Nothing
tests/testthat/_snaps/count_occurrences.md
In tern: Create Common TLGs Used in Clinical Trials
s_count_occurrences functions as expected with valid input and default arguments
Code
res
Output
$count
$count$MH1
[1] 3
$count$MH2
[1] 1
$count$MH3
[1] 1
$count_fraction
$count_fraction$MH1
[1] 3.00 0.75
$count_fraction$MH2
[1] 1.00 0.25
$count_fraction$MH3
[1] 1.00 0.25
$fraction
$fraction$MH1
num denom
3 4
$fraction$MH2
num denom
1 4
$fraction$MH3
num denom
1 4
s_count_occurrences functions as expected when requesting different denominator
Code
res
Output
$count
$count$MH1
[1] 3
$count$MH2
[1] 1
$count$MH3
[1] 1
$count_fraction
$count_fraction$MH1
[1] 3 1
$count_fraction$MH2
[1] 1.0000000 0.3333333
$count_fraction$MH3
[1] 1.0000000 0.3333333
$fraction
$fraction$MH1
num denom
3 3
$fraction$MH2
num denom
1 3
$fraction$MH3
num denom
1 3
a_count_occurrences works with custom input.
Code
res
Output
RowsVerticalSection (in_rows) object print method:
----------------------------
row_name formatted_cell indent_mod row_label
1 Level: a 3 1 Level: a
2 LVL B 1 2 LVL B
3 Count of c 1 0 Count of c
4 Missing D 0 3 Missing D
5 Level: a 3 (60%) 1 Level: a
6 LVL B 1 (20%) 2 LVL B
7 c 1 (20%) 0 c
8 Missing D 0 (0%) 0 Missing D
count_occurrences functions as expected with valid input and default arguments
Code
res
Output
A B
(N=5) (N=4)
———————————————————————————
MH1 3 (60.0%) 1 (25.0%)
MH2 1 (20.0%) 2 (50.0%)
MH3 1 (20.0%) 1 (25.0%)
MH4 0 1 (25.0%)
count_occurrences functions as expected with label row specified
Code
res
Output
all obs
———————————————————
MH Term
MH1 4 (44.4%)
MH2 3 (33.3%)
count_occurrences works as expected with risk difference column
Code
res
Output
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=202) (N=177) (N=162) (N=379)
———————————————————————————————————————————————————————————————————————————————————————
dcd A.1.1.1.1 17 (8.4%) 17 (9.6%) 14 (8.6%) -1.2 (-7.0 - 4.6)
dcd A.1.1.1.2 17 (8.4%) 14 (7.9%) 17 (10.5%) 0.5 (-5.0 - 6.0)
dcd B.1.1.1.1 15 (7.4%) 19 (10.7%) 15 (9.3%) -3.3 (-9.1 - 2.5)
dcd B.2.1.2.1 17 (8.4%) 16 (9.0%) 13 (8.0%) -0.6 (-6.3 - 5.1)
dcd B.2.2.3.1 17 (8.4%) 15 (8.5%) 16 (9.9%) -0.1 (-5.7 - 5.6)
dcd C.1.1.1.3 15 (7.4%) 13 (7.3%) 18 (11.1%) 0.1 (-5.2 - 5.4)
dcd C.2.1.2.1 20 (9.9%) 14 (7.9%) 10 (6.2%) 2.0 (-3.7 - 7.7)
dcd D.1.1.1.1 17 (8.4%) 18 (10.2%) 7 (4.3%) -1.8 (-7.6 - 4.1)
dcd D.1.1.4.2 16 (7.9%) 13 (7.3%) 16 (9.9%) 0.6 (-4.8 - 5.9)
dcd D.2.1.5.3 21 (10.4%) 20 (11.3%) 12 (7.4%) -0.9 (-7.2 - 5.4)
Code
res
Output
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=202) (N=177) (N=162) (N=379)
