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tests/testthat/_snaps/survival_biomarkers_subgroups.md
In tern: Create Common TLGs Used in Clinical Trials
extract_survival_biomarkers functions as expected with valid input and default arguments
Code
res
Output
biomarker biomarker_label n_tot n_tot_events median hr
1 AGE Age 200 141 753.5176 1.0113037
2 BMRKR1 Continuous Level Biomarker 1 200 141 753.5176 0.9987473
3 AGE Age 110 79 685.2335 0.9974417
4 BMRKR1 Continuous Level Biomarker 1 110 79 685.2335 1.0145281
5 AGE Age 90 62 888.4916 1.0213080
6 BMRKR1 Continuous Level Biomarker 1 90 62 888.4916 0.9829857
7 AGE Age 70 52 735.4722 1.0139949
8 BMRKR1 Continuous Level Biomarker 1 70 52 735.4722 0.9991674
9 AGE Age 68 42 858.9952 1.0332689
10 BMRKR1 Continuous Level Biomarker 1 68 42 858.9952 0.9709938
11 AGE Age 62 47 727.8043 0.9964359
12 BMRKR1 Continuous Level Biomarker 1 62 47 727.8043 1.0611819
lcl ucl conf_level pval pval_label subgroup var
1 0.9880703 1.035084 0.95 0.3431854 p-value (Wald) All Patients ALL
2 0.9521917 1.047579 0.95 0.9589522 p-value (Wald) All Patients ALL
3 0.9646002 1.031401 0.95 0.8807989 p-value (Wald) F SEX
4 0.9580753 1.074307 0.95 0.6214667 p-value (Wald) F SEX
5 0.9890882 1.054577 0.95 0.1973532 p-value (Wald) M SEX
6 0.9024823 1.070670 0.95 0.6938508 p-value (Wald) M SEX
7 0.9678771 1.062310 0.95 0.5584219 p-value (Wald) LOW BMRKR2
8 0.9243879 1.079996 0.95 0.9832563 p-value (Wald) LOW BMRKR2
9 0.9768608 1.092934 0.95 0.2531999 p-value (Wald) MEDIUM BMRKR2
10 0.8873583 1.062512 0.95 0.5218385 p-value (Wald) MEDIUM BMRKR2
11 0.9646222 1.029299 0.95 0.8292481 p-value (Wald) HIGH BMRKR2
12 0.9643359 1.167754 0.95 0.2239082 p-value (Wald) HIGH BMRKR2
var_label row_type
1 All Patients content
2 All Patients content
3 Sex analysis
4 Sex analysis
5 Sex analysis
6 Sex analysis
7 Continuous Level Biomarker 2 analysis
8 Continuous Level Biomarker 2 analysis
9 Continuous Level Biomarker 2 analysis
10 Continuous Level Biomarker 2 analysis
11 Continuous Level Biomarker 2 analysis
12 Continuous Level Biomarker 2 analysis
extract_survival_biomarkers works as expected with groups_lists
Code
res
Output
biomarker subgroup
7 AGE low
8 BMRKR1 low
9 AGE low/medium
10 BMRKR1 low/medium
11 AGE low/medium/high
12 BMRKR1 low/medium/high
tabulate_survival_biomarkers works as expected with valid input
Code
res
Output
Total n Total Events Median (DAYS) Hazard Ratio 95% Wald CI p-value (Wald)
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Age
All Patients 200 141 753.5 1.01 (0.99, 1.04) 0.3432
Sex
F 110 79 685.2 1.00 (0.96, 1.03) 0.8808
M 90 62 888.5 1.02 (0.99, 1.05) 0.1974
Continuous Level Biomarker 2
LOW 70 52 735.5 1.01 (0.97, 1.06) 0.5584
MEDIUM 68 42 859.0 1.03 (0.98, 1.09) 0.2532
HIGH 62 47 727.8 1.00 (0.96, 1.03) 0.8292
Continuous Level Biomarker 1
All Patients 200 141 753.5 1.00 (0.95, 1.05) 0.9590
