Nothing
tests/testthat/_snaps/response_subgroups.md
In tern: Create Common TLGs Used in Clinical Trials
extract_rsp_subgroups functions as expected with valid input and default arguments
Code
res
Output
$prop
arm n n_rsp prop subgroup var var_label
1 B: Placebo 51 36 0.7058824 All Patients ALL All Patients
2 A: Drug X 49 41 0.8367347 All Patients ALL All Patients
3 B: Placebo 29 19 0.6551724 F SEX Sex
4 A: Drug X 25 24 0.9600000 F SEX Sex
5 B: Placebo 22 17 0.7727273 M SEX Sex
6 A: Drug X 24 17 0.7083333 M SEX Sex
7 B: Placebo 25 18 0.7200000 S1 STRATA2 Stratification Factor 2
8 A: Drug X 26 22 0.8461538 S1 STRATA2 Stratification Factor 2
9 B: Placebo 26 18 0.6923077 S2 STRATA2 Stratification Factor 2
10 A: Drug X 23 19 0.8260870 S2 STRATA2 Stratification Factor 2
row_type
1 content
2 content
3 analysis
4 analysis
5 analysis
6 analysis
7 analysis
8 analysis
9 analysis
10 analysis
$or
arm n_tot or lcl ucl conf_level subgroup var
1 100 2.1354167 0.8112648 5.620858 0.95 All Patients ALL
2 54 12.6315770 1.4840381 107.515254 0.95 F SEX
3 46 0.7142857 0.1889048 2.700853 0.95 M SEX
4 51 2.1388889 0.5395114 8.479609 0.95 S1 STRATA2
5 49 2.1111111 0.5405387 8.245089 0.95 S2 STRATA2
var_label row_type
1 All Patients content
2 Sex analysis
3 Sex analysis
4 Stratification Factor 2 analysis
5 Stratification Factor 2 analysis
extract_rsp_subgroups functions as expected with NULL subgroups
Code
res
Output
$prop
arm n n_rsp prop subgroup var var_label row_type
1 B: Placebo 51 36 0.7058824 All Patients ALL All Patients content
2 A: Drug X 49 41 0.8367347 All Patients ALL All Patients content
$or
arm n_tot or lcl ucl conf_level subgroup var
1 100 2.135417 0.8112648 5.620858 0.95 All Patients ALL
var_label row_type
1 All Patients content
extract_rsp_subgroups works as expected with groups_lists
Code
res
Output
[1] "low" "low" "low/medium" "low/medium"
[5] "low/medium/high" "low/medium/high"
Code
res
Output
[1] "low" "low/medium" "low/medium/high"
extract_rsp_subgroups functions as expected with strata
Code
res
Output
$prop
arm n n_rsp prop subgroup var var_label
1 B: Placebo 51 36 0.7058824 ALL ALL ALL
2 A: Drug X 49 41 0.8367347 ALL ALL ALL
3 B: Placebo 29 19 0.6551724 F SEX Sex
4 A: Drug X 25 24 0.9600000 F SEX Sex
5 B: Placebo 22 17 0.7727273 M SEX Sex
6 A: Drug X 24 17 0.7083333 M SEX Sex
7 B: Placebo 25 18 0.7200000 S1 STRATA2 Stratification Factor 2
8 A: Drug X 26 22 0.8461538 S1 STRATA2 Stratification Factor 2
9 B: Placebo 26 18 0.6923077 S2 STRATA2 Stratification Factor 2
10 A: Drug X 23 19 0.8260870 S2 STRATA2 Stratification Factor 2
row_type
1 content
2 content
3 analysis
4 analysis
5 analysis
6 analysis
7 analysis
8 analysis
9 analysis
10 analysis
$or
arm n_tot or lcl ucl conf_level pval
1 100 2.0600522 0.9213863 4.605902 0.9 0.135169890
2 54 11.2344101 1.8870687 66.882551 0.9 0.007819801
3 46 0.6700931 0.2220166 2.022483 0.9 0.549837487
4 51 2.2252093 0.6800882 7.280756 0.9 0.260432159
5 49 1.9373524 0.6160317 6.092761 0.9 0.337843302
pval_label subgroup var
1 p-value (Cochran-Mantel-Haenszel Test) ALL ALL
