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tern

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install.packages('tern')

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Version

0.9.5

License

Apache License 2.0

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Repository

https://github.com/insightsengineering/tern/

Homepage

https://insightsengineering.github.io/tern/

Maintainer

Joe Zhu

Last Published

April 14th, 2025

Functions in tern (0.9.5)

Analysis function to calculate risk difference column values

afun_selected_stats

Get selected statistics names

abnormal_by_worst_grade_worsen

Patient counts for laboratory events (worsen from baseline) by highest grade post-baseline

Split function to configure risk difference column

analyze_colvars_functions

Analyze functions on columns

Convert to rtable

append_varlabels

Add variable labels to top left corner in table

analyze_functions

Analyze functions

control_analyze_vars

Control function for descriptive statistics

apply_auto_formatting

Apply automatic formatting

Control functions for Kaplan-Meier plot annotation tables

Patient counts with abnormal range values

as_factor_keep_attributes

Conversion of a vector to a factor

abnormal_by_baseline

Patient counts with abnormal range values by baseline status

Additional assertions to use with checkmate

Layout-creating function to add row total counts

abnormal_by_marked

Count patients with marked laboratory abnormalities

combination_function

Class for CombinationFunction

check_diff_prop_ci

Check proportion difference arguments

Check element dimension

abnormal_by_worst_grade

Patient counts with the most extreme post-baseline toxicity grade per direction of abnormality

bins_percent_labels

Labels for bins in percent

Labels for adverse event baskets

count_patients_events_in_cols

Count patients and events in columns

Reference and treatment group combination

count_patients_with_event

Count the number of patients with a particular event

Combine factor levels

count_cumulative

Cumulative counts with thresholds

count_missed_doses

Count missed doses

Cox proportional hazards regression

analyze_variables

Analyze variables

cox_regression_inter

Cox regression helper function for interactions

control_incidence_rate

Control function for incidence rate

argument_convention

Standard arguments

combine_vectors

Element-wise combination of two vectors

control_lineplot_vars

Control function for g_lineplot()

Arrange multiple grobs

analyze_vars_in_cols

Summarize numeric variables in columns

Content row function to add alt_counts_df row total to labels

Add titles, footnotes, page Number, and a bounding box to a grid grob

control_logistic

Control function for logistic regression model fitting

compare_variables

Compare variables between groups

d_test_proportion_diff

Description of the difference test between two proportions

Conversion of days to months

default_stats_formats_labels

Get default statistical methods and their associated formats, labels, and indent modifiers

Control function for subgroup treatment effect pattern (STEP) calculations

Bland-Altman analysis

Content row function to add row total to labels

decorate_grob_factory

Update page number

desctools_binom

Confidence intervals for a difference of binomials

Utility function to create label for confidence interval

Control function for Cox-PH model

Utility function to create label for p-value

extract_survival_subgroups

Prepare survival data for population subgroups in data frames

Format extreme values

d_onco_rsp_label

Description of standard oncology response

Control function for Cox regression

Format automatically using data significant digits

Generate PK reference dataset

format_count_fraction

Format count and fraction

control_surv_time

Control function for survfit models for survival time

count_occurrences

Occurrence counts

count_occurrences_by_grade

Occurrence counts by grade

estimate_multinomial_rsp

Estimation of proportions per level of factor

Constructor for content functions given a data frame with flag input

format_fraction_threshold

Format fraction with lower threshold

estimate_proportions

Estimation of proportions

format_extreme_values

Format a single extreme value

control_surv_timepoint

Control function for survfit models for patients' survival rate at time points

count_patients_with_flags

Count the number of patients with particular flags

cut_quantile_bins

Cut numeric vector into empirical quantile bins

fct_collapse_only

Collapse factor levels and keep only those new group levels

d_count_cumulative

Description of cumulative count

Discard specified levels of a factor

format_extreme_values_ci

Format extreme values part of a confidence interval

Create a forest plot from an rtable

Format numeric values by significant figures

count_values_funs

Count specific values

d_count_missed_doses

Description function that calculates labels for s_count_missed_doses()

d_count_abnormal_by_baseline

Description function for s_count_abnormal_by_baseline()

Description of the proportion summary

decorate_grob_set

Decorate set of grobs and add page numbering

Default string replacement for NA values

d_proportion_diff

Description of method used for proportion comparison

groups_list_to_df

Convert list of groups to a data frame

d_rsp_subgroups_colvars

Labels for column variables in binary response by subgroup table

.is_equal_float

Utility function to check if a float value is equal to another float value

empty_vector_if_na

Return an empty numeric if all elements are NA.

