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Epi (version 2.61)

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

21,467

Version

2.61

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

October 7th, 2025

Functions in Epi (2.61)

Icens

Fits a regression model to interval censored data.
Epi

Epi: Functions for manipulation and statistical analysis of epidemiological data
AaJ

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

Births in Denmark by year and month of birth and sex
DMlate

The Danish National Diabetes Register.
DMconv

Conversion to diabetes
DMepi

Epidemiological rates for diabetes in Denmark 1996--2015
BrCa

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

Create a Lexis object of follow-up
LCa.fit

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

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

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

Mortality in Denmark 1974 ff.
N2Y

Create risk time ("Person-Years") in Lexis triangles from population count data.
Lexis2msm

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

Function to compute and draw ROC-curves.
N.dk

Population size in Denmark
Lexis.lines

Draw life lines in a Lexis diagram.
Lexis.diagram

Plot a Lexis diagram
Life.lines

Compute dates/ages for life lines in a Lexis diagram
apc.LCa

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

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.
apc.frame

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

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

Population risk time in Denmark
S.typh

Salmonella Typhimurium outbreak 1996 in Denmark.
addDrug

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

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

Bereavement in an elderly cohort
bdendo

A case-control study of endometrial cancer
Relevel

Reorder and combine levels of a factor
bootLexis

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

Births in a London Hospital
ci.cum

Compute cumulative sum of estimates.
blcaIT

Bladder cancer mortality in Italian males
cal.yr

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

Draw boxes and arrows for illustration of multistate models.
ccwc

Generate a nested case-control study
ci.Crisk

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

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

Diet and heart data
crr.Lexis

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

Conditional logistic regression
effx

Function to calculate effects
contr.cum

Contrast matrices
cutLexis

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

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

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

Function to calculate effects for individually matched case-control studies
ci.pd

Compute confidence limits for a difference of two independent proportions.
ftrend

Fit a floating trend to a factor in generalized linear model
foreign.Lexis

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

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

Calculate floated variances
expand.data

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

Fit an additive excess risk model to interval censored data.
fit.baseline

Fit a piecewise contsnt intesity model for interval censored data.
gen.exp

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

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

Functions to manage and explore the workspace
lungDK

Male lung cancer incidence in Denmark
legendbox

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

An unmatched case-control study of leprosy incidence
lgrep

Convenience versions of grep
apc.lines

Plot APC-estimates in an APC-frame.
in.span

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

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

hivDK: seroconversion in a cohort of Danish men
harm

Create a basis of harmonic functions.
fit.mult

Fits a multiplicative relative risk model to interval censored data.
matshade

Plot confidence intervals as shaded areas around lines.
mat2pol

Plot columns of a matrix as stacked areas.
nice

Nice breakpoints for axes on plots
nickel

A Cohort of Nickel Smelters in South Wales
mcutLexis

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

Mantel-Haenszel analyses of cohort and case-control studies
mod.Lexis

Fit intensity models to follow-up data in Lexis objects
merge.Lexis

Merge a Lexis object with a data frame
paths.Lexis

Generate paths traveled through a Lexis multistate model data frame.
occup

A small occupational cohort
plotevent

Plot Equivalence Classes
poisreg

Family Object for Poisson Regression
pctab

Create percentages in a table
mortDK

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

Function to group a variable in intervals.
plot.apc

Plot the estimates from a fitted Age-Period-Cohort model
pc.lines

Plot period and cohort effects in an APC-frame.
plot.Lexis

Lexis diagrams
plotCIF

Plotting Aalen-Johansen curves for competing events
rcutLexis

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

Split follow-up time in a Lexis object
rm.tr

Remove transitions from a Lexis object.
projection.ip

Projection of columns of a matrix.
simLexis

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

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

Plot estimates with confidence limits (forest plot)
thoro

Thorotrast Study
summary.Lexis

Summarize transitions and risk time from a Lexis object
testisDK

Testis cancer incidence in Denmark, 1943--1996
pr

Diabetes prevance as of 2010-01-01 in Denmark
unLexis

Remove Lexis attributes from a Lexis object.
entry.Lexis

Time series and other methods for Lexis objects
stat.table

Tables of summary statistics
stack.Lexis

Functions to facilitate analysis of multistate models.
timeBand

Extract time band data from a split Lexis object
transform.Lexis

Transform a Lexis (or stacked.Lexis) object
cbind.Lexis

Combining a Lexis objects with data frames or other Lexis objects
timeScales

The time scales of a Lexis object
stattable.funs

Special functions for use in stat.table
twoby2

Analysis of a two by two table
subset.Lexis

Subsetting Lexis (and stacked.Lexis) objects
xcutLexis

Cut follow-up in a Lexis object by event date(s) while preserving the original states. This is essentially a cross-classification of the original states and the new ones, hence the "x".
steno2

Clinical trial: Steno2 baseline and follow-up.