2 p-value (Cochran-Mantel-Haenszel Test) F SEX
3 p-value (Cochran-Mantel-Haenszel Test) M SEX
4 p-value (Cochran-Mantel-Haenszel Test) S1 STRATA2
5 p-value (Cochran-Mantel-Haenszel Test) S2 STRATA2
var_label row_type
1 ALL content
2 Sex analysis
3 Sex analysis
4 Stratification Factor 2 analysis
5 Stratification Factor 2 analysis
a_response_subgroups functions as expected with valid input
Code
res
Output
prop pval
——————————————————
M 0.12 <0.0001
F 0.57 0.9838
tabulate_rsp_subgroups functions as expected with valid input
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total n n Response (%) n Response (%) Odds Ratio 95% CI p-value (Chi-Squared Test)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 142 73 68.5% 69 85.5% 2.71 (1.18, 6.24) 0.0164
Sex
F 78 40 62.5% 38 94.7% 10.80 (2.27, 51.45) 0.0006
M 64 33 75.8% 31 74.2% 0.92 (0.30, 2.85) 0.8852
Stratification Factor 2
S1 73 34 70.6% 39 87.2% 2.83 (0.86, 9.35) 0.0801
S2 69 39 66.7% 30 83.3% 2.50 (0.78, 8.04) 0.1181
tabulate_rsp_subgroups correctly calculates column indices
Code
res
Output
$col_x
[1] 6
$col_ci
[1] 7
$col_symbol_size
[1] 1
Code
res
Output
$col_x
[1] 1
$col_ci
[1] 3
$col_symbol_size
[1] 2
tabulate_rsp_subgroups functions as expected with valid input extreme values in OR table
Code
res
Output
REF COMP
Baseline Risk Factors Total n n Response (%) n Response (%) Odds Ratio 95% CI
——————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 62 40 82.5% 22 9.1% 0.02 (<0.01, 0.11)
var1
subgroup1 50 30 100.0% 20 0.0% <0.01 (0.00, >999.99)
subgroup2 12 10 30.0% 2 100.0% >999.99 (0.00, >999.99)
tabulate_rsp_subgroups functions as expected with NULL subgroups
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total n n Response (%) n Response (%) Odds Ratio 95% CI p-value (Chi-Squared Test)
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 142 73 68.5% 69 85.5% 2.71 (1.18, 6.24) 0.0164
tabulate_rsp_subgroups functions as expected when 0 obs in one arm
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total n n Response (%) n Response (%) Odds Ratio 95% CI p-value (Chi-Squared Test)
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 142 73 68.5% 69 85.5% 2.71 (1.18, 6.24) 0.0164
Race
ASIAN 81 43 69.8% 38 92.1% 5.06 (1.31, 19.44) 0.0117
BLACK OR AFRICAN AMERICAN 28 13 69.2% 15 73.3% 1.22 (0.24, 6.31) 0.8106
WHITE 23 12 75.0% 11 72.7% 0.89 (0.14, 5.72) 0.9013
AMERICAN INDIAN OR ALASKA NATIVE 7 3 0.0% 4 100.0% >999.99 (0.00, >999.99) 0.0082
MULTIPLE 2 1 100.0% 1 100.0% 1.00 (0.00, >999.99) 1.0000
NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER 1 1 100.0% 0 NA NA NA NA
d_rsp_subgroups_colvars functions as expected with valid input
Code
res
Output
$vars
[1] "n" "n_rsp" "prop" "n_tot" "or" "lcl" "pval"
$labels
n n_rsp
"n" "Responders"
prop n_tot
"Response (%)" "Total n"
or ci
"Odds Ratio" "90% CI"
pval
"p-value (Chi-Squared Test)"
tabulate_rsp_subgroups .formats argument works as expected
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total n n Response (%) n Response (%) Odds Ratio 95% CI p-value (Chi-Squared Test)