Sex
F 110 79 685.2 1.01 (0.96, 1.07) 0.6215
M 90 62 888.5 0.98 (0.90, 1.07) 0.6939
Continuous Level Biomarker 2
LOW 70 52 735.5 1.00 (0.92, 1.08) 0.9833
MEDIUM 68 42 859.0 0.97 (0.89, 1.06) 0.5218
HIGH 62 47 727.8 1.06 (0.96, 1.17) 0.2239
Code
res
Output
$col_x
[1] 4
$col_ci
[1] 5
$col_symbol_size
[1] 1
$forest_header
[1] "Higher\nBetter" "Lower\nBetter"
tabulate_survival_biomarkers functions as expected with NULL subgroups
Code
res
Output
Total n Total Events Median (DAYS) Hazard Ratio 95% Wald CI p-value (Wald)
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Age
All Patients 200 141 753.5 1.01 (0.99, 1.04) 0.3432
Continuous Level Biomarker 1
All Patients 200 141 753.5 1.00 (0.95, 1.05) 0.9590
tabulate_survival_biomarkers works with only a single biomarker in the data frame
Code
res
Output
Total n Total Events Median Hazard Ratio 95% Wald CI p-value (Wald)
—————————————————————————————————————————————————————————————————————————————————————————————————————————————
Continuous Level Biomarker 1
All Patients 400 282 680.0 0.98 (0.95, 1.01) 0.3000
tabulate_survival_biomarkers na_str argument works as expected
Code
res
Output
Total n Total Events Median (DAYS) Hazard Ratio 95% Wald CI p-value (Wald)
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Age
All Patients 200 141 753.5 1.01 (0.99, 1.04) 0.3432
Sex
F 110 79 685.2 <No data> (0.96, 1.03) 0.8808
M 90 62 888.5 <No data> (0.99, 1.05) 0.1974
Continuous Level Biomarker 2
LOW 70 52 735.5 1.01 (0.97, 1.06) 0.5584
MEDIUM 68 42 859.0 1.03 (0.98, 1.09) 0.2532
HIGH 62 47 727.8 1.00 (0.96, 1.03) 0.8292
Continuous Level Biomarker 1
All Patients 200 141 753.5 <No data> (0.95, 1.05) 0.9590
Sex
F 110 79 685.2 <No data> (0.96, 1.07) 0.6215
M 90 62 888.5 0.98 (0.90, 1.07) 0.6939
Continuous Level Biomarker 2
LOW 70 52 735.5 1.00 (0.92, 1.08) 0.9833
MEDIUM 68 42 859.0 0.97 (0.89, 1.06) 0.5218
HIGH 62 47 727.8 1.06 (0.96, 1.17) 0.2239
label_all argument to extract_survival_subgroups works as expected
Code
res
Output
Total n Total Events Median (DAYS) Hazard Ratio 95% Wald CI p-value (Wald)
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Age
Full Analysis Set 200 141 753.5 1.01 (0.99, 1.04) 0.3432
Sex
F 110 79 685.2 1.00 (0.96, 1.03) 0.8808
M 90 62 888.5 1.02 (0.99, 1.05) 0.1974
Continuous Level Biomarker 2
LOW 70 52 735.5 1.01 (0.97, 1.06) 0.5584
MEDIUM 68 42 859.0 1.03 (0.98, 1.09) 0.2532
HIGH 62 47 727.8 1.00 (0.96, 1.03) 0.8292
Continuous Level Biomarker 1
Full Analysis Set 200 141 753.5 1.00 (0.95, 1.05) 0.9590
Sex
F 110 79 685.2 1.01 (0.96, 1.07) 0.6215
M 90 62 888.5 0.98 (0.90, 1.07) 0.6939
Continuous Level Biomarker 2
LOW 70 52 735.5 1.00 (0.92, 1.08) 0.9833
MEDIUM 68 42 859.0 0.97 (0.89, 1.06) 0.5218
HIGH 62 47 727.8 1.06 (0.96, 1.17) 0.2239
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tern documentation built on June 22, 2024, 10:25 a.m.