—————————————————————————————————————————————————————————————————————————————————————————————
dcd A.1.1.1.1 8 11 11 -2.3 (-6.7 - 2.2)
dcd A.1.1.1.2 11 10 13 -0.2 (-4.8 - 4.4)
dcd B.1.1.1.1 12 14 11 -2.0 (-7.1 - 3.2)
dcd B.2.1.2.1 11 12 9 -1.3 (-6.2 - 3.5)
dcd B.2.2.3.1 7 9 15 -1.6 (-5.7 - 2.5)
dcd C.1.1.1.3 10 10 16 -0.7 (-5.2 - 3.8)
dcd C.2.1.2.1 13 12 7 -0.3 (-5.4 - 4.7)
dcd D.1.1.1.1 12 13 6 -1.4 (-6.4 - 3.6)
dcd D.1.1.4.2 12 8 15 1.4 (-3.1 - 5.9)
dcd D.2.1.5.3 14 16 10 -2.1 (-7.6 - 3.4)
dcd A.1.1.1.1 8 (4.0%) 11 (6.2%) 11 (6.8%) -2.3 (-6.7 - 2.2)
dcd A.1.1.1.2 11 (5.4%) 10 (5.6%) 13 (8.0%) -0.2 (-4.8 - 4.4)
dcd B.1.1.1.1 12 (5.9%) 14 (7.9%) 11 (6.8%) -2.0 (-7.1 - 3.2)
dcd B.2.1.2.1 11 (5.4%) 12 (6.8%) 9 (5.6%) -1.3 (-6.2 - 3.5)
dcd B.2.2.3.1 7 (3.5%) 9 (5.1%) 15 (9.3%) -1.6 (-5.7 - 2.5)
dcd C.1.1.1.3 10 (5.0%) 10 (5.6%) 16 (9.9%) -0.7 (-5.2 - 3.8)
dcd C.2.1.2.1 13 (6.4%) 12 (6.8%) 7 (4.3%) -0.3 (-5.4 - 4.7)
dcd D.1.1.1.1 12 (5.9%) 13 (7.3%) 6 (3.7%) -1.4 (-6.4 - 3.6)
dcd D.1.1.4.2 12 (5.9%) 8 (4.5%) 15 (9.3%) 1.4 (-3.1 - 5.9)
dcd D.2.1.5.3 14 (6.9%) 16 (9.0%) 10 (6.2%) -2.1 (-7.6 - 3.4)
dcd A.1.1.1.1 8/202 (4.0%) 11/177 (6.2%) 11/162 (6.8%) -2.3 (-6.7 - 2.2)
dcd A.1.1.1.2 11/202 (5.4%) 10/177 (5.6%) 13/162 (8.0%) -0.2 (-4.8 - 4.4)
dcd B.1.1.1.1 12/202 (5.9%) 14/177 (7.9%) 11/162 (6.8%) -2.0 (-7.1 - 3.2)
dcd B.2.1.2.1 11/202 (5.4%) 12/177 (6.8%) 9/162 (5.6%) -1.3 (-6.2 - 3.5)
dcd B.2.2.3.1 7/202 (3.5%) 9/177 (5.1%) 15/162 (9.3%) -1.6 (-5.7 - 2.5)
dcd C.1.1.1.3 10/202 (5.0%) 10/177 (5.6%) 16/162 (9.9%) -0.7 (-5.2 - 3.8)
dcd C.2.1.2.1 13/202 (6.4%) 12/177 (6.8%) 7/162 (4.3%) -0.3 (-5.4 - 4.7)
dcd D.1.1.1.1 12/202 (5.9%) 13/177 (7.3%) 6/162 (3.7%) -1.4 (-6.4 - 3.6)
dcd D.1.1.4.2 12/202 (5.9%) 8/177 (4.5%) 15/162 (9.3%) 1.4 (-3.1 - 5.9)
dcd D.2.1.5.3 14/202 (6.9%) 16/177 (9.0%) 10/162 (6.2%) -2.1 (-7.6 - 3.4)
Code
res
Output
F M
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI) A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=122) (N=97) (N=98) (N=219) (N=80) (N=80) (N=64) (N=160)
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
dcd A.1.1.1.1 9 (7.4%) 10 (10.3%) 8 (8.2%) -2.9 (-10.6 - 4.7) 8 (10.0%) 7 (8.8%) 6 (9.4%) 1.3 (-7.8 - 10.3)
dcd A.1.1.1.2 6 (4.9%) 9 (9.3%) 12 (12.2%) -4.4 (-11.3 - 2.6) 11 (13.8%) 5 (6.2%) 5 (7.8%) 7.5 (-1.7 - 16.7)
dcd B.1.1.1.1 11 (9.0%) 10 (10.3%) 7 (7.1%) -1.3 (-9.2 - 6.6) 4 (5.0%) 9 (11.2%) 8 (12.5%) -6.2 (-14.7 - 2.2)
dcd B.2.1.2.1 10 (8.2%) 7 (7.2%) 10 (10.2%) 1.0 (-6.1 - 8.1) 7 (8.8%) 9 (11.2%) 3 (4.7%) -2.5 (-11.8 - 6.8)
dcd B.2.2.3.1 10 (8.2%) 11 (11.3%) 10 (10.2%) -3.1 (-11.1 - 4.8) 7 (8.8%) 4 (5.0%) 6 (9.4%) 3.7 (-4.1 - 11.6)
