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Epi (version 2.41)

A Package for 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 and simulation of multistate data - the Lexis suite of functions, which includes interfaces to 'mstate', 'etm' and 'cmprsk' packages. Also 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

8,038

Version

2.41

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

August 7th, 2020

Functions in Epi (2.41)

The Danish National Diabetes Register.

Epi: Functions for manipulation and statistical analysis of epidemiological data

Conversion to diabetes

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

Births in Denmark by year and month of birth and sex

Plot a Lexis diagram

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

Fits a regression model to interval censored data.

Create a Lexis object

Epidemiological rates for diabetes in Denmark 1996--2015

Mortality in Denmark 1974 ff.

Population size in Denmark

Draw life lines in a Lexis diagram.

Compute dates/ages for life lines in a Lexis diagram

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

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

Population risk time in Denmark

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.

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

Bladder cancer mortality in Italian males

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

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

Births in a London Hospital

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

A case-control study of endometrial cancer

Function to compute and draw ROC-curves.

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

Generate a nested case-control study

Compute cumulative sum of estimates.

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

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

Draw boxes and arrows for illustration of multistate models.

Bereavement in an elderly cohort

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

Function to calculate effects for individually matched case-control studies

Diet and heart data

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

Function to calculate effects

Fit a floating trend to a factor in generalized linear model

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

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

Contrast matrices

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

Fits a multiplicative relative risk model to interval censored data.

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

Calculate floated variances

An unmatched case-control study of leprosy incidence

Mantel-Haenszel analyses of cohort and case-control studies

Nice breakpoints

Function to group a variable in intervals.

Reorder and combine levels of a factor

Compute confidence limits for a difference of two independent proportions.

Merge a Lexis object with a data frame

Salmonella Typhimurium outbreak 1996 in Denmark.

Conditional logistic regression

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

Convenience versions of grep

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

Family Object for Poisson Regression

Plot APC-estimates in an APC-frame.

Plot Equivalence Classes

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

Extract time band data from a split Lexis object

Fit intensity models to follow-up data in Lexis objects

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

Fit a piecewise contsnt intesity model for interval censored data.

Thorotrast Study

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

A small occupational cohort

A Cohort of Nickel Smelters in South Wales

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

Fit an addive excess risk model to interval censored data.

Plot confidence intervals as shaded areas around lines.

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

hivDK: seroconversion in a cohort of Danish men

Create a basis of harmonic functions.

Plotting Aalen-Johansen curves for competing events

Summarize transitions and risk time from a Lexis object

Remove transitions from a Lexis object.

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

Combining a Lexis objects with data frames or other Lexis objects

Plot estimates with confidence limits (forest plot)

Male lung cancer incidence in Denmark

Testis cancer incidence in Denmark, 1943--1996

Analysis of a two by two table

Compact printing of Lexis object

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

Functions to manage and explore the workspace

Plot period and cohort effects in an APC-frame.

Tables of summary statistics

Time series and other methods for Lexis objects

Plot columns of a matrix as stacked areas.

Split follow-up time in a Lexis object

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

The time scales of a Lexis object

Functions to facilitate analysis of multistate models.

Create percentages in a table

transform.Lexis

Transform a Lexis (or stacked.Lexis) object

Projection of columns of a matrix.

Diabetes prevance as of 2010-01-01 in Denmark

Special functions for use in stat.table

Subsetting Lexis (and stacked.Lexis) objects