24.4)
SAE with fatal outcome 50 (72.5%) 47 (64.4%) 42 (72.4%) 8.1 (-7.1 - 23.3)
Code
res
Output
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=202) (N=177) (N=162) (N=379)
————————————————————————————————————————————————————————————————————————————————————————————————
SAE 53 49 39 -1.4 (-10.4 - 7.5)
SAE with fatal outcome 50 47 42 -1.8 (-10.6 - 7.0)
SAE 53 (26.2%) 49 (27.7%) 39 (24.1%) -1.4 (-10.4 - 7.5)
SAE with fatal outcome 50 (24.8%) 47 (26.6%) 42 (25.9%) -1.8 (-10.6 - 7.0)
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s_count_patients_with_flags handles NA
Code
res
Output
$n
$n$TRTEMFL
[1] 2
$count
$count$TRTEMFL
[1] 2
$count_fraction
$count_fraction$TRTEMFL
[1] 2 1
$n_blq
$n_blq[[1]]
[1] 0
s_count_patients_with_flags handles multiple columns
Code
res
Output
$n
$n$TRTEMFL
[1] 3
$n$AEOUTFL
[1] 3
$count
$count$TRTEMFL
[1] 3
$count$AEOUTFL
[1] 1
$count_fraction
$count_fraction$TRTEMFL
[1] 3 1
$count_fraction$AEOUTFL
[1] 1.0000000 0.3333333
$n_blq
$n_blq$TRTEMFL
[1] 0
$n_blq$AEOUTFL
[1] 0
s_count_patients_with_flags custom variable label behaviour works
Code
res
Output
$n
$n$SER
[1] 164
$n$REL
[1] 164
$n$CTC35
[1] 164
$n$CTC45
[1] 164
$count
$count$SER
[1] 128
$count$REL
[1] 137
$count$CTC35
[1] 134
$count$CTC45
[1] 104
$count_fraction
$count_fraction$SER
[1] 128.0000000 0.7804878
$count_fraction$REL
[1] 137.0000000 0.8353659
$count_fraction$CTC35
[1] 134.0000000 0.8170732
$count_fraction$CTC45
[1] 104.0000000 0.6341463
$n_blq
$n_blq$SER
[1] 0
$n_blq$REL
[1] 0
$n_blq$CTC35
[1] 0
$n_blq$CTC45
[1] 0
Code
res
Output
$n
$n$`Serious AE`
[1] 164
$n$`Related AE`
[1] 164
$n$`Grade 3-5 AE`
[1] 164
$n$`Grade 4/5 AE`
[1] 164
$count
$count$`Serious AE`
[1] 128
$count$`Related AE`
[1] 137
$count$`Grade 3-5 AE`
[1] 134
$count$`Grade 4/5 AE`
[1] 104
$count_fraction
$count_fraction$`Serious AE`
[1] 128.0000000 0.7804878
$count_fraction$`Related AE`
[1] 137.0000000 0.8353659
$count_fraction$`Grade 3-5 AE`
[1] 134.0000000 0.8170732
$count_fraction$`Grade 4/5 AE`
[1] 104.0000000 0.6341463
$n_blq
$n_blq$`Serious AE`
[1] 0
$n_blq$`Related AE`
[1] 0
$n_blq$`Grade 3-5 AE`
[1] 0
$n_blq$`Grade 4/5 AE`
[1] 0
Code
res
Output
$n
$n$`Category 1`
[1] 164
$n$`Category 2`
[1] 164
$n$`Category 3`
[1] 164
$n$`Category 4`
[1] 164
$count
$count$`Category 1`
[1] 128
$count$`Category 2`
[1] 137
$count$`Category 3`
[1] 134
$count$`Category 4`
[1] 104
$count_fraction
$count_fraction$`Category 1`
[1] 128.0000000 0.7804878
$count_fraction$`Category 2`
[1] 137.0000000 0.8353659
$count_fraction$`Category 3`
[1] 134.0000000 0.8170732
$count_fraction$`Category 4`
[1] 104.0000000 0.6341463
$n_blq
$n_blq$`Category 1`
[1] 0
$n_blq$`Category 2`
[1] 0
$n_blq$`Category 3`
[1] 0
$n_blq$`Category 4`
[1] 0
Code
res
Output
$n
$n$`Serious AE`
[1] 164
$n$`Related AE`
[1] 164
$n$`Grade 3-5 AE`
[1] 164
$n$`Grade 4/5 AE`
[1] 164
$count
$count$`Serious AE`
[1] 128
$count$`Related AE`
[1] 137
$count$`Grade 3-5 AE`
[1] 134
$count$`Grade 4/5 AE`
[1] 104
$count_fraction
$count_fraction$`Serious AE`
[1] 128.0000000 0.7804878
$count_fraction$`Related AE`
[1] 137.0000000 0.8353659
$count_fraction$`Grade 3-5 AE`
[1] 134.0000000 0.8170732
$count_fraction$`Grade 4/5 AE`
[1] 104.0000000 0.6341463
$n_blq
$n_blq$`Serious AE`
[1] 0
$n_blq$`Related AE`
