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Epi (version 2.0)

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 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

11,182

Version

2.0

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

January 6th, 2016

Functions in Epi (2.0)

Compute dates/ages for life lines in a Lexis diagram

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

Fits a regression model to interval censored data.

Function to calculate effects

Salmonella Typhimurium outbreak 1996 in Denmark.

merge.data.frame

Merge data frame with a Lexis object

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

Plot APC-estimates in an APC-frame.

Reorder and combine levels of a factor

Plot a Lexis diagram

Create a Lexis object

Bladder cancer mortality in Italian males

Fit a floating trend to a factor in generalized linear model

Merge a Lexis object with a data frame

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

Population size in Denmark

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

hivDK: seroconversion in a cohort of Danish men

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

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

An unmatched case-control study of leprosy incidence

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

Births in Denmark by year and month of birth and sex

Functions to facilitate analysis of multistate models.

Split follow-up time in a Lexis object

Compute linear functions of parameters with standard errors and confidence limits

Nice breakpoints

Generate a nested case-control study

Conversion to diabetes

Functions to manage and explore the workspace

Conditional logistic regression

Tables of summary statistics

Fit an addive excess risk model to interval censored data.

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.

A case-control study of endometrial cancer

Testis cancer incidence in Denmark, 1943--1996

Population risk time in Denmark

Mortality in Denmark 1974 ff.

Time series methods for Lexis objects

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

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

Compute confidence limits for a difference of two independent proportions.

Fits a multiplicative relative risk model to interval censored data.

Contrast matrices

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

A Cohort of Nickel Smelters in South Wales

The time scales of a Lexis object

Compute cumulative sum of estimates.

Thorotrast Study

Subsetting Lexis (and stacked.Lexis) objects

Analysis of a two by two table

Create percentages in a table

Draw life lines in a Lexis diagram.

Function to compute and draw ROC-curves.

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

Draw boxes and arrows for illustration of multistate models.

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

Function to calculate effects for individually matched case-control studies

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

transform.Lexis

Transform a Lexis (or stacked.Lexis) objects

Extract time band data from a split Lexis object

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

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

The Danish National Diabetes Register.

Births in a London Hospital

Calculate floated variances

Diet and heart data

A small occupational cohort

Function to group a variable in intervals.

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

Combining a Lexis objects with data frames or other Lexis objects

Bereavement in an elderly cohort

Plot estimates with confidence limits (forest plot)

Plot period and cohort effects in an APC-frame.

Mantel-Haenszel analyses of cohort and case-control studies

Special functions for use in stat.table

Male lung cancer incidence in Denmark

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

hivDK: seroconversion in a cohort of Danish men