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 142.00 73 68.5% 69 85.5% 2.71 1.2 to 6.2 0.0164
Sex
F 78.00 40 62.5% 38 94.7% 10.80 2.3 to 51.5 0.0006
M 64.00 33 75.8% 31 74.2% 0.92 0.3 to 2.9 0.8852
Stratification Factor 2
S1 73.00 34 70.6% 39 87.2% 2.83 0.9 to 9.4 0.0801
S2 69.00 39 66.7% 30 83.3% 2.50 0.8 to 8.0 0.1181
tabulate_rsp_subgroups na_str argument works as expected
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total n n Response (%) n Response (%) Odds Ratio 95% CI p-value (Chi-Squared Test)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 142 73 68.5% 69 85.5% 2.71 (1.18, 6.24) 0.0164
Sex
F 78 40 62.5% 38 94.7% <No data> (2.27, 51.45) 0.0006
M 64 33 75.8% 31 74.2% <No data> (0.30, 2.85) 0.8852
Stratification Factor 2
S1 73 34 70.6% 39 87.2% <No data> (0.86, 9.35) 0.0801
S2 69 39 66.7% 30 83.3% <No data> (0.78, 8.04) 0.1181
tabulate_rsp_subgroups riskdiff argument works as expected
Code
res
Output
B: Placebo A: Drug X
Prop. Diff
Baseline Risk Factors Total n n Response (%) n Response (%) Odds Ratio 95% CI p-value (Chi-Squared Test) (95% CI)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 142 73 68.5% 69 85.5% 2.71 (1.18, 6.24) 0.0164 -17.0 (-30.5 - -3.5)
Sex
F 78 40 62.5% 38 94.7% 10.80 (2.27, 51.45) 0.0006 -32.2 (-48.8 - -15.6)
M 64 33 75.8% 31 74.2% 0.92 (0.30, 2.85) 0.8852 1.6 (-19.7 - 22.8)
Stratification Factor 2
S1 73 34 70.6% 39 87.2% 2.83 (0.86, 9.35) 0.0801 -16.6 (-35.2 - 2.0)
S2 69 39 66.7% 30 83.3% 2.50 (0.78, 8.04) 0.1181 -16.7 (-36.6 - 3.3)
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extract_rsp_subgroups functions as expected with valid input and default arguments
Code
res
Output
$prop
arm n n_rsp prop subgroup var var_label
1 B: Placebo 51 36 0.7058824 All Patients ALL All Patients
2 A: Drug X 49 41 0.8367347 All Patients ALL All Patients
3 B: Placebo 29 19 0.6551724 F SEX Sex
4 A: Drug X 25 24 0.9600000 F SEX Sex
5 B: Placebo 22 17 0.7727273 M SEX Sex
6 A: Drug X 24 17 0.7083333 M SEX Sex
7 B: Placebo 25 18 0.7200000 S1 STRATA2 Stratification Factor 2
8 A: Drug X 26 22 0.8461538 S1 STRATA2 Stratification Factor 2
9 B: Placebo 26 18 0.6923077 S2 STRATA2 Stratification Factor 2
10 A: Drug X 23 19 0.8260870 S2 STRATA2 Stratification Factor 2
row_type
1 content
2 content
3 analysis
4 analysis
5 analysis
6 analysis
7 analysis
8 analysis
9 analysis
10 analysis
$or
arm n_tot or lcl ucl conf_level subgroup var
1 100 2.1354167 0.8112648 5.620858 0.95 All Patients ALL
2 54 12.6315770 1.4840381 107.515254 0.95 F SEX
3 46 0.7142857 0.1889048 2.700853 0.95 M SEX
4 51 2.1388889 0.5395114 8.479609 0.95 S1 STRATA2
5 49 2.1111111 0.5405387 8.245089 0.95 S2 STRATA2
var_label row_type
1 All Patients content
2 Sex analysis
3 Sex analysis
4 Stratification Factor 2 analysis
5 Stratification Factor 2 analysis
extract_rsp_subgroups functions as expected with NULL subgroups
Code
res
Output
$prop
arm n n_rsp prop subgroup var var_label row_type
1 B: Placebo 51 36 0.7058824 All Patients ALL All Patients content
2 A: Drug X 49 41 0.8367347 All Patients ALL All Patients content