dcd C.1.1.1.3 10 (8.2%) 8 (8.2%) 12 (12.2%) -0.1 (-7.4 - 7.3) 5 (6.2%) 5 (6.2%) 6 (9.4%) 0.0 (-7.5 - 7.5)
dcd C.2.1.2.1 13 (10.7%) 6 (6.2%) 6 (6.1%) 4.5 (-2.8 - 11.7) 7 (8.8%) 8 (10.0%) 4 (6.2%) -1.3 (-10.3 - 7.8)
dcd D.1.1.1.1 10 (8.2%) 12 (12.4%) 4 (4.1%) -4.2 (-12.3 - 4.0) 7 (8.8%) 6 (7.5%) 3 (4.7%) 1.2 (-7.2 - 9.7)
dcd D.1.1.4.2 10 (8.2%) 5 (5.2%) 7 (7.1%) 3.0 (-3.5 - 9.6) 6 (7.5%) 8 (10.0%) 9 (14.1%) -2.5 (-11.2 - 6.2)
dcd D.2.1.5.3 12 (9.8%) 10 (10.3%) 9 (9.2%) -0.5 (-8.5 - 7.6) 9 (11.2%) 10 (12.5%) 3 (4.7%) -1.2 (-11.3 - 8.8)
summarize_occurrences functions as expected with valid input and default arguments
Code
res
Output
A B
(N=5) (N=4)
—————————————————————————————
F
MH1 1 (20.0%) 0
MH2 1 (20.0%) 1 (25.0%)
MH3 0 1 (25.0%)
MH4 0 1 (25.0%)
M
MH1 2 (40.0%) 1 (25.0%)
MH2 0 1 (25.0%)
MH3 1 (20.0%) 0
summarize_occurrences works as expected with risk difference column
Code
res
Output
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=202) (N=177) (N=162) (N=379)
—————————————————————————————————————————————————————————————————————————————————
F
LOW 12 (5.9%) 11 (6.2%) 10 (6.2%) -0.3 (-5.1 - 4.6)
MEDIUM 11 (5.4%) 13 (7.3%) 10 (6.2%) -1.9 (-6.9 - 3.1)
HIGH 10 (5.0%) 7 (4.0%) 7 (4.3%) 1.0 (-3.2 - 5.1)
M
LOW 12 (5.9%) 5 (2.8%) 6 (3.7%) 3.1 (-1.0 - 7.2)
MEDIUM 10 (5.0%) 9 (5.1%) 4 (2.5%) -0.1 (-4.5 - 4.3)
HIGH 4 (2.0%) 12 (6.8%) 11 (6.8%) -4.8 (-9.0 - -0.6)
Code
res
Output
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=202) (N=177) (N=162) (N=379)
————————————————————————————————————————————————————————————————————————————————————————
F
LOW 10 6 8 1.6 (-2.4 - 5.6)
MEDIUM 9 11 9 -1.8 (-6.3 - 2.8)
HIGH 6 6 7 -0.4 (-4.0 - 3.1)
LOW 10 (5.0%) 6 (3.4%) 8 (4.9%) 1.6 (-2.4 - 5.6)
MEDIUM 9 (4.5%) 11 (6.2%) 9 (5.6%) -1.8 (-6.3 - 2.8)
HIGH 6 (3.0%) 6 (3.4%) 7 (4.3%) -0.4 (-4.0 - 3.1)
LOW 10/202 (5.0%) 6/177 (3.4%) 8/162 (4.9%) 1.6 (-2.4 - 5.6)
MEDIUM 9/202 (4.5%) 11/177 (6.2%) 9/162 (5.6%) -1.8 (-6.3 - 2.8)
HIGH 6/202 (3.0%) 6/177 (3.4%) 7/162 (4.3%) -0.4 (-4.0 - 3.1)
M
LOW 7 5 6 0.6 (-2.9 - 4.2)
MEDIUM 9 7 4 0.5 (-3.5 - 4.5)
HIGH 4 11 8 -4.2 (-8.3 - -0.2)
LOW 7 (3.5%) 5 (2.8%) 6 (3.7%) 0.6 (-2.9 - 4.2)
MEDIUM 9 (4.5%) 7 (4.0%) 4 (2.5%) 0.5 (-3.5 - 4.5)
HIGH 4 (2.0%) 11 (6.2%) 8 (4.9%) -4.2 (-8.3 - -0.2)
LOW 7/202 (3.5%) 5/177 (2.8%) 6/162 (3.7%) 0.6 (-2.9 - 4.2)
MEDIUM 9/202 (4.5%) 7/177 (4.0%) 4/162 (2.5%) 0.5 (-3.5 - 4.5)
HIGH 4/202 (2.0%) 11/177 (6.2%) 8/162 (4.9%) -4.2 (-8.3 - -0.2)
Code
res
Output
A B C