Simulated CDISC data for examples

h_adlb_abnormal_by_worst_grade

Helper function to prepare ADLB for count_abnormal_by_worst_grade()

ggplot decomposition

Individual patient plots

Obtain column indices

Helper function to create simple line plot over time

h_count_cumulative

Helper function for s_count_cumulative()

Helper function to create a KM plot

Helper function to format the optional g_lineplot table

Hazard ratio estimation in interactions

h_prop_diff_test

Helper functions to test proportion differences

Helper functions for calculating proportion confidence intervals

fit_survival_step

Subgroup treatment effect pattern (STEP) fit for survival outcome

h_tbl_median_surv

Helper function for survival estimations

forest_viewport

Create a viewport tree for the forest plot

h_grob_median_surv

Helper function to create survival estimation grobs

Helper functions for Poisson models

d_survival_subgroups_colvars

Labels for column variables in survival duration by subgroup table

h_grob_tbl_at_risk

Helper function to create patient-at-risk grobs

Convert data.frame object to ggplot object

Format XX as a formatting function

Encode categorical missing values in a data frame

h_response_biomarkers_subgroups

Helper functions for tabulating biomarker effects on binary response by subgroup

extract_rsp_subgroups

Prepare response data for population subgroups in data frames

h_split_by_subgroups

Split data frame by subgroups

Helper function to create Cox-PH grobs

Split parameters

h_survival_biomarkers_subgroups

Helper functions for tabulating biomarker effects on survival by subgroup

h_worsen_counter

Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline()

extract_by_name

Extract elements by name

formatting_functions

Formatting functions

extract_survival_biomarkers

Prepare survival data estimates for multiple biomarkers in a single data frame

Utility function to return a named list of covariate names

Smooth function with optional grouping

Helper function to return results of a linear model

h_response_subgroups

Helper functions for tabulating binary response by subgroup

h_tab_one_biomarker

Helper function for tabulation of a single biomarker result

h_survival_duration_subgroups

Helper functions for tabulating survival duration by subgroup

labels_or_names

Labels or names of list elements

response_subgroups

Tabulate binary response by subgroup

Conversion of months to days

muffled_car_anova

Muffled car::Anova

Convert rtable objects to ggplot objects

prune_occurrences

Occurrence table pruning

Fit for logistic regression

Subgroup treatment effect pattern (STEP) fit for binary (response) outcome

extract_rsp_biomarkers

Prepare response data estimates for multiple biomarkers in a single data frame

fct_explicit_na_if

Insertion of explicit missing values in a factor

Fitting functions for Cox proportional hazards regression

Re-implemented range() default S3 method for numerical objects

h_tbl_coxph_pairwise

Helper function for generating a pairwise Cox-PH table

format_count_fraction_fixed_dp

Format count and percentage with fixed single decimal place

stat_propdiff_ci

Proportion difference and confidence interval

labels_use_control

Update labels according to control specifications

strata_normal_quantile

Helper function for the estimation of stratified quantiles

logistic_regression_cols

Logistic regression multivariate column layout function

Stack multiple grobs

Proportion difference

Confidence interval for mean

summarize_logistic

Multivariate logistic regression table

format_count_fraction_lt10

Format count and fraction with special case for count < 10

Difference test for two proportions

summarize_num_patients

Number of patients

split_cols_by_groups

Split columns by groups of levels

summarize_functions

Summarize functions

h_append_grade_groups

Helper function for s_count_occurrences_by_grade()

split_text_grob

Split text according to available text width

Replicate entries of a vector if required

summarize_change

Summarize the change from baseline or absolute baseline values

format_fraction

Format fraction and percentage

summarize_glm_count

Summarize Poisson negative binomial regression

format_fraction_fixed_dp

Format fraction and percentage with fixed single decimal place

Helper function to calculate x-tick positions

Kaplan-Meier plot

Line plot with optional table

imputation_rule

Apply 1/3 or 1/2 imputation rule to data

Create a STEP graph

Helper function to prepare ADLB with worst labs

to_string_matrix

Convert table into matrix of strings

Horizontal waterfall plot

h_adsl_adlb_merge_using_worst_flag

Helper function for deriving analysis datasets for select laboratory tables

h_cox_regression

Helper functions for Cox proportional hazards regression

Helper function to tidy survival fit data

Custom tidy method for STEP results

tryCatch around car::Anova

Helper function to create grid object with y-axis annotation

logistic_summary_by_flag

Logistic regression summary table

h_incidence_rate

Helper functions for incidence rate

Sort pharmacokinetic data by PARAM variable

Helper functions to calculate proportion difference

Helper function to prepare a KM layout

Number of available (non-missing entries) in a vector

Odds ratio estimation

Make names without dots

reapply_varlabels

Reapply variable labels

summarize_colvars

Summarize variables in columns

h_logistic_regression

Helper functions for multivariate logistic regression

update_weights_strat_wilson

Helper function for the estimation of weights for prop_strat_wilson()

response_biomarkers_subgroups

Tabulate biomarker effects on binary response by subgroup

utils_split_funs

Custom split functions

Ungroup non-numeric statistics

Helper functions for accessing information from rtables

h_map_for_count_abnormal

Helper function to create a map data frame for trim_levels_to_map()

Custom tidy methods for Cox regression

Univariate formula special term

unlist_and_blank_na

Blank for missing input

p-Value of the mean

Confidence interval for median

Helper functions for odds ratio estimation

s_cox_multivariate

Multivariate Cox model - summarized results

summarize_patients_exposure_in_cols

Count patients and sum exposure across all patients in columns

Convert strings to NA

h_stack_by_baskets

Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records.

survival_biomarkers_subgroups

Tabulate biomarker effects on survival by subgroup

survival_coxph_pairwise

Pairwise Cox-PH model

score_occurrences

Occurrence table sorting

Indicate study arm variable in formula

Helper functions for subgroup treatment effect pattern (STEP) calculations

summarize_ancova

Summary for analysis of covariance (ANCOVA).

survival_duration_subgroups

Tabulate survival duration by subgroup

Survival time analysis

survival_timepoint

Survival time point analysis

Custom tidy method for binomial GLM results