$or
arm n_tot or lcl ucl conf_level subgroup var
1 100 2.135417 0.8112648 5.620858 0.95 All Patients ALL
var_label row_type
1 All Patients content
extract_rsp_subgroups works as expected with groups_lists
Code
res
Output
[1] "low" "low" "low/medium" "low/medium"
[5] "low/medium/high" "low/medium/high"
Code
res
Output
[1] "low" "low/medium" "low/medium/high"
extract_rsp_subgroups functions as expected with strata
Code
res
Output
$prop
arm n n_rsp prop subgroup var var_label
1 B: Placebo 51 36 0.7058824 ALL ALL ALL
2 A: Drug X 49 41 0.8367347 ALL ALL ALL
3 B: Placebo 29 19 0.6551724 F SEX Sex
4 A: Drug X 25 24 0.9600000 F SEX Sex
5 B: Placebo 22 17 0.7727273 M SEX Sex
6 A: Drug X 24 17 0.7083333 M SEX Sex
7 B: Placebo 25 18 0.7200000 S1 STRATA2 Stratification Factor 2
8 A: Drug X 26 22 0.8461538 S1 STRATA2 Stratification Factor 2
9 B: Placebo 26 18 0.6923077 S2 STRATA2 Stratification Factor 2
10 A: Drug X 23 19 0.8260870 S2 STRATA2 Stratification Factor 2
row_type
1 content
2 content
3 analysis
4 analysis
5 analysis
6 analysis
7 analysis
8 analysis
9 analysis
10 analysis
$or
arm n_tot or lcl ucl conf_level pval
1 100 2.0600522 0.9213863 4.605902 0.9 0.135169890
2 54 11.2344101 1.8870687 66.882551 0.9 0.007819801
3 46 0.6700931 0.2220166 2.022483 0.9 0.549837487
4 51 2.2252093 0.6800882 7.280756 0.9 0.260432159
5 49 1.9373524 0.6160317 6.092761 0.9 0.337843302
pval_label subgroup var
1 p-value (Cochran-Mantel-Haenszel Test) ALL ALL
2 p-value (Cochran-Mantel-Haenszel Test) F SEX
3 p-value (Cochran-Mantel-Haenszel Test) M SEX
4 p-value (Cochran-Mantel-Haenszel Test) S1 STRATA2
5 p-value (Cochran-Mantel-Haenszel Test) S2 STRATA2
var_label row_type
1 ALL content
2 Sex analysis
3 Sex analysis
4 Stratification Factor 2 analysis
5 Stratification Factor 2 analysis
a_response_subgroups functions as expected with valid input
Code
res
Output
prop pval
——————————————————
M 0.12 <0.0001
F 0.57 0.9838
tabulate_rsp_subgroups functions as expected with valid input
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total n n Response (%) n Response (%) Odds Ratio 95% CI p-value (Chi-Squared Test)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 142 73 68.5% 69 85.5% 2.71 (1.18, 6.24) 0.0164
Sex
F 78 40 62.5% 38 94.7% 10.80 (2.27, 51.45) 0.0006
M 64 33 75.8% 31 74.2% 0.92 (0.30, 2.85) 0.8852
Stratification Factor 2
S1 73 34 70.6% 39 87.2% 2.83 (0.86, 9.35) 0.0801
S2 69 39 66.7% 30 83.3% 2.50 (0.78, 8.04) 0.1181
tabulate_rsp_subgroups correctly calculates column indices
Code
res
Output
$col_x
[1] 6
$col_ci
[1] 7
$col_symbol_size
[1] 1
Code
res
Output
$col_x
[1] 1
$col_ci
[1] 3
$col_symbol_size
[1] 2
tabulate_rsp_subgroups functions as expected with valid input extreme values in OR table
Code
res
Output
REF COMP
Baseline Risk Factors Total n n Response (%) n Response (%) Odds Ratio 95% CI
——————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 62 40 82.5% 22 9.1% 0.02 (<0.01, 0.11)
var1
subgroup1 50 30 100.0% 20 0.0% <0.01 (0.00, >999.99)
subgroup2 12 10 30.0% 2 100.0% >999.99 (0.00, >999.99)