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI) A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI) A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=64) (N=67) (N=62) (N=131) (N=78) (N=64) (N=45) (N=142) (N=60) (N=46) (N=55) (N=106)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
F
LOW 6 (9.4%) 4 (6.0%) 1 (1.6%) 3.4 (-5.7 - 12.5) 3 (3.8%) 5 (7.8%) 6 (13.3%) -4.0 (-11.8 - 3.9) 3 (5.0%) 2 (4.3%) 3 (5.5%) 0.7 (-7.4 - 8.7)
MEDIUM 1 (1.6%) 4 (6.0%) 4 (6.5%) -4.4 (-10.8 - 2.0) 6 (7.7%) 4 (6.2%) 2 (4.4%) 1.4 (-6.9 - 9.8) 4 (6.7%) 5 (10.9%) 4 (7.3%) -4.2 (-15.2 - 6.8)
HIGH 3 (4.7%) 4 (6.0%) 3 (4.8%) -1.3 (-9.0 - 6.4) 3 (3.8%) 2 (3.1%) 0 0.7 (-5.3 - 6.8) 4 (6.7%) 1 (2.2%) 4 (7.3%) 4.5 (-3.1 - 12.1)
M
LOW 1 (1.6%) 2 (3.0%) 2 (3.2%) -1.4 (-6.5 - 3.7) 7 (9.0%) 2 (3.1%) 3 (6.7%) 5.8 (-1.8 - 13.5) 4 (6.7%) 1 (2.2%) 1 (1.8%) 4.5 (-3.1 - 12.1)
MEDIUM 5 (7.8%) 2 (3.0%) 1 (1.6%) 4.8 (-2.9 - 12.6) 2 (2.6%) 3 (4.7%) 2 (4.4%) -2.1 (-8.4 - 4.1) 3 (5.0%) 4 (8.7%) 1 (1.8%) -3.7 (-13.5 - 6.1)
HIGH 2 (3.1%) 5 (7.5%) 5 (8.1%) -4.3 (-11.9 - 3.3) 2 (2.6%) 5 (7.8%) 3 (6.7%) -5.2 (-12.7 - 2.2) 0 2 (4.3%) 3 (5.5%) -4.3 (-10.2 - 1.5)
Code
res
Output
Risk Difference (%) (95% CI) Risk Difference (%) (95% CI)
A: Drug X B: Placebo C: Combination A: Drug X vs. B: Placebo A: Drug X vs. C: Combination
(N=202) (N=177) (N=162) (N=379) (N=364)
————————————————————————————————————————————————————————————————————————————————————————————————————————————————
F
LOW 12 (5.9%) 11 (6.2%) 10 (6.2%) -0.3 (-5.1 - 4.6) -0.2 (-5.2 - 4.7)
MEDIUM 11 (5.4%) 13 (7.3%) 10 (6.2%) -1.9 (-6.9 - 3.1) -0.7 (-5.6 - 4.1)
HIGH 10 (5.0%) 7 (4.0%) 7 (4.3%) 1.0 (-3.2 - 5.1) 0.6 (-3.7 - 5.0)
M
LOW 12 (5.9%) 5 (2.8%) 6 (3.7%) 3.1 (-1.0 - 7.2) 2.2 (-2.1 - 6.6)
MEDIUM 10 (5.0%) 9 (5.1%) 4 (2.5%) -0.1 (-4.5 - 4.3) 2.5 (-1.3 - 6.3)
HIGH 4 (2.0%) 12 (6.8%) 11 (6.8%) -4.8 (-9.0 - -0.6) -4.8 (-9.1 - -0.5)
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s_count_occurrences functions as expected with valid input and default arguments
Code
res
Output
$count
$count$MH1
[1] 3
$count$MH2
[1] 1
$count$MH3
[1] 1
$count_fraction
$count_fraction$MH1
[1] 3.00 0.75
$count_fraction$MH2
[1] 1.00 0.25
$count_fraction$MH3
[1] 1.00 0.25
$fraction
$fraction$MH1
num denom
3 4
$fraction$MH2
num denom
1 4
$fraction$MH3
num denom
1 4
s_count_occurrences functions as expected when requesting different denominator
Code
res
Output
$count
$count$MH1
[1] 3
$count$MH2
[1] 1
$count$MH3
[1] 1
$count_fraction
$count_fraction$MH1
[1] 3 1
$count_fraction$MH2
[1] 1.0000000 0.3333333
$count_fraction$MH3
[1] 1.0000000 0.3333333
$fraction
$fraction$MH1
num denom
3 3
$fraction$MH2
num denom
1 3
$fraction$MH3
num denom
1 3
a_count_occurrences works with custom input.
