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Epi (version 2.26)

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

8,952

Version

2.26

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

March 11th, 2018

Functions in Epi (2.26)

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

Compute dates/ages for life lines in a Lexis diagram

Mortality in Denmark 1974 ff.

Conversion to diabetes

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

Epidmiological rates for diabetes in Denmark 1996--2015

Population risk time in Denmark

Reorder and combine levels of a factor

Function to compute and draw ROC-curves.

The Danish National Diabetes Register.

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

Fits a regression model to interval censored data.

A 1:1 subset of the endometrial cancer case-control study

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

Plot a Lexis diagram

Compute cumulative sum of estimates.

Function to calculate effects for individually matched case-control studies

Draw life lines in a Lexis diagram.

Compute linear functions of parameters with standard errors and confidence limits

Contrast matrices

Salmonella Typhimurium outbreak 1996 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.

Convenience versions of grep

Plot APC-estimates in an APC-frame.

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

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

Function to group a variable in intervals.

Fit an addive excess risk model to interval censored data.

Nice breakpoints

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

Special functions for use in stat.table

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

Subsetting Lexis (and stacked.Lexis) objects

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

Fit a piecewise contsnt intesity model for interval censored data.

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

hivDK: seroconversion in a cohort of Danish men

An unmatched case-control study of leprosy incidence

Bladder cancer mortality in Italian males

Functions to manage and explore the workspace

Create a Lexis object

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

Male lung cancer incidence in Denmark

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

Population size in Denmark

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

Compute confidence limits for a difference of two independent proportions.

Combining a Lexis objects with data frames or other Lexis objects

Conditional logistic regression

Remove transitions from a Lexis object.

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

Draw boxes and arrows for illustration of multistate models.

Bereavement in an elderly cohort

Function to calculate effects

Diet and heart data

Fits a multiplicative relative risk model to interval censored data.

Calculate floated variances

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

A case-control study of endometrial cancer

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

A Cohort of Nickel Smelters in South Wales

A small occupational cohort

Plot Equivalence Classes

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

Projection of columns of a matrix.

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

Projection of a model matrix on to the orthogonal complement of a trend.

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

Mantel-Haenszel analyses of cohort and case-control studies

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

Plot period and cohort effects in an APC-frame.

Create percentages in a table

Time series methods for Lexis objects

Tables of summary statistics

Analysis of a two by two table

Split follow-up time in a Lexis object

Generate a nested case-control study

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

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

Functions to facilitate analysis of multistate models.

The time scales of a Lexis object

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

Fit a floating trend to a factor in generalized linear model

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

transform.Lexis

Transform a Lexis (or stacked.Lexis) objects

Merge a Lexis object with a data frame

Plot estimates with confidence limits (forest plot)

Plotting Aalen-Johansen curves for competing events

Summarize transitions and risk time from a Lexis object

Testis cancer incidence in Denmark, 1943--1996

Thorotrast Study

Extract time band data from a split Lexis object

Births in Denmark by year and month of birth and sex