From 9cfefae2482644b671810004946c40eef7cec0d0 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Fri, 8 Sep 2023 19:18:12 +0000 Subject: [PATCH] Update pkgdown documentation 5dee25f174a69df9429b3ab12b66be374dd8276b --- main/404.html | 25 +-- main/CODE_OF_CONDUCT.html | 25 +-- main/CONTRIBUTING.html | 25 +-- main/LICENSE-text.html | 25 +-- main/SECURITY.html | 25 +-- main/articles/index.html | 25 +-- main/articles/missing_values.html | 25 +-- main/articles/tables.html | 25 +-- main/articles/tern.html | 25 +-- main/articles/tern_formats.html | 25 +-- main/authors.html | 29 +-- main/index.html | 25 +-- main/news/index.html | 36 +--- main/pkgdown.yml | 2 +- main/pull_request_template.html | 25 +-- main/reference/a_summary_internal.html | 25 +-- main/reference/abnormal.html | 25 +-- main/reference/abnormal_by_baseline.html | 25 +-- main/reference/abnormal_by_marked.html | 25 +-- main/reference/abnormal_by_worst_grade.html | 25 +-- .../abnormal_by_worst_grade_worsen.html | 25 +-- main/reference/add_riskdiff.html | 25 +-- main/reference/add_rowcounts.html | 32 +--- main/reference/aesi_label.html | 25 +-- main/reference/afun_riskdiff.html | 25 +-- main/reference/afun_selected_stats.html | 25 +-- main/reference/analyze_colvars_functions.html | 25 +-- main/reference/analyze_functions.html | 25 +-- main/reference/analyze_variables.html | 101 ++++------ main/reference/analyze_vars_in_cols.html | 56 +++--- main/reference/append_varlabels.html | 25 +-- main/reference/argument_convention.html | 30 +-- main/reference/arrange_grobs.html | 25 +-- main/reference/as.rtable.html | 45 ++--- main/reference/as_factor_keep_attributes.html | 25 +-- main/reference/assertions.html | 25 +-- main/reference/bins_percent_labels.html | 25 +-- main/reference/c_label_n.html | 42 ++--- main/reference/c_label_n_alt.html | 119 ++++++++++++ main/reference/cfun_by_flag.html | 25 +-- main/reference/check_diff_prop_ci.html | 25 +-- main/reference/check_same_n.html | 25 +-- main/reference/combination_function.html | 25 +-- main/reference/combine_counts.html | 25 +-- main/reference/combine_groups.html | 25 +-- main/reference/combine_levels.html | 25 +-- main/reference/combine_vectors.html | 25 +-- main/reference/compare_variables.html | 131 ++++++------- main/reference/control_analyze_vars.html | 25 +-- main/reference/control_coxph.html | 25 +-- main/reference/control_coxreg.html | 25 +-- main/reference/control_incidence_rate.html | 25 +-- main/reference/control_lineplot_vars.html | 25 +-- main/reference/control_logistic.html | 25 +-- main/reference/control_step.html | 25 +-- main/reference/control_surv_time.html | 25 +-- main/reference/control_surv_timepoint.html | 25 +-- main/reference/count_cumulative.html | 25 +-- main/reference/count_missed_doses.html | 25 +-- main/reference/count_occurrences.html | 25 +-- .../reference/count_occurrences_by_grade.html | 25 +-- .../count_patients_events_in_cols.html | 25 +-- 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main/reference/decorate_grob_set.html | 25 +-- main/reference/desctools_binom.html | 25 +-- main/reference/df_explicit_na.html | 25 +-- main/reference/draw_grob.html | 25 +-- main/reference/empty_vector_if_na.html | 25 +-- main/reference/estimate_coef.html | 25 +-- main/reference/estimate_multinomial_rsp.html | 25 +-- main/reference/estimate_proportions.html | 25 +-- main/reference/ex_data.html | 25 +-- main/reference/explicit_na.html | 25 +-- main/reference/extract_by_name.html | 25 +-- main/reference/extract_rsp_biomarkers.html | 25 +-- main/reference/extract_rsp_subgroups.html | 25 +-- .../extract_survival_biomarkers.html | 25 +-- .../reference/extract_survival_subgroups.html | 25 +-- main/reference/extreme_format.html | 26 +-- main/reference/f_conf_level.html | 25 +-- main/reference/f_pval.html | 25 +-- main/reference/fct_collapse_only.html | 25 +-- main/reference/fct_discard.html | 25 +-- main/reference/fct_explicit_na_if.html | 25 +-- main/reference/fit_coxreg.html | 25 +-- main/reference/fit_logistic.html | 25 +-- main/reference/fit_rsp_step.html | 25 +-- main/reference/fit_survival_step.html | 25 +-- main/reference/forest_viewport.html | 25 +-- main/reference/format_count_fraction.html | 26 +-- .../format_count_fraction_fixed_dp.html | 26 +-- main/reference/format_extreme_values.html | 26 +-- main/reference/format_extreme_values_ci.html | 26 +-- main/reference/format_fraction.html | 26 +-- main/reference/format_fraction_fixed_dp.html | 26 +-- main/reference/format_fraction_threshold.html | 26 +-- main/reference/format_sigfig.html | 132 +++++++++++++ main/reference/format_xx.html | 26 +-- main/reference/formatting_functions.html | 26 +-- main/reference/g_forest.html | 25 +-- main/reference/g_km.html | 25 +-- main/reference/g_lineplot.html | 25 +-- main/reference/g_step.html | 25 +-- main/reference/g_waterfall.html | 25 +-- main/reference/get_covariates.html | 25 +-- main/reference/get_smooths.html | 25 +-- main/reference/groups_list_to_df.html | 25 +-- main/reference/h_adlb_worsen.html | 25 +-- .../h_adsl_adlb_merge_using_worst_flag.html | 25 +-- main/reference/h_ancova.html | 25 +-- main/reference/h_append_grade_groups.html | 25 +-- main/reference/h_col_indices.html | 25 +-- main/reference/h_count_cumulative.html | 25 +-- main/reference/h_cox_regression.html | 25 +-- main/reference/h_data_plot.html | 25 +-- main/reference/h_decompose_gg.html | 25 +-- main/reference/h_format_row.html | 25 +-- main/reference/h_g_ipp.html | 25 +-- main/reference/h_ggkm.html | 25 +-- main/reference/h_glm_count.html | 25 +-- main/reference/h_grob_coxph.html | 25 +-- main/reference/h_grob_median_surv.html | 25 +-- main/reference/h_grob_tbl_at_risk.html | 25 +-- main/reference/h_grob_y_annot.html | 25 +-- main/reference/h_incidence_rate.html | 25 +-- main/reference/h_km_layout.html | 25 +-- main/reference/h_logistic_regression.html | 25 +-- main/reference/h_map_for_count_abnormal.html | 25 +-- main/reference/h_odds_ratio.html | 25 +-- main/reference/h_pkparam_sort.html | 25 +-- main/reference/h_prop_diff.html | 25 +-- main/reference/h_prop_diff_test.html | 25 +-- main/reference/h_proportions.html | 25 +-- .../h_response_biomarkers_subgroups.html | 25 +-- main/reference/h_response_subgroups.html | 25 +-- main/reference/h_split_by_subgroups.html | 25 +-- main/reference/h_split_param.html | 25 +-- main/reference/h_stack_by_baskets.html | 25 +-- main/reference/h_step.html | 25 +-- .../h_survival_biomarkers_subgroups.html | 25 +-- .../h_survival_duration_subgroups.html | 25 +-- main/reference/h_tab_one_biomarker.html | 25 +-- main/reference/h_tbl_coxph_pairwise.html | 25 +-- main/reference/h_tbl_median_surv.html | 25 +-- main/reference/h_worsen_counter.html | 25 +-- main/reference/h_xticks.html | 25 +-- main/reference/imputation_rule.html | 173 ++++++++++++++++++ main/reference/incidence_rate.html | 25 +-- main/reference/index.html | 35 ++-- main/reference/individual_patient_plot.html | 25 +-- main/reference/labels_or_names.html | 25 +-- main/reference/logistic_regression_cols.html | 25 +-- main/reference/logistic_summary_by_flag.html | 25 +-- main/reference/make_names.html | 25 +-- main/reference/month2day.html | 25 +-- main/reference/muffled_car_anova.html | 25 +-- main/reference/n_available.html | 25 +-- main/reference/odds_ratio.html | 25 +-- main/reference/prop_diff.html | 25 +-- main/reference/prop_diff_test.html | 25 +-- main/reference/prune_occurrences.html | 25 +-- main/reference/range_noinf.html | 25 +-- main/reference/reapply_varlabels.html | 25 +-- .../response_biomarkers_subgroups.html | 25 +-- main/reference/response_subgroups.html | 25 +-- main/reference/rtables_access.html | 25 +-- main/reference/s_cox_multivariate.html | 25 +-- main/reference/sas_na.html | 25 +-- main/reference/score_occurrences.html | 25 +-- main/reference/split_cols_by_groups.html | 25 +-- main/reference/split_text_grob.html | 25 +-- main/reference/stack_grobs.html | 25 +-- main/reference/stat_mean_ci.html | 25 +-- main/reference/stat_mean_pval.html | 25 +-- main/reference/stat_median_ci.html | 25 +-- main/reference/stat_propdiff_ci.html | 25 +-- main/reference/strata_normal_quantile.html | 25 +-- main/reference/study_arm.html | 25 +-- main/reference/summarize_ancova.html | 25 +-- main/reference/summarize_change.html | 25 +-- main/reference/summarize_colvars.html | 25 +-- main/reference/summarize_functions.html | 25 +-- main/reference/summarize_glm_count.html | 25 +-- main/reference/summarize_logistic.html | 25 +-- main/reference/summarize_num_patients.html | 25 +-- .../summarize_patients_exposure_in_cols.html | 25 +-- main/reference/summary_stats.html | 25 +-- .../survival_biomarkers_subgroups.html | 25 +-- main/reference/survival_coxph_pairwise.html | 25 +-- .../survival_duration_subgroups.html | 25 +-- main/reference/survival_time.html | 25 +-- main/reference/survival_timepoint.html | 25 +-- main/reference/tern-package.html | 25 +-- main/reference/tidy.glm.html | 25 +-- main/reference/tidy.step.html | 25 +-- main/reference/tidy_coxreg.html | 25 +-- main/reference/to_n.html | 25 +-- main/reference/to_string_matrix.html | 25 +-- main/reference/try_car_anova.html | 25 +-- main/reference/ungroup_stats.html | 25 +-- main/reference/univariate.html | 25 +-- main/reference/unlist_and_blank_na.html | 25 +-- .../update_weights_strat_wilson.html | 25 +-- main/search.json | 2 +- main/sitemap.xml | 9 + 225 files changed, 841 insertions(+), 5368 deletions(-) create mode 100644 main/reference/c_label_n_alt.html create mode 100644 main/reference/format_sigfig.html create mode 100644 main/reference/imputation_rule.html diff --git a/main/404.html b/main/404.html index 7abee9ab4f..ac76873ee2 100644 --- a/main/404.html +++ b/main/404.html @@ -25,7 +25,7 @@ tern - 0.9.0.9000 + 0.9.0.9001
part of NESTpharmaverse
+ + + + + +
+
+
+