Code
res
Output
RowsVerticalSection (in_rows) object print method:
----------------------------
row_name formatted_cell indent_mod row_label
1 Level: a 3 1 Level: a
2 LVL B 1 2 LVL B
3 Count of c 1 0 Count of c
4 Missing D 0 3 Missing D
5 Level: a 3 (60%) 1 Level: a
6 LVL B 1 (20%) 2 LVL B
7 c 1 (20%) 0 c
8 Missing D 0 (0%) 0 Missing D
count_occurrences functions as expected with valid input and default arguments
Code
res
Output
A B
(N=5) (N=4)
———————————————————————————
MH1 3 (60.0%) 1 (25.0%)
MH2 1 (20.0%) 2 (50.0%)
MH3 1 (20.0%) 1 (25.0%)
MH4 0 1 (25.0%)
count_occurrences functions as expected with label row specified
Code
res
Output
all obs
———————————————————
MH Term
MH1 4 (44.4%)
MH2 3 (33.3%)
count_occurrences works as expected with risk difference column
Code
res
Output
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=202) (N=177) (N=162) (N=379)
———————————————————————————————————————————————————————————————————————————————————————
dcd A.1.1.1.1 17 (8.4%) 17 (9.6%) 14 (8.6%) -1.2 (-7.0 - 4.6)
dcd A.1.1.1.2 17 (8.4%) 14 (7.9%) 17 (10.5%) 0.5 (-5.0 - 6.0)
dcd B.1.1.1.1 15 (7.4%) 19 (10.7%) 15 (9.3%) -3.3 (-9.1 - 2.5)
dcd B.2.1.2.1 17 (8.4%) 16 (9.0%) 13 (8.0%) -0.6 (-6.3 - 5.1)
dcd B.2.2.3.1 17 (8.4%) 15 (8.5%) 16 (9.9%) -0.1 (-5.7 - 5.6)
dcd C.1.1.1.3 15 (7.4%) 13 (7.3%) 18 (11.1%) 0.1 (-5.2 - 5.4)
dcd C.2.1.2.1 20 (9.9%) 14 (7.9%) 10 (6.2%) 2.0 (-3.7 - 7.7)
dcd D.1.1.1.1 17 (8.4%) 18 (10.2%) 7 (4.3%) -1.8 (-7.6 - 4.1)
dcd D.1.1.4.2 16 (7.9%) 13 (7.3%) 16 (9.9%) 0.6 (-4.8 - 5.9)
dcd D.2.1.5.3 21 (10.4%) 20 (11.3%) 12 (7.4%) -0.9 (-7.2 - 5.4)
Code
res
Output
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=202) (N=177) (N=162) (N=379)
—————————————————————————————————————————————————————————————————————————————————————————————
dcd A.1.1.1.1 8 11 11 -2.3 (-6.7 - 2.2)
dcd A.1.1.1.2 11 10 13 -0.2 (-4.8 - 4.4)
dcd B.1.1.1.1 12 14 11 -2.0 (-7.1 - 3.2)
dcd B.2.1.2.1 11 12 9 -1.3 (-6.2 - 3.5)
dcd B.2.2.3.1 7 9 15 -1.6 (-5.7 - 2.5)
dcd C.1.1.1.3 10 10 16 -0.7 (-5.2 - 3.8)
dcd C.2.1.2.1 13 12 7 -0.3 (-5.4 - 4.7)
dcd D.1.1.1.1 12 13 6 -1.4 (-6.4 - 3.6)
dcd D.1.1.4.2 12 8 15 1.4 (-3.1 - 5.9)
dcd D.2.1.5.3 14 16 10 -2.1 (-7.6 - 3.4)