[1] 0
$n_blq$`Grade 3-5 AE`
[1] 0
$n_blq$`Grade 4/5 AE`
[1] 0
count_patients_with_flags works as expected
Code
res
Output
A B
(N=6) (N=4)
————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one adverse event 1 (16.7%) 1 (25.0%)
Total number of patients with fatal AEs 0 1 (25.0%)
count_patients_with_flags works as expected when specifying table_names
Code
res
Output
A B
(N=6) (N=4)
————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one adverse event 1 (16.7%) 1 (25.0%)
Total number of patients with fatal AEs 0 1 (25.0%)
Total number of patients with at least one adverse event 1 (16.7%) 1 (25.0%)
Total number of patients with fatal AEs 0 1 (25.0%)
count_patients_with_flags works with label row specified
Code
res
Output
A: Drug X B: Placebo C: Combination
(N=69) (N=73) (N=58)
———————————————————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one adverse event 59 (85.5%) 57 (78.1%) 48 (82.8%)
Total number of patients with at least one
Serious AE 45 (65.2%) 46 (63.0%) 37 (63.8%)
Related AE 49 (71.0%) 48 (65.8%) 40 (69.0%)
Grade 3-5 AE 47 (68.1%) 46 (63.0%) 41 (70.7%)
Grade 4/5 AE 34 (49.3%) 38 (52.1%) 32 (55.2%)
count_patients_with_flags custom variable label behaviour works with var_labels specified
Code
res
Output
A: Drug X B: Placebo C: Combination
—————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one
SER 45 (65.2%) 46 (63.0%) 37 (63.8%)
REL 49 (71.0%) 48 (65.8%) 40 (69.0%)
CTC35 47 (68.1%) 46 (63.0%) 41 (70.7%)
CTC45 34 (49.3%) 38 (52.1%) 32 (55.2%)
Code
res
Output
A: Drug X B: Placebo C: Combination
—————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one
Serious AE 45 (65.2%) 46 (63.0%) 37 (63.8%)
Related AE 49 (71.0%) 48 (65.8%) 40 (69.0%)
Grade 3-5 AE 47 (68.1%) 46 (63.0%) 41 (70.7%)
Grade 4/5 AE 34 (49.3%) 38 (52.1%) 32 (55.2%)
Code
res
Output
A: Drug X B: Placebo C: Combination
—————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one
Category 1 45 (65.2%) 46 (63.0%) 37 (63.8%)
Category 2 49 (71.0%) 48 (65.8%) 40 (69.0%)
Category 3 47 (68.1%) 46 (63.0%) 41 (70.7%)
Category 4 34 (49.3%) 38 (52.1%) 32 (55.2%)
Code
res
Output
A: Drug X B: Placebo C: Combination
—————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one
Serious AE 45 (65.2%) 46 (63.0%) 37 (63.8%)
Related AE 49 (71.0%) 48 (65.8%) 40 (69.0%)
Grade 3-5 AE 47 (68.1%) 46 (63.0%) 41 (70.7%)
Grade 4/5 AE 34 (49.3%) 38 (52.1%) 32 (55.2%)
count_patients_with_flags works as expected with risk difference column
Code
res
Output
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=69) (N=73) (N=58) (N=142)
————————————————————————————————————————————————————————————————————————————————————————————————
SAE 53 (76.8%) 49 (67.1%) 39 (67.2%) 9.7 (-5.0 - 24.4)
SAE with fatal outcome 50 (72.5%) 47 (64.4%) 42 (72.4%) 8.1 (-7.1 - 23.3)
Code
res
Output
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=202) (N=177) (N=162) (N=379)
————————————————————————————————————————————————————————————————————————————————————————————————
SAE 53 49 39 -1.4 (-10.4 - 7.5)
SAE with fatal outcome 50 47 42 -1.8 (-10.6 - 7.0)
SAE 53 (26.2%) 49 (27.7%) 39 (24.1%) -1.4 (-10.4 - 7.5)
SAE with fatal outcome 50 (24.8%) 47 (26.6%) 42 (25.9%) -1.8 (-10.6 - 7.0)
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