tests/testthat/_snaps/h_survival_duration_subgroups.md

In tern: Create Common TLGs Used in Clinical Trials

h_survtime_df functions as expected with valid input and default arguments

Code
  res
Output
           arm  n n_events   median
  1 B: Placebo 73       57 727.8043
  2  A: Drug X 69       44 974.6402

h_survtime_df functions as expected when median is NA

Code
  res
Output
    arm n n_events median
  1   A 3        1     NA
  2   B 3        3      2

h_survtime_df functions as expected when 0 records in one group

Code
  res
Output
    arm n n_events median
  1   A 0       NA     NA
  2   B 6        4      5

h_split_by_subgroups functions as expected with valid input and default arguments

Code
  res
Output
  $y.B
  $y.B$df
    x y z
  1 2 B D

  $y.B$df_labels
    subgroup var   var_label
  1        B   y label for y


  $y.A
  $y.A$df
    x y z
  1 1 A D

  $y.A$df_labels
    subgroup var   var_label
  1        A   y label for y


  $z.D
  $z.D$df
    x y z
  1 1 A D
  2 2 B D

  $z.D$df_labels
    subgroup var   var_label
  1        D   z label for z

h_split_by_subgroups works as expected with groups_lists

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  res
Output
  [1] "y.AB" "z.D"

Code
  res
Output
  $y.AB
  $y.AB$df
    x y z
  1 1 A D
  2 2 B D

  $y.AB$df_labels
    subgroup var   var_label
  1       AB   y label for y


  $z.D
  $z.D$df
    x y z
  1 1 A D
  2 2 B D

  $z.D$df_labels
    subgroup var   var_label
  1        D   z label for z

h_survtime_subgroups_df functions as expected with valid input and default arguments

Code
  res
Output
            arm  n n_events    median     subgroup    var
  1  B: Placebo 73       57  727.8043 All Patients    ALL
  2   A: Drug X 69       44  974.6402 All Patients    ALL
  3  B: Placebo 40       31  599.1772            F    SEX
  4   A: Drug X 38       24 1016.2982            F    SEX
  5  B: Placebo 33       26  888.4916            M    SEX
  6   A: Drug X 31       20  974.6402            M    SEX
  7  B: Placebo 24       21  735.4722          LOW BMRKR2
  8   A: Drug X 26       15  974.6402          LOW BMRKR2
  9  B: Placebo 23       14  731.8352       MEDIUM BMRKR2
  10  A: Drug X 26       17  964.2197       MEDIUM BMRKR2
  11 B: Placebo 26       22  654.8245         HIGH BMRKR2
  12  A: Drug X 17       12 1016.2982         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

h_survtime_subgroups_df functions as expected when subgroups is NULL.

Code
  res
Output
           arm  n n_events   median     subgroup var    var_label row_type
  1 B: Placebo 73       57 727.8043 All Patients ALL All Patients  content
  2  A: Drug X 69       44 974.6402 All Patients ALL All Patients  content

h_survtime_subgroups_df works as expected with groups_lists

Code
  res
Output
  [1] "low"             "low"             "low/medium"      "low/medium"     
  [5] "low/medium/high" "low/medium/high"

h_coxph_df functions as expected with valid input and default arguments

Code
  res
Output
    arm n_tot n_tot_events        hr       lcl      ucl conf_level       pval
  1       142          101 0.7108557 0.4779138 1.057337       0.95 0.09049511
            pval_label
  1 p-value (log-rank)

h_coxph_df functions as expected with one stratification factor

Code
  res
Output
    arm n_tot n_tot_events        hr       lcl     ucl conf_level       pval
  1       142          101 0.6646586 0.4399495 1.00414       0.95 0.05089188
            pval_label
  1 p-value (log-rank)

h_coxph_df functions as expected with multiple stratification factors

Code
  res
Output
    arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval
  1       142          101 0.6126133 0.3913507 0.9589739       0.95 0.03086774
            pval_label
  1 p-value (log-rank)

h_coxph_df functions as expected when 0 records in one group

Code
  res
Output
    arm n_tot n_tot_events hr lcl ucl conf_level pval pval_label
  1        69           44 NA  NA  NA       0.95   NA         NA

h_coxph_subgroups_df functions as expected with valid input and default arguments

Code
  res
Output
    arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval
  1       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511
  2        78           55 0.5595391 0.3246658 0.9643271       0.95 0.03411759
  3        64           46 0.9102874 0.5032732 1.6464678       0.95 0.75582028
  4        50           36 0.7617717 0.3854349 1.5055617       0.95 0.43236030
  5        49           31 0.7651261 0.3641277 1.6077269       0.95 0.47860004
  6        43           34 0.6662356 0.3257413 1.3626456       0.95 0.26285846
            pval_label     subgroup    var                    var_label row_type
  1 p-value (log-rank) All Patients    ALL                 All Patients  content
  2 p-value (log-rank)            F    SEX                          Sex analysis
  3 p-value (log-rank)            M    SEX                          Sex analysis
  4 p-value (log-rank)          LOW BMRKR2 Continuous Level Biomarker 2 analysis
  5 p-value (log-rank)       MEDIUM BMRKR2 Continuous Level Biomarker 2 analysis
  6 p-value (log-rank)         HIGH BMRKR2 Continuous Level Biomarker 2 analysis

Code
  res
Output
    arm n_tot n_tot_events           hr lcl ucl conf_level      pval
  1         3            2 1.056023e-09   0 Inf       0.95 0.4795001
  2         1            0           NA  NA  NA       0.95        NA
  3         2            2           NA  NA  NA       0.95        NA
            pval_label     subgroup     var    var_label row_type
  1 p-value (log-rank) All Patients     ALL All Patients  content
  2               <NA>          GBR COUNTRY      Country analysis
  3               <NA>          CAN COUNTRY      Country analysis

h_coxph_subgroups_df functions as expected with stratification factors

Code
  res
Output
    arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval
  1       142          101 0.6646586 0.4399495 1.0041404       0.95 0.05089188
  2        78           55 0.4824037 0.2671020 0.8712529       0.95 0.01372098
  3        64           46 0.8256627 0.4434121 1.5374387       0.95 0.54529396
            pval_label     subgroup var    var_label row_type
  1 p-value (log-rank) All Patients ALL All Patients  content
  2 p-value (log-rank)            F SEX          Sex analysis
  3 p-value (log-rank)            M SEX          Sex analysis

h_coxph_subgroups_df functions as expected when subgroups is NULL.

Code
  res
Output
    arm n_tot n_tot_events        hr       lcl      ucl conf_level       pval
  1       142          101 0.7108557 0.4779138 1.057337       0.95 0.09049511
            pval_label     subgroup var    var_label row_type
  1 p-value (log-rank) All Patients ALL All Patients  content

h_coxph_subgroups_df works as expected with groups_lists

Code
  res
Output
  [1] "low"             "low/medium"      "low/medium/high"

tern documentation built on June 22, 2024, 10:25 a.m.