dcd A.1.1.1.1 8 (4.0%) 11 (6.2%) 11 (6.8%) -2.3 (-6.7 - 2.2)
dcd A.1.1.1.2 11 (5.4%) 10 (5.6%) 13 (8.0%) -0.2 (-4.8 - 4.4)
dcd B.1.1.1.1 12 (5.9%) 14 (7.9%) 11 (6.8%) -2.0 (-7.1 - 3.2)
dcd B.2.1.2.1 11 (5.4%) 12 (6.8%) 9 (5.6%) -1.3 (-6.2 - 3.5)
dcd B.2.2.3.1 7 (3.5%) 9 (5.1%) 15 (9.3%) -1.6 (-5.7 - 2.5)
dcd C.1.1.1.3 10 (5.0%) 10 (5.6%) 16 (9.9%) -0.7 (-5.2 - 3.8)
dcd C.2.1.2.1 13 (6.4%) 12 (6.8%) 7 (4.3%) -0.3 (-5.4 - 4.7)
dcd D.1.1.1.1 12 (5.9%) 13 (7.3%) 6 (3.7%) -1.4 (-6.4 - 3.6)
dcd D.1.1.4.2 12 (5.9%) 8 (4.5%) 15 (9.3%) 1.4 (-3.1 - 5.9)
dcd D.2.1.5.3 14 (6.9%) 16 (9.0%) 10 (6.2%) -2.1 (-7.6 - 3.4)
dcd A.1.1.1.1 8/202 (4.0%) 11/177 (6.2%) 11/162 (6.8%) -2.3 (-6.7 - 2.2)
dcd A.1.1.1.2 11/202 (5.4%) 10/177 (5.6%) 13/162 (8.0%) -0.2 (-4.8 - 4.4)
dcd B.1.1.1.1 12/202 (5.9%) 14/177 (7.9%) 11/162 (6.8%) -2.0 (-7.1 - 3.2)
dcd B.2.1.2.1 11/202 (5.4%) 12/177 (6.8%) 9/162 (5.6%) -1.3 (-6.2 - 3.5)
dcd B.2.2.3.1 7/202 (3.5%) 9/177 (5.1%) 15/162 (9.3%) -1.6 (-5.7 - 2.5)
dcd C.1.1.1.3 10/202 (5.0%) 10/177 (5.6%) 16/162 (9.9%) -0.7 (-5.2 - 3.8)
dcd C.2.1.2.1 13/202 (6.4%) 12/177 (6.8%) 7/162 (4.3%) -0.3 (-5.4 - 4.7)
dcd D.1.1.1.1 12/202 (5.9%) 13/177 (7.3%) 6/162 (3.7%) -1.4 (-6.4 - 3.6)
dcd D.1.1.4.2 12/202 (5.9%) 8/177 (4.5%) 15/162 (9.3%) 1.4 (-3.1 - 5.9)
dcd D.2.1.5.3 14/202 (6.9%) 16/177 (9.0%) 10/162 (6.2%) -2.1 (-7.6 - 3.4)
Code
res
Output
F M
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI) A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=122) (N=97) (N=98) (N=219) (N=80) (N=80) (N=64) (N=160)
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
dcd A.1.1.1.1 9 (7.4%) 10 (10.3%) 8 (8.2%) -2.9 (-10.6 - 4.7) 8 (10.0%) 7 (8.8%) 6 (9.4%) 1.3 (-7.8 - 10.3)
dcd A.1.1.1.2 6 (4.9%) 9 (9.3%) 12 (12.2%) -4.4 (-11.3 - 2.6) 11 (13.8%) 5 (6.2%) 5 (7.8%) 7.5 (-1.7 - 16.7)
dcd B.1.1.1.1 11 (9.0%) 10 (10.3%) 7 (7.1%) -1.3 (-9.2 - 6.6) 4 (5.0%) 9 (11.2%) 8 (12.5%) -6.2 (-14.7 - 2.2)
dcd B.2.1.2.1 10 (8.2%) 7 (7.2%) 10 (10.2%) 1.0 (-6.1 - 8.1) 7 (8.8%) 9 (11.2%) 3 (4.7%) -2.5 (-11.8 - 6.8)
dcd B.2.2.3.1 10 (8.2%) 11 (11.3%) 10 (10.2%) -3.1 (-11.1 - 4.8) 7 (8.8%) 4 (5.0%) 6 (9.4%) 3.7 (-4.1 - 11.6)