Content Row Function to Add alt_counts_df Row Total to Labels

+ Source: R/utils_rtables.R +
c_label_n_alt.Rd
+
+ +
+

This takes the label of the latest row split level and adds the row total from alt_counts_df +in parentheses. This function differs from c_label_n() by taking row counts from alt_counts_df +rather than df, and is used by add_rowcounts() when alt_counts is set to TRUE.

+
+ +
+

Usage

+ 
c_label_n_alt(df, labelstr, .alt_df_row)
+
+ +
+

Arguments

+
df
+

(data.frame)
data set containing all analysis variables.

+ + +
labelstr
+

(character)
label of the level of the parent split currently being summarized +(must be present as second argument in Content Row Functions). See rtables::summarize_row_groups() +for more information.

+ +
+
+

Value

+ + +

A list with formatted rtables::CellValue() with the row count value and the correct label.

+
+
+

See also

+

c_label_n() which performs the same function but retrieves row counts from df instead +of alt_counts_df.

+
+ +
+ + +
+ + + + + + + diff --git a/main/reference/cfun_by_flag.html b/main/reference/cfun_by_flag.html index e64fcf7c13..ff03dd4ae3 100644 --- a/main/reference/cfun_by_flag.html +++ b/main/reference/cfun_by_flag.html @@ -10,7 +10,7 @@ tern - 0.9.0.9000 + 0.9.0.9001
part of NESTpharmaverse
+ + + + + +
+
+
+

Formatting Numeric Values By Significant Figures

+ Source: R/formatting_functions.R +
format_sigfig.Rd
+
+ +
+

Format numeric values to print with a specified number of significant figures.

