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tern

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install.packages('tern')

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2,254

Version

0.9.7

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 (0.9.7)

Layout-creating function to add row total counts

afun_selected_stats

Get selected statistics names

Split function to configure risk difference column

Labels for adverse event baskets

Analysis function to calculate risk difference column values

abnormal_by_marked

Count patients with marked laboratory abnormalities

abnormal_by_worst_grade_worsen

Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline

Count patients with abnormal range values

abnormal_by_worst_grade

Count patients by most extreme post-baseline toxicity grade per direction of abnormality

abnormal_by_baseline

Count patients with abnormal analysis range values by baseline status

analyze_functions

Analyze functions

as_factor_keep_attributes

Conversion of a vector to a factor

analyze_colvars_functions

Analyze functions in columns

Convert to rtable

append_varlabels

Add variable labels to top left corner in table

analyze_variables

Analyze variables

analyze_vars_in_cols

Analyze numeric variables in columns

apply_auto_formatting

Apply automatic formatting

Reference and treatment group combination

Check element dimension

combination_function

Class for CombinationFunction

Additional assertions to use with checkmate

bins_percent_labels

Labels for bins in percent

Constructor for content functions given a data frame with flag input

check_diff_prop_ci

Check proportion difference arguments

Arrange multiple grobs

Content row function to add alt_counts_df row total to labels

Content row function to add row total to labels

argument_convention

Standard arguments

control_lineplot_vars

Control function for g_lineplot()

Control function for Cox regression

Combine factor levels

combine_vectors

Element-wise combination of two vectors

control_incidence_rate

Control function for incidence rate

Control function for Cox-PH model

Control functions for Kaplan-Meier plot annotation tables

compare_variables

Compare variables between groups

control_logistic

Control function for logistic regression model fitting

control_analyze_vars

Control function for descriptive statistics

Control function for subgroup treatment effect pattern (STEP) calculations

count_cumulative

Cumulative counts of numeric variable by thresholds

count_patients_with_event

Count the number of patients with a particular event

control_surv_time

Control function for survfit models for survival time

count_occurrences

Count occurrences

control_riskdiff

Control function for risk difference column

control_surv_timepoint

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

count_occurrences_by_grade

Count occurrences by grade

count_patients_events_in_cols

Count patient events in columns

count_missed_doses

Count number of patients with missed doses by thresholds

d_onco_rsp_label

Description of standard oncology response

d_count_missed_doses

Description function that calculates labels for s_count_missed_doses()

d_count_cumulative

Description of cumulative count

Generate PK reference dataset

count_patients_with_flags

Count the number of patients with particular flags

Count specific values

Cox proportional hazards regression

cox_regression_inter

Cox regression helper function for interactions

d_rsp_subgroups_colvars

Labels for column variables in binary response by subgroup table

decorate_grob_set

Decorate set of grobs and add page numbering

decorate_grob_factory

Update page number

d_survival_subgroups_colvars

Labels for column variables in survival duration by subgroup table

cut_quantile_bins

Cut numeric vector into empirical quantile bins

d_count_abnormal_by_baseline

Description function for s_count_abnormal_by_baseline()

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

Description of the proportion summary

d_proportion_diff

Description of method used for proportion comparison

Default string replacement for NA values

Conversion of days to months

d_test_proportion_diff

Description of the difference test between two proportions

estimate_multinomial_rsp

Estimate proportions of each level of a variable

empty_vector_if_na

Return an empty numeric if all elements are NA.

desctools_binom

Confidence intervals for a difference of binomials

.is_equal_float

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

default_stats_formats_labels

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

estimate_proportion

Proportion estimation

Convert data.frame object to ggplot object

Hazard ratio estimation in interactions

Simulated CDISC data for examples

extract_by_name

Extract elements by name

extract_rsp_subgroups

Prepare response data for population subgroups in data frames

extract_survival_subgroups

Prepare survival data for population subgroups in data frames

Encode categorical missing values in a data frame

Format extreme values

Utility function to create label for confidence interval

extract_rsp_biomarkers

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

Utility function to create label for p-value

Discard specified levels of a factor

fct_collapse_only

Collapse factor levels and keep only those new group levels

Format automatically using data significant digits

format_count_fraction

Format count and fraction

format_fraction_fixed_dp

Format fraction and percentage with fixed single decimal place

format_fraction

Format fraction and percentage

Fit for logistic regression

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

Format numeric values by significant figures

format_fraction_threshold

Format fraction with lower threshold

format_count_fraction_fixed_dp

Format count and percentage with fixed single decimal place

format_count_fraction_lt10

Format count and fraction with special case for count < 10

Fitting functions for Cox proportional hazards regression

fct_explicit_na_if

Insertion of explicit missing values in a factor

Format XX as a formatting function

extract_survival_biomarkers

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

fit_survival_step

Subgroup treatment effect pattern (STEP) fit for survival outcome

Bland-Altman plot

Smooth function with optional grouping

groups_list_to_df

Convert list of groups to a data frame

Create a forest plot from an rtable

forest_viewport

Create a viewport tree for the forest plot

Individual patient plots

formatting_functions

Formatting functions

format_extreme_values_ci

Format extreme values part of a confidence interval

format_extreme_values

Format a single extreme value

Horizontal waterfall plot

Line plot with optional table

Kaplan-Meier plot

Create a STEP graph

Utility function to return a named list of covariate names

Helper function to tidy survival fit data

h_adlb_abnormal_by_worst_grade

Helper function to prepare ADLB for count_abnormal_by_worst_grade()

ggplot decomposition

Helper function to prepare ADLB with worst labs

h_append_grade_groups

Helper function for s_count_occurrences_by_grade()