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extract_survival_biomarkers functions as expected with valid input and default arguments
Code
res
Output
biomarker biomarker_label n_tot n_tot_events median hr
1 AGE Age 200 141 753.5176 1.0113037
2 BMRKR1 Continuous Level Biomarker 1 200 141 753.5176 0.9987473
3 AGE Age 110 79 685.2335 0.9974417
4 BMRKR1 Continuous Level Biomarker 1 110 79 685.2335 1.0145281
5 AGE Age 90 62 888.4916 1.0213080
6 BMRKR1 Continuous Level Biomarker 1 90 62 888.4916 0.9829857
7 AGE Age 70 52 735.4722 1.0139949
8 BMRKR1 Continuous Level Biomarker 1 70 52 735.4722 0.9991674
9 AGE Age 68 42 858.9952 1.0332689
10 BMRKR1 Continuous Level Biomarker 1 68 42 858.9952 0.9709938
11 AGE Age 62 47 727.8043 0.9964359
12 BMRKR1 Continuous Level Biomarker 1 62 47 727.8043 1.0611819
lcl ucl conf_level pval pval_label subgroup var
1 0.9880703 1.035084 0.95 0.3431854 p-value (Wald) All Patients ALL
2 0.9521917 1.047579 0.95 0.9589522 p-value (Wald) All Patients ALL
3 0.9646002 1.031401 0.95 0.8807989 p-value (Wald) F SEX
4 0.9580753 1.074307 0.95 0.6214667 p-value (Wald) F SEX
5 0.9890882 1.054577 0.95 0.1973532 p-value (Wald) M SEX
6 0.9024823 1.070670 0.95 0.6938508 p-value (Wald) M SEX
7 0.9678771 1.062310 0.95 0.5584219 p-value (Wald) LOW BMRKR2
8 0.9243879 1.079996 0.95 0.9832563 p-value (Wald) LOW BMRKR2
9 0.9768608 1.092934 0.95 0.2531999 p-value (Wald) MEDIUM BMRKR2
10 0.8873583 1.062512 0.95 0.5218385 p-value (Wald) MEDIUM BMRKR2
11 0.9646222 1.029299 0.95 0.8292481 p-value (Wald) HIGH BMRKR2
12 0.9643359 1.167754 0.95 0.2239082 p-value (Wald) HIGH BMRKR2
var_label row_type
1 All Patients content
2 All Patients content
3 Sex analysis
4 Sex analysis
5 Sex analysis
6 Sex analysis
7 Continuous Level Biomarker 2 analysis
8 Continuous Level Biomarker 2 analysis
9 Continuous Level Biomarker 2 analysis
10 Continuous Level Biomarker 2 analysis
11 Continuous Level Biomarker 2 analysis
12 Continuous Level Biomarker 2 analysis
extract_survival_biomarkers works as expected with groups_lists
Code
res
Output
biomarker subgroup
7 AGE low
8 BMRKR1 low
9 AGE low/medium
10 BMRKR1 low/medium
11 AGE low/medium/high
12 BMRKR1 low/medium/high
tabulate_survival_biomarkers works as expected with valid input
Code
res
Output
Total n Total Events Median (DAYS) Hazard Ratio 95% Wald CI p-value (Wald)
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Age
All Patients 200 141 753.5 1.01 (0.99, 1.04) 0.3432
Sex
F 110 79 685.2 1.00 (0.96, 1.03) 0.8808
M 90 62 888.5 1.02 (0.99, 1.05) 0.1974
Continuous Level Biomarker 2
LOW 70 52 735.5 1.01 (0.97, 1.06) 0.5584
MEDIUM 68 42 859.0 1.03 (0.98, 1.09) 0.2532
HIGH 62 47 727.8 1.00 (0.96, 1.03) 0.8292
Continuous Level Biomarker 1
All Patients 200 141 753.5 1.00 (0.95, 1.05) 0.9590
Sex
F 110 79 685.2 1.01 (0.96, 1.07) 0.6215
M 90 62 888.5 0.98 (0.90, 1.07) 0.6939