tabulate_rsp_subgroups functions as expected with NULL subgroups
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total n n Response (%) n Response (%) Odds Ratio 95% CI p-value (Chi-Squared Test)
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 142 73 68.5% 69 85.5% 2.71 (1.18, 6.24) 0.0164
tabulate_rsp_subgroups functions as expected when 0 obs in one arm
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total n n Response (%) n Response (%) Odds Ratio 95% CI p-value (Chi-Squared Test)
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 142 73 68.5% 69 85.5% 2.71 (1.18, 6.24) 0.0164
Race
ASIAN 81 43 69.8% 38 92.1% 5.06 (1.31, 19.44) 0.0117
BLACK OR AFRICAN AMERICAN 28 13 69.2% 15 73.3% 1.22 (0.24, 6.31) 0.8106
WHITE 23 12 75.0% 11 72.7% 0.89 (0.14, 5.72) 0.9013
AMERICAN INDIAN OR ALASKA NATIVE 7 3 0.0% 4 100.0% >999.99 (0.00, >999.99) 0.0082
MULTIPLE 2 1 100.0% 1 100.0% 1.00 (0.00, >999.99) 1.0000
NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER 1 1 100.0% 0 NA NA NA NA
d_rsp_subgroups_colvars functions as expected with valid input
Code
res
Output
$vars
[1] "n" "n_rsp" "prop" "n_tot" "or" "lcl" "pval"
$labels
n n_rsp
"n" "Responders"
prop n_tot
"Response (%)" "Total n"
or ci
"Odds Ratio" "90% CI"
pval
"p-value (Chi-Squared Test)"
tabulate_rsp_subgroups .formats argument works as expected
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total n n Response (%) n Response (%) Odds Ratio 95% CI p-value (Chi-Squared Test)
—————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 142.00 73 68.5% 69 85.5% 2.71 1.2 to 6.2 0.0164
Sex
F 78.00 40 62.5% 38 94.7% 10.80 2.3 to 51.5 0.0006
M 64.00 33 75.8% 31 74.2% 0.92 0.3 to 2.9 0.8852
Stratification Factor 2
S1 73.00 34 70.6% 39 87.2% 2.83 0.9 to 9.4 0.0801
S2 69.00 39 66.7% 30 83.3% 2.50 0.8 to 8.0 0.1181
tabulate_rsp_subgroups na_str argument works as expected
Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total n n Response (%) n Response (%) Odds Ratio 95% CI p-value (Chi-Squared Test)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 142 73 68.5% 69 85.5% 2.71 (1.18, 6.24) 0.0164
Sex
F 78 40 62.5% 38 94.7% <No data> (2.27, 51.45) 0.0006
M 64 33 75.8% 31 74.2% <No data> (0.30, 2.85) 0.8852
Stratification Factor 2
S1 73 34 70.6% 39 87.2% <No data> (0.86, 9.35) 0.0801
S2 69 39 66.7% 30 83.3% <No data> (0.78, 8.04) 0.1181
tabulate_rsp_subgroups riskdiff argument works as expected
Code
res
Output
B: Placebo A: Drug X
Prop. Diff
Baseline Risk Factors Total n n Response (%) n Response (%) Odds Ratio 95% CI p-value (Chi-Squared Test) (95% CI)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
All Patients 142 73 68.5% 69 85.5% 2.71 (1.18, 6.24) 0.0164 -17.0 (-30.5 - -3.5)
Sex
F 78 40 62.5% 38 94.7% 10.80 (2.27, 51.45) 0.0006 -32.2 (-48.8 - -15.6)
M 64 33 75.8% 31 74.2% 0.92 (0.30, 2.85) 0.8852 1.6 (-19.7 - 22.8)
Stratification Factor 2
S1 73 34 70.6% 39 87.2% 2.83 (0.86, 9.35) 0.0801 -16.6 (-35.2 - 2.0)
S2 69 39 66.7% 30 83.3% 2.50 (0.78, 8.04) 0.1181 -16.7 (-36.6 - 3.3)
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