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Epi (version 1.1.71)

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 and manipulation of multistate data - the Lexis suite of functions, which includes interfaces to mstate, etm and cmprsk packages. Also contains functions for Age-Period-Cohort modeling and a function for interval censored data and some useful functions for tabulation and plotting, as well some epidemiological datasets.

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Version

Install

install.packages('Epi')

Monthly Downloads

6,284

Version

1.1.71

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

September 17th, 2015

Functions in Epi (1.1.71)

Merge a Lexis object with a data frame

Function to calculate effects

Compute confidence limits for a difference of two independent proportions.

Compute dates/ages for life lines in a Lexis diagram

Fit a floating trend to a factor in generalized linear model

merge.data.frame

Merge data frame with a Lexis object

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

Draw life lines in a Lexis diagram.

Salmonella Typhimurium outbreak 1996 in Denmark.

Tables of summary statistics

Plot period and cohort effects in an APC-frame.

Mortality in Denmark 1974 ff.

Functions to manage and explore the workspace

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

Conditional logistic regression

The time scales of a Lexis object

Function to compute and draw ROC-curves.

Births in Denmark by year and month of birth and sex

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

Conversion to diabetes

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

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

Contrast matrices

Reorder and combine levels of a factor

Split follow-up time in a Lexis object

A small occupational cohort

Births in a London Hospital

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

Mantel-Haenszel analyses of cohort and case-control studies

Create a Lexis object

Fits a regression model to interval censored data.

Population size in Denmark

Compute cumulative sum of estimates.

An unmatched case-control study of leprosy incidence

A case-control study of endometrial cancer

Create percentages in a table

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

Plot APC-estimates in an APC-frame.

Compute linear functions of parameters with standard errors and confidence limits

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

Male lung cancer incidence in Denmark

Diet and heart data

Function to group a variable in intervals.

Plot a Lexis diagram

Bladder cancer mortality in Italian males

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

Nice breakpoints

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

Fit an addive excess risk model to interval censored data.

Thorotrast Study

Analysis of a two by two table

Population risk time in Denmark

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

Calculate floated variances

hivDK: seroconversion in a cohort of Danish men

Draw boxes and arrows for illustration of multistate models.

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

transform.Lexis

Transform a Lexis (or stacked.Lexis) objects

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

The Danish National Diabetes Register.

Functions to facilitate analysis of multistate models.

Testis cancer incidence in Denmark, 1943--1996

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

Plot estimates with confidence limits (forest plot)

Subsetting Lexis (and stacked.Lexis) objects

Extract time band data from a split Lexis object

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

A Cohort of Nickel Smelters in South Wales

Special functions for use in stat.table

Time series methods for Lexis objects

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

Function to calculate effects for individually matched case-control studies

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

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.

Generate a nested case-control study

Fits a multiplicative relative risk model to interval censored data.

Bereavement in an elderly cohort