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Epi (version 2.60)

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 and some useful functions for tabulation and plotting, as well as a number of epidemiological data sets.

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Version

Install

install.packages('Epi')

Monthly Downloads

6,284

Version

2.60

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

July 8th, 2025

Functions in Epi (2.60)

Mortality in Denmark 1974 ff.

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

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

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

Population size in Denmark

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

Function to compute and draw ROC-curves.

Compute dates/ages for life lines in a Lexis diagram

Plot a Lexis diagram

Draw life lines in a Lexis diagram.

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.

Salmonella Typhimurium outbreak 1996 in Denmark.

Reorder and combine levels of a factor

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

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

Population risk time in Denmark

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

A case-control study of endometrial cancer

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

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

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

Bladder cancer mortality in Italian males

Births in a London Hospital

Draw boxes and arrows for illustration of multistate models.

Bereavement in an elderly cohort

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

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

Generate a nested case-control study

Compute cumulative sum of estimates.

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

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)

Contrast matrices

Diet and heart data

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

Calculate floated variances

Fit a floating trend to a factor in generalized linear model

Compute confidence limits for a difference of two independent proportions.

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

Fit an additive excess risk model to interval censored data.

Fit a piecewise contsnt intesity model for interval censored data.

Fits a multiplicative relative risk model to interval censored data.

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

Convenience versions of grep

Plot APC-estimates in an APC-frame.

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

Male lung cancer incidence in Denmark

Functions to manage and explore the workspace

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

Nice breakpoints for axes on plots

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

Fit intensity models to follow-up data in Lexis objects

Plot columns of a matrix as stacked areas.

A Cohort of Nickel Smelters in South Wales

Plot confidence intervals as shaded areas around lines.

hivDK: seroconversion in a cohort of Danish men

Function to group a variable in intervals.

Mantel-Haenszel analyses of cohort and case-control studies

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

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

An unmatched case-control study of leprosy incidence

Generate paths travelled through a Lexis multistate model data frame.

Function to calculate effects

A small occupational cohort

Plot Equivalence Classes

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

Function to calculate effects for individually matched case-control studies

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

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

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

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

Plotting Aalen-Johansen curves for competing events

Create a basis of harmonic functions.

Merge a Lexis object with a data frame

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

Plot estimates with confidence limits (forest plot)

Combining a Lexis objects with data frames or other Lexis objects

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

Family Object for Poisson Regression

Functions to facilitate analysis of multistate models.

Time series and other methods for Lexis objects

Remove Lexis attributes from a Lexis object.

The time scales of a Lexis object

Summarize transitions and risk time from a Lexis object

transform.Lexis

Transform a Lexis (or stacked.Lexis) object

Testis cancer incidence in Denmark, 1943--1996

Analysis of a two by two table

Plot period and cohort effects in an APC-frame.

Tables of summary statistics

Special functions for use in stat.table

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

Create percentages in a table

Remove transitions from a Lexis object.

Extract time band data from a split Lexis object

Subsetting Lexis (and stacked.Lexis) objects

Diabetes prevance as of 2010-01-01 in Denmark

Projection of columns of a matrix.

Split follow-up time in a Lexis object

Thorotrast Study

Clinical trial: Steno2 baseline and follow-up.

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

Conversion to diabetes

Epidemiological rates for diabetes in Denmark 1996--2015

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

Births in Denmark by year and month of birth and sex

The Danish National Diabetes Register.

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

Create a Lexis object of follow-up

Epi: Functions for manipulation and statistical analysis of epidemiological data

Fits a regression model to interval censored data.