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tern

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install.packages('tern')

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2,254

Version

0.9.4

License

Apache License 2.0

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Maintainer

Joe Zhu

Last Published

April 14th, 2025

Functions in tern (0.9.4)

abnormal_by_marked

Count patients with marked laboratory abnormalities
aesi_label

Labels for adverse event baskets
add_riskdiff

Split function to configure risk difference column
add_rowcounts

Layout-creating function to add row total counts
afun_selected_stats

Get selected statistics names
afun_riskdiff

Analysis function to calculate risk difference column values
abnormal_by_worst_grade

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

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

Patient counts with abnormal range values
abnormal_by_baseline

Patient counts with abnormal range values by baseline status
argument_convention

Standard arguments
analyze_functions

Analyze functions
analyze_vars_in_cols

Summarize numeric variables in columns
append_varlabels

Add variable labels to top left corner in table
as.rtable

Convert to rtable
analyze_colvars_functions

Analyze functions on columns
apply_auto_formatting

Apply automatic formatting
as_factor_keep_attributes

Conversion of a vector to a factor
arrange_grobs

Arrange multiple grobs
analyze_variables

Analyze variables
assertions

Additional assertions to use with checkmate
combination_function

Class for CombinationFunction
combine_counts

Combine counts
c_label_n

Content row function to add row total to labels
bins_percent_labels

Labels for bins in percent
c_label_n_alt

Content row function to add alt_counts_df row total to labels
check_same_n

Check element dimension
check_diff_prop_ci

Check proportion difference arguments
bland_altman

Bland-Altman analysis
cfun_by_flag

Constructor for content functions given a data frame with flag input
combine_vectors

Element-wise combination of two vectors
control_analyze_vars

Control function for descriptive statistics
control_coxph

Control function for Cox-PH model
control_incidence_rate

Control function for incidence rate
combine_levels

Combine factor levels
combine_groups

Reference and treatment group combination
control_coxreg

Control function for Cox regression
compare_variables

Compare variables between groups
control_lineplot_vars

Control function for g_lineplot()
control_annot

Control functions for Kaplan-Meier plot annotation tables
count_occurrences_by_grade

Occurrence counts by grade
control_surv_time

Control function for survfit models for survival time
count_patients_events_in_cols

Count patients and events in columns
control_logistic

Control function for logistic regression model fitting
count_occurrences

Occurrence counts
control_surv_timepoint

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

Count missed doses
count_cumulative

Cumulative counts with thresholds
control_step

Control function for subgroup treatment effect pattern (STEP) calculations
count_patients_with_event

Count the number of patients with a particular event
cox_regression

Cox proportional hazards regression
d_count_cumulative

Description of cumulative count
cut_quantile_bins

Cut numeric vector into empirical quantile bins
count_values_funs

Count specific values
count_patients_with_flags

Count the number of patients with particular flags
d_onco_rsp_label

Description of standard oncology response
d_count_missed_doses

Description function that calculates labels for s_count_missed_doses()
decorate_grob

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

Cox regression helper function for interactions
d_count_abnormal_by_baseline

Description function for s_count_abnormal_by_baseline()
d_pkparam

Generate PK reference dataset
day2month

Conversion of days to months
decorate_grob_set

Decorate set of grobs and add page numbering
default_na_str

Default string replacement for NA values
d_proportion

Description of the proportion summary
d_test_proportion_diff

Description of the difference test between two proportions
decorate_grob_factory

Update page number
d_proportion_diff

Description of method used for proportion comparison
d_survival_subgroups_colvars

Labels for column variables in survival duration by subgroup table
d_rsp_subgroups_colvars

Labels for column variables in binary response by subgroup table
df2gg

Convert data.frame object to ggplot object
estimate_multinomial_rsp

Estimation of proportions per level of factor
.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.
draw_grob

Draw grob
df_explicit_na

Encode categorical missing values in a data frame
extract_rsp_biomarkers

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

Confidence intervals for a difference of binomials
f_pval

Utility function to create label for p-value
estimate_proportions

Estimation of proportions
f_conf_level

Utility function to create label for confidence interval
default_stats_formats_labels

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

Extract elements by name
extract_survival_subgroups

Prepare survival data for population subgroups in data frames
extreme_format

Format extreme values
estimate_coef

Hazard ratio estimation in interactions
extract_survival_biomarkers

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

Prepare response data for population subgroups in data frames
format_count_fraction

Format count and fraction
format_auto

Format automatically using data significant digits
fct_collapse_only

Collapse factor levels and keep only those new group levels
fct_discard

Discard specified levels of a factor
format_fraction

Format fraction and percentage
ex_data

Simulated CDISC data for examples
explicit_na

Missing data
fit_rsp_step

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

Fit for logistic regression
format_fraction_threshold

Format fraction with lower threshold
format_sigfig

Format numeric values by significant figures
fit_survival_step

Subgroup treatment effect pattern (STEP) fit for survival outcome
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
forest_viewport

Create a viewport tree for the forest plot
format_fraction_fixed_dp

Format fraction and percentage with fixed single decimal place
format_extreme_values_ci