Continuous Level Biomarker 2
LOW 70 52 735.5 1.00 (0.92, 1.08) 0.9833
MEDIUM 68 42 859.0 0.97 (0.89, 1.06) 0.5218
HIGH 62 47 727.8 1.06 (0.96, 1.17) 0.2239
Code
res
Output
$col_x
[1] 4
$col_ci
[1] 5
$col_symbol_size
[1] 1
$forest_header
[1] "Higher\nBetter" "Lower\nBetter"
tabulate_survival_biomarkers functions as expected with NULL subgroups
Code
res
Output
Total n Total Events Median (DAYS) Hazard Ratio 95% Wald CI p-value (Wald)
————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Age
All Patients 200 141 753.5 1.01 (0.99, 1.04) 0.3432
Continuous Level Biomarker 1
All Patients 200 141 753.5 1.00 (0.95, 1.05) 0.9590
tabulate_survival_biomarkers works with only a single biomarker in the data frame
Code
res
Output
Total n Total Events Median Hazard Ratio 95% Wald CI p-value (Wald)
—————————————————————————————————————————————————————————————————————————————————————————————————————————————
Continuous Level Biomarker 1
All Patients 400 282 680.0 0.98 (0.95, 1.01) 0.3000
tabulate_survival_biomarkers na_str argument works as expected
Code
res
Output
Total n Total Events Median (DAYS) Hazard Ratio 95% Wald CI p-value (Wald)
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Age
All Patients 200 141 753.5 1.01 (0.99, 1.04) 0.3432
Sex
F 110 79 685.2 <No data> (0.96, 1.03) 0.8808
M 90 62 888.5 <No data> (0.99, 1.05) 0.1974
Continuous Level Biomarker 2
LOW 70 52 735.5 1.01 (0.97, 1.06) 0.5584
MEDIUM 68 42 859.0 1.03 (0.98, 1.09) 0.2532
HIGH 62 47 727.8 1.00 (0.96, 1.03) 0.8292
Continuous Level Biomarker 1
All Patients 200 141 753.5 <No data> (0.95, 1.05) 0.9590
Sex
F 110 79 685.2 <No data> (0.96, 1.07) 0.6215
M 90 62 888.5 0.98 (0.90, 1.07) 0.6939
Continuous Level Biomarker 2
LOW 70 52 735.5 1.00 (0.92, 1.08) 0.9833
MEDIUM 68 42 859.0 0.97 (0.89, 1.06) 0.5218
HIGH 62 47 727.8 1.06 (0.96, 1.17) 0.2239
label_all argument to extract_survival_subgroups works as expected
Code
res
Output
Total n Total Events Median (DAYS) Hazard Ratio 95% Wald CI p-value (Wald)
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Age
Full Analysis Set 200 141 753.5 1.01 (0.99, 1.04) 0.3432
Sex
F 110 79 685.2 1.00 (0.96, 1.03) 0.8808
M 90 62 888.5 1.02 (0.99, 1.05) 0.1974
Continuous Level Biomarker 2
LOW 70 52 735.5 1.01 (0.97, 1.06) 0.5584
MEDIUM 68 42 859.0 1.03 (0.98, 1.09) 0.2532
HIGH 62 47 727.8 1.00 (0.96, 1.03) 0.8292
Continuous Level Biomarker 1
Full Analysis Set 200 141 753.5 1.00 (0.95, 1.05) 0.9590
Sex
F 110 79 685.2 1.01 (0.96, 1.07) 0.6215
M 90 62 888.5 0.98 (0.90, 1.07) 0.6939
Continuous Level Biomarker 2
LOW 70 52 735.5 1.00 (0.92, 1.08) 0.9833
MEDIUM 68 42 859.0 0.97 (0.89, 1.06) 0.5218
HIGH 62 47 727.8 1.06 (0.96, 1.17) 0.2239
Try the tern package in your browser
Any scripts or data that you put into this service are public.
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