dcd C.1.1.1.3 10 (8.2%) 8 (8.2%) 12 (12.2%) -0.1 (-7.4 - 7.3) 5 (6.2%) 5 (6.2%) 6 (9.4%) 0.0 (-7.5 - 7.5)
dcd C.2.1.2.1 13 (10.7%) 6 (6.2%) 6 (6.1%) 4.5 (-2.8 - 11.7) 7 (8.8%) 8 (10.0%) 4 (6.2%) -1.3 (-10.3 - 7.8)
dcd D.1.1.1.1 10 (8.2%) 12 (12.4%) 4 (4.1%) -4.2 (-12.3 - 4.0) 7 (8.8%) 6 (7.5%) 3 (4.7%) 1.2 (-7.2 - 9.7)
dcd D.1.1.4.2 10 (8.2%) 5 (5.2%) 7 (7.1%) 3.0 (-3.5 - 9.6) 6 (7.5%) 8 (10.0%) 9 (14.1%) -2.5 (-11.2 - 6.2)
dcd D.2.1.5.3 12 (9.8%) 10 (10.3%) 9 (9.2%) -0.5 (-8.5 - 7.6) 9 (11.2%) 10 (12.5%) 3 (4.7%) -1.2 (-11.3 - 8.8)
summarize_occurrences functions as expected with valid input and default arguments
Code
res
Output
A B
(N=5) (N=4)
—————————————————————————————
F
MH1 1 (20.0%) 0
MH2 1 (20.0%) 1 (25.0%)
MH3 0 1 (25.0%)
MH4 0 1 (25.0%)
M
MH1 2 (40.0%) 1 (25.0%)
MH2 0 1 (25.0%)
MH3 1 (20.0%) 0
summarize_occurrences works as expected with risk difference column
Code
res
Output
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=202) (N=177) (N=162) (N=379)
—————————————————————————————————————————————————————————————————————————————————
F
LOW 12 (5.9%) 11 (6.2%) 10 (6.2%) -0.3 (-5.1 - 4.6)
MEDIUM 11 (5.4%) 13 (7.3%) 10 (6.2%) -1.9 (-6.9 - 3.1)
HIGH 10 (5.0%) 7 (4.0%) 7 (4.3%) 1.0 (-3.2 - 5.1)
M
LOW 12 (5.9%) 5 (2.8%) 6 (3.7%) 3.1 (-1.0 - 7.2)
MEDIUM 10 (5.0%) 9 (5.1%) 4 (2.5%) -0.1 (-4.5 - 4.3)
HIGH 4 (2.0%) 12 (6.8%) 11 (6.8%) -4.8 (-9.0 - -0.6)
Code
res
Output
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=202) (N=177) (N=162) (N=379)
————————————————————————————————————————————————————————————————————————————————————————
F
LOW 10 6 8 1.6 (-2.4 - 5.6)
MEDIUM 9 11 9 -1.8 (-6.3 - 2.8)
HIGH 6 6 7 -0.4 (-4.0 - 3.1)
LOW 10 (5.0%) 6 (3.4%) 8 (4.9%) 1.6 (-2.4 - 5.6)
MEDIUM 9 (4.5%) 11 (6.2%) 9 (5.6%) -1.8 (-6.3 - 2.8)
HIGH 6 (3.0%) 6 (3.4%) 7 (4.3%) -0.4 (-4.0 - 3.1)
LOW 10/202 (5.0%) 6/177 (3.4%) 8/162 (4.9%) 1.6 (-2.4 - 5.6)
MEDIUM 9/202 (4.5%) 11/177 (6.2%) 9/162 (5.6%) -1.8 (-6.3 - 2.8)
HIGH 6/202 (3.0%) 6/177 (3.4%) 7/162 (4.3%) -0.4 (-4.0 - 3.1)
M
LOW 7 5 6 0.6 (-2.9 - 4.2)
MEDIUM 9 7 4 0.5 (-3.5 - 4.5)
HIGH 4 11 8 -4.2 (-8.3 - -0.2)
LOW 7 (3.5%) 5 (2.8%) 6 (3.7%) 0.6 (-2.9 - 4.2)
MEDIUM 9 (4.5%) 7 (4.0%) 4 (2.5%) 0.5 (-3.5 - 4.5)
HIGH 4 (2.0%) 11 (6.2%) 8 (4.9%) -4.2 (-8.3 - -0.2)