Format extreme values part of a confidence interval
format_extreme_values

Format a single extreme value
format_xx

Format XX as a formatting function
formatting_functions

Formatting functions
fit_coxreg

Fitting functions for Cox proportional hazards regression
fct_explicit_na_if

Insertion of explicit missing values in a factor
g_lineplot

Line plot with optional table
g_km

Kaplan-Meier plot
h_adlb_abnormal_by_worst_grade

Helper function to prepare ADLB for count_abnormal_by_worst_grade()
g_step

Create a STEP graph
get_covariates

Utility function to return a named list of covariate names
g_ipp

Individual patient plots
groups_list_to_df

Convert list of groups to a data frame
g_forest

Create a forest plot from an rtable
get_smooths

Smooth function with optional grouping
h_ancova

Helper function to return results of a linear model
h_decompose_gg

ggplot decomposition
h_format_row

Helper function to format the optional g_lineplot table
h_append_grade_groups

Helper function for s_count_occurrences_by_grade()
h_cox_regression

Helper functions for Cox proportional hazards regression
g_waterfall

Horizontal waterfall plot
h_adsl_adlb_merge_using_worst_flag

Helper function for deriving analysis datasets for select laboratory tables
h_data_plot

Helper function to tidy survival fit data
h_adlb_worsen

Helper function to prepare ADLB with worst labs
h_count_cumulative

Helper function for s_count_cumulative()
h_col_indices

Obtain column indices
h_km_layout

Helper function to prepare a KM layout
h_grob_median_surv

Helper function to create survival estimation grobs
h_glm_count

Helper functions for Poisson models
h_g_ipp

Helper function to create simple line plot over time
h_grob_tbl_at_risk

Helper function to create patient-at-risk grobs
h_ggkm

Helper function to create a KM plot
h_logistic_regression

Helper functions for multivariate logistic regression
h_grob_coxph

Helper function to create Cox-PH grobs
h_incidence_rate

Helper functions for incidence rate
h_grob_y_annot

Helper function to create grid object with y-axis annotation
h_pkparam_sort

Sort pharmacokinetic data by PARAM variable
h_prop_diff

Helper functions to calculate proportion difference
h_split_by_subgroups

Split data frame by subgroups
h_split_param

Split parameters
h_proportions

Helper functions for calculating proportion confidence intervals
h_prop_diff_test

Helper functions to test proportion differences
h_map_for_count_abnormal

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

Helper functions for odds ratio estimation
h_tbl_median_surv

Helper function for survival estimations
h_xticks

Helper function to calculate x-tick positions
h_worsen_counter

Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline()
h_response_subgroups

Helper functions for tabulating binary response by subgroup
h_response_biomarkers_subgroups

Helper functions for tabulating biomarker effects on binary response by subgroup
h_stack_by_baskets

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

Helper functions for subgroup treatment effect pattern (STEP) calculations
imputation_rule

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

Helper functions for tabulating survival duration by subgroup
h_survival_biomarkers_subgroups

Helper functions for tabulating biomarker effects on survival by subgroup
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
logistic_regression_cols

Logistic regression multivariate column layout function
make_names

Make names without dots
labels_use_control

Update labels according to control specifications
logistic_summary_by_flag

Logistic regression summary table
odds_ratio

Odds ratio estimation
n_available

Number of available (non-missing entries) in a vector
month2day

Conversion of months to days
muffled_car_anova

Muffled car::Anova
labels_or_names

Labels or names of list elements
incidence_rate

Incidence rate
prop_diff_test

Difference test for two proportions
rtable2gg

Convert rtable objects to ggplot objects
response_biomarkers_subgroups

Tabulate biomarker effects on binary response by subgroup
reapply_varlabels

Reapply variable labels
prune_occurrences

Occurrence table pruning
prop_diff

Proportion difference
range_noinf

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

Multivariate Cox model - summarized results
rtables_access

Helper functions for accessing information from rtables
response_subgroups

Tabulate binary response by subgroup
split_text_grob

Split text according to available text width
split_cols_by_groups

Split columns by groups of levels
stat_median_ci

Confidence interval for median
score_occurrences

Occurrence table sorting
sas_na

Convert strings to NA
stat_propdiff_ci

Proportion difference and confidence interval
strata_normal_quantile

Helper function for the estimation of stratified quantiles
stat_mean_pval

p-Value of the mean
stack_grobs

Stack multiple grobs
stat_mean_ci

Confidence interval for mean
study_arm

Indicate study arm variable in formula
summarize_num_patients

Number of patients
summarize_logistic

Multivariate logistic regression table
survival_biomarkers_subgroups

Tabulate biomarker effects on survival by subgroup
summarize_functions

Summarize functions
summarize_change

Summarize the change from baseline or absolute baseline values
summarize_colvars

Summarize variables in columns
summarize_glm_count

Summarize Poisson negative binomial regression
summarize_patients_exposure_in_cols

Count patients and sum exposure across all patients in columns
summarize_ancova

Summary for analysis of covariance (ANCOVA).
survival_time

Survival time analysis
tidy.step

Custom tidy method for STEP results
to_n

Replicate entries of a vector if required
tidy_coxreg

Custom tidy methods for Cox regression
to_string_matrix

Convert table into matrix of strings
tidy.glm

Custom tidy method for binomial GLM results
tern-package

tern Package
survival_coxph_pairwise

Pairwise Cox-PH model
survival_duration_subgroups

Tabulate survival duration by subgroup
survival_timepoint

Survival time point analysis
utils_split_funs

Custom split functions
unlist_and_blank_na

Blank for missing input
update_weights_strat_wilson

Helper function for the estimation of weights for prop_strat_wilson()
univariate

Univariate formula special term
try_car_anova

tryCatch around car::Anova
ungroup_stats

Ungroup non-numeric statistics