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Epi (version 2.63)

Statistical Analysis in Epidemiology

Description

Functions for demographic and epidemiological analysis in the Lexis diagram, i.e. register and cohort follow-up data. In particular representation, manipulation, rate estimation and simulation for multistate data - the Lexis suite of functions, which includes interfaces to 'mstate', 'etm' and 'cmprsk' packages. Contains functions for Age-Period-Cohort and Lee-Carter modeling and a function for interval censored data. Has functions for extracting and manipulating parameter estimates and predicted values (ci.lin and its cousins), as well as a number of epidemiological data sets.

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Version

Install

install.packages('Epi')

Monthly Downloads

8,621

Version

2.63

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

March 20th, 2026

Functions in Epi (2.63)

Plot a Lexis diagram

Set up an array of NAs, solely from the list of dimnames

Create risk time ("Person-Years") in Lexis triangles from population count data.

Population size in Denmark

Mortality in Denmark 1974 ff.

Natural splines - (cubic splines linear beyond outermost knots) with convenient specification of knots and possibility of centering, detrending and clamping.

Generate a knitting pattern for a tube-shaped scarf with Lexis lines

Compute dates/ages for life lines in a Lexis diagram

Draw life lines in a Lexis diagram.

Convert a Lexis obejct to a data set suitable for input to the msm:msm function.

A wrapper for termplot that optionally (but by default) exponentiates terms, and plot them on a common log-scale. Also scales x-axes to the same physical scale.

Produce an empty frame for display of parameter-estimates from Age-Period-Cohort-models.

Add covariates (typically clinical measurements) taken at known times to a Lexis object.

Salmonella Typhimurium outbreak 1996 in Denmark.

Population risk time in Denmark

Reorder and combine levels of a factor

Function to compute and draw ROC-curves.

Expand a Lexis object with information of drug exposure based on purchase dates and -amounts

Fit Age-Period-Cohort models and Lee-Carter models with effects modeled by natural splines.

Fit an Age-Period-Cohort model to tabular data.

Bladder cancer mortality in Italian males

Generate a nested case-control study

A case-control study of endometrial cancer

Compute cumulative risks and expected sojourn times from models for cause-specific rates.

Bereavement in an elderly cohort

Create a bootstrap sample of persons (as identified by lex.id) from a Lexis object

Births in a London Hospital

Functions to convert character, factor and various date objects into a number, and vice versa.

Compute cumulative sum of estimates.

Draw boxes and arrows for illustration of multistate models.

Projection of a model matrix on the orthogonal complement of a trend or curvature.

Diet and heart data

Contrast matrices

Conditional logistic regression

Cut follow-up at a specified date for each person.

Fit a competing risks regression model (Fine-Gray model) using a Lexis object)

Compute linear functions of parameters with standard errors and confidence limits, optionally transforming to a different scale.

Compute confidence limits for a difference of two independent proportions.

Function to calculate effects

Linear predictor (eta) from a formula, coefficients, vcov and a prediction frame.

Create a data structures suitable for use with packages mstate or etm.

Fit a floating trend to a factor in generalized linear model

Rates of lung and nasal cancer mortality, and total mortality.

Fits a multiplicative relative risk model to interval censored data.

Function to calculate effects for individually matched case-control studies

Compute survival functions from rates and expected residual lifetime in an illness-death model as well as years of life lost to disease.

Fit an additive excess risk model to interval censored data.

Calculate floated variances

Fit a piecewise contsnt intesity model for interval censored data.

Function to expand data for regression analysis of interval censored data.

Draw a box with text explaining the numbers in and between boxes from boxes.MS and boxes.Lexis

Is x in the column span of matrix A and what columns are linearly dependent?

Population mortality rates for Denmark in 5-years age groups.

An unmatched case-control study of leprosy incidence

Plot APC-estimates in an APC-frame.

hivDK: seroconversion in a cohort of Danish men

Convenience versions of grep

Functions to manage and explore the workspace

Generate covariates for drug-exposure follow-up from drug purchase records.

Create a basis of harmonic functions.

Function to group a variable in intervals.

Nice breakpoints for axes on plots

Plot confidence intervals as shaded areas around lines.

Mantel-Haenszel analyses of cohort and case-control studies

Cut follow-up at multiple event dates and keep track of order of events

Merge a Lexis object with a data frame

Plot columns of a matrix as stacked areas.

Male lung cancer incidence in Denmark

Population mortality rates for Denmark in 1-year age-classes.

Fit intensity models to follow-up data in Lexis objects

Generate paths traveled through a Lexis multistate model data frame.

A small occupational cohort

Check if records in a Lexis object represent overlapping epochs

A Cohort of Nickel Smelters in South Wales

Plot period and cohort effects in an APC-frame.

Plot the estimates from a fitted Age-Period-Cohort model

Create percentages in a table

Plot estimates with confidence limits (forest plot)

Plotting Aalen-Johansen curves for competing events

Diabetes prevance as of 2010-01-01 in Denmark

Family Object for Poisson Regression

Projection of columns of a matrix.

A function to cut follow-up at intermediate event times.

Remove transitions from a Lexis object.

Functions to plot rates from a table classified by age and calendar time (period)

Simulate a Lexis object representing follow-up in a multistate model.

Split follow-up time in a Lexis object

Plot Equivalence Classes

Combining a Lexis objects with data frames or other Lexis objects

Time series and other methods for Lexis objects

Functions to facilitate analysis of multistate models.

Clinical trial: Steno2 baseline and follow-up.

Thorotrast Study

Testis cancer incidence in Denmark, 1943--1996

Tables of summary statistics

Extract time band data from a split Lexis object

Summarize transitions and risk time from a Lexis object

Subsetting Lexis (and stacked.Lexis) objects

Special functions for use in stat.table

Cut follow-up in a Lexis object by event date(s) while preserving the original states.

Analysis of a two by two table

Remove Lexis attributes from a Lexis object.

transform.Lexis

Transform a Lexis (or stacked.Lexis) object

The time scales of a Lexis object

Epidemiological rates for diabetes in Denmark 1996--2015

Epi: Functions for manipulation and statistical analysis of epidemiological data

Clinical status, relapse, metastasis and death in 2982 women with breast cancer.

Births in Denmark by year and month of birth and sex

The Aalen-Johansen estimator of state probabilities from a multistate Lexis object.

The Danish National Diabetes Register.

Conversion to diabetes

Fits a regression model to interval censored data.

Create a Lexis object of follow-up

Fit Lee-Carter-type models for rates to arbitrarily shaped observations of rates in a Lexis diagram.