+
+ +
+

Usage

+ 
format_sigfig(sigfig)
+
+ +
+

Arguments

+
sigfig
+

(integer)
number of significant figures to display.

+ +
+
+

Value

+ + +

An rtables formatting function.

+
+
+

See also

+

Other formatting functions: +extreme_format, +format_count_fraction_fixed_dp(), +format_count_fraction(), +format_extreme_values_ci(), +format_extreme_values(), +format_fraction_fixed_dp(), +format_fraction_threshold(), +format_fraction(), +format_xx(), +formatting_functions

+
+ +
+

Examples

+ 
fmt_3sf <- format_sigfig(3)
+fmt_3sf(1.658)
+#> [1] "1.66"
+fmt_3sf(1e1)
+#> [1] "10.0"
+
+fmt_5sf <- format_sigfig(5)
+fmt_5sf(0.57)
+#> [1] "0.57000"
+fmt_5sf(0.000025645)
+#> [1] "0.000025645"
+
+
+
+
+ + +
+ + + + + + + diff --git a/main/reference/format_xx.html b/main/reference/format_xx.html index 17ec423104..090db00fd9 100644 --- a/main/reference/format_xx.html +++ b/main/reference/format_xx.html @@ -12,7 +12,7 @@ tern - 0.9.0.9000 + 0.9.0.9001
part of NESTpharmaverse
+ + + + + +
+
+
+

Apply 1/3 or 1/2 Imputation Rule to Data

+ Source: R/imputation_rule.R +
imputation_rule.Rd
+
+ +
+

[Stable]

+
+ +
+

Usage

+ 
imputation_rule(
+  df,
+  x_stats,
+  stat,
+  imp_rule,
+  post = FALSE,
+  avalcat_var = "AVALCAT1"
+)
+
+ +
+

Arguments

+
df
+

(data.frame)
data set containing all analysis variables.

+ + +
x_stats
+

(named list)
a named list of statistics, typically the results of s_summary().

+ + +
stat
+

(character)
statistic to return the value/NA level of according to the imputation +rule applied.

+ + +
imp_rule
+

(character)
imputation rule setting. Set to "1/3" to implement 1/3 imputation +rule or "1/2" to implement 1/2 imputation rule.

+ + +
post
+

(flag)
whether the data corresponds to a post-dose time-point (defaults to FALSE). +This parameter is only used when imp_rule is set to "1/3".

+ + +
avalcat_var
+

(character)
name of variable that indicates whether a row in df corresponds +to an analysis value in category "BLQ", "LTR", "<PCLLOQ", or none of the above +(defaults to "AVALCAT1"). Variable avalcat_var must be present in df.

+ +
+
+

Value

+ + +

A list containing statistic value (val) and NA level (na_level) that should be displayed +according to the specified imputation rule.

+
+
+

See also

+

analyze_vars_in_cols() where this function can be implemented by setting the imp_rule +argument.

+
+ +
+

Examples

+ 
set.seed(1)
+df <- data.frame(
+  AVAL = runif(50, 0, 1),
+  AVALCAT1 = sample(c(1, "BLQ"), 50, replace = TRUE)
+)
+x_stats <- s_summary(df$AVAL)
+imputation_rule(df, x_stats, "max", "1/3")
+#> $val
+#>       max 
+#> 0.9919061 
+#> 
+#> $na_level
+#> [1] "ND"
+#> 
+imputation_rule(df, x_stats, "geom_mean", "1/3")
+#> $val
+#> [1] NA
+#> 
+#> $na_level
+#> [1] "NE"
+#> 
+imputation_rule(df, x_stats, "mean", "1/2")
+#> $val
+#> [1] NA
+#> 
+#> $na_level
+#> [1] "ND"
+#> 
+
+
+
+
+ + +
+ + + + + + + diff --git a/main/reference/incidence_rate.html b/main/reference/incidence_rate.html index 0e8eb77431..e9bc74e1aa 100644 --- a/main/reference/incidence_rate.html +++ b/main/reference/incidence_rate.html @@ -14,7 +14,7 @@ tern - 0.9.0.9000 + 0.9.0.9001
part of NESTpharmaverse