Obtain column indices

h_count_cumulative

Helper function for s_count_cumulative()

h_cox_regression

Helper functions for Cox proportional hazards regression

Helper function to create grid object with y-axis annotation

h_grob_tbl_at_risk

Helper function to create patient-at-risk grobs

h_adsl_adlb_merge_using_worst_flag

Helper function for deriving analysis datasets for select laboratory tables

Helper function to return results of a linear model

h_grob_median_surv

Helper function to create survival estimation grobs

Helper function to create Cox-PH grobs

Helper function to prepare a KM layout

h_incidence_rate

Helper functions for incidence rate

Helper function to format the optional g_lineplot table

Helper function to create simple line plot over time

Helper function to create a KM plot

Helper functions for Poisson models

h_response_biomarkers_subgroups

Helper functions for tabulating biomarker effects on binary response by subgroup

h_prop_diff_test

Helper functions to test proportion differences

h_response_subgroups

Helper functions for tabulating binary response by subgroup

h_logistic_regression

Helper functions for multivariate logistic regression

Helper functions for calculating proportion confidence intervals

Helper functions for odds ratio estimation

Sort pharmacokinetic data by PARAM variable

Function to return the estimated means using predicted probabilities

Helper functions to calculate proportion difference

h_map_for_count_abnormal

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

h_tbl_median_surv

Helper function for survival estimations

h_split_by_subgroups

Split data frame by subgroups

h_tbl_coxph_pairwise

Helper function for generating a pairwise Cox-PH table

h_tab_one_biomarker

Helper function for tabulation of a single biomarker result

h_worsen_counter

Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline()

Incidence rate estimation

logistic_regression_cols

Logistic regression multivariate column layout function

Split parameters

Helper function to calculate x-tick positions

imputation_rule

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

labels_use_control

Update labels according to control specifications

labels_or_names

Labels or names of list elements

h_survival_biomarkers_subgroups

Helper functions for tabulating biomarker effects on survival by subgroup

h_survival_duration_subgroups

Helper functions for tabulating survival duration by subgroup

Conversion of months to days

muffled_car_anova

Muffled car::Anova

h_stack_by_baskets

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

logistic_summary_by_flag

Logistic regression summary table

Helper functions for subgroup treatment effect pattern (STEP) calculations

Proportion difference estimation

Make names without dots

prune_occurrences

Occurrence table pruning

Difference test for two proportions

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

reapply_varlabels

Reapply variable labels

response_biomarkers_subgroups

Tabulate biomarker effects on binary response by subgroup

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

response_subgroups

Tabulate binary response by subgroup

s_cox_multivariate

Multivariate Cox model - summarized results

Bland-Altman analysis

Helper functions for accessing information from rtables

Odds ratio estimation

Confidence interval for mean

Stack multiple grobs

split_text_grob

Split text according to available text width

p-Value of the mean

Convert rtable objects to ggplot objects

Convert strings to NA

score_occurrences

Occurrence table sorting

Confidence interval for median

split_cols_by_groups

Split columns by groups of levels

stat_propdiff_ci

Proportion difference and confidence interval

summarize_glm_count

Summarize Poisson negative binomial regression

summarize_change

Summarize change from baseline values or absolute baseline values

summarize_colvars

Summarize variables in columns

summarize_functions

Summarize functions

summarize_ancova

Summarize analysis of covariance (ANCOVA) results

summarize_logistic

Multivariate logistic regression table

strata_normal_quantile

Helper function for the estimation of stratified quantiles

Indicate study arm variable in formula

survival_duration_subgroups

Tabulate survival duration by subgroup

Custom tidy method for binomial GLM results

summarize_num_patients

Count number of patients

survival_coxph_pairwise

Analyze a pairwise Cox-PH model

survival_biomarkers_subgroups

Tabulate biomarker effects on survival by subgroup

summarize_patients_exposure_in_cols

Count number of patients and sum exposure across all patients in columns

survival_timepoint

Survival time point analysis

Survival time analysis

Custom tidy method for STEP results

Ungroup non-numeric statistics

unlist_and_blank_na

Blank for missing input

Custom tidy methods for Cox regression

Univariate formula special term

update_weights_strat_wilson

Helper function for the estimation of weights for prop_strat_wilson()

Replicate entries of a vector if required

util_handling_additional_fun_params

Utilities to handle extra arguments in analysis functions

utils_split_funs

Custom split functions

to_string_matrix

Convert table into matrix of strings

tryCatch around car::Anova