LOW 7/202 (3.5%) 5/177 (2.8%) 6/162 (3.7%) 0.6 (-2.9 - 4.2)
MEDIUM 9/202 (4.5%) 7/177 (4.0%) 4/162 (2.5%) 0.5 (-3.5 - 4.5)
HIGH 4/202 (2.0%) 11/177 (6.2%) 8/162 (4.9%) -4.2 (-8.3 - -0.2)
Code
res
Output
A B C
A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI) A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI) A: Drug X B: Placebo C: Combination Risk Difference (%) (95% CI)
(N=64) (N=67) (N=62) (N=131) (N=78) (N=64) (N=45) (N=142) (N=60) (N=46) (N=55) (N=106)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
F
LOW 6 (9.4%) 4 (6.0%) 1 (1.6%) 3.4 (-5.7 - 12.5) 3 (3.8%) 5 (7.8%) 6 (13.3%) -4.0 (-11.8 - 3.9) 3 (5.0%) 2 (4.3%) 3 (5.5%) 0.7 (-7.4 - 8.7)
MEDIUM 1 (1.6%) 4 (6.0%) 4 (6.5%) -4.4 (-10.8 - 2.0) 6 (7.7%) 4 (6.2%) 2 (4.4%) 1.4 (-6.9 - 9.8) 4 (6.7%) 5 (10.9%) 4 (7.3%) -4.2 (-15.2 - 6.8)
HIGH 3 (4.7%) 4 (6.0%) 3 (4.8%) -1.3 (-9.0 - 6.4) 3 (3.8%) 2 (3.1%) 0 0.7 (-5.3 - 6.8) 4 (6.7%) 1 (2.2%) 4 (7.3%) 4.5 (-3.1 - 12.1)
M
LOW 1 (1.6%) 2 (3.0%) 2 (3.2%) -1.4 (-6.5 - 3.7) 7 (9.0%) 2 (3.1%) 3 (6.7%) 5.8 (-1.8 - 13.5) 4 (6.7%) 1 (2.2%) 1 (1.8%) 4.5 (-3.1 - 12.1)
MEDIUM 5 (7.8%) 2 (3.0%) 1 (1.6%) 4.8 (-2.9 - 12.6) 2 (2.6%) 3 (4.7%) 2 (4.4%) -2.1 (-8.4 - 4.1) 3 (5.0%) 4 (8.7%) 1 (1.8%) -3.7 (-13.5 - 6.1)
HIGH 2 (3.1%) 5 (7.5%) 5 (8.1%) -4.3 (-11.9 - 3.3) 2 (2.6%) 5 (7.8%) 3 (6.7%) -5.2 (-12.7 - 2.2) 0 2 (4.3%) 3 (5.5%) -4.3 (-10.2 - 1.5)
Code
res
Output
Risk Difference (%) (95% CI) Risk Difference (%) (95% CI)
A: Drug X B: Placebo C: Combination A: Drug X vs. B: Placebo A: Drug X vs. C: Combination
(N=202) (N=177) (N=162) (N=379) (N=364)
————————————————————————————————————————————————————————————————————————————————————————————————————————————————
F
LOW 12 (5.9%) 11 (6.2%) 10 (6.2%) -0.3 (-5.1 - 4.6) -0.2 (-5.2 - 4.7)
MEDIUM 11 (5.4%) 13 (7.3%) 10 (6.2%) -1.9 (-6.9 - 3.1) -0.7 (-5.6 - 4.1)
HIGH 10 (5.0%) 7 (4.0%) 7 (4.3%) 1.0 (-3.2 - 5.1) 0.6 (-3.7 - 5.0)
M
LOW 12 (5.9%) 5 (2.8%) 6 (3.7%) 3.1 (-1.0 - 7.2) 2.2 (-2.1 - 6.6)
MEDIUM 10 (5.0%) 9 (5.1%) 4 (2.5%) -0.1 (-4.5 - 4.3) 2.5 (-1.3 - 6.3)
HIGH 4 (2.0%) 12 (6.8%) 11 (6.8%) -4.8 (-9.0 - -0.6) -4.8 (-9.1 - -0.5)
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