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Epi (version 2.7)

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 some epidemiological datasets.

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Version

Install

install.packages('Epi')

Monthly Downloads

8,038

Version

2.7

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

October 4th, 2016

Functions in Epi (2.7)

Births in a London Hospital

Plot APC-estimates in an APC-frame.

Merge a Lexis object with a data frame

Mantel-Haenszel analyses of cohort and case-control studies

Plot estimates with confidence limits (forest plot)

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

Split follow-up time in a Lexis object

The time scales of a Lexis object

transform.Lexis

Transform a Lexis (or stacked.Lexis) objects

Bladder cancer mortality in Italian males

Conversion to diabetes

Diet and heart data

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

Fit a floating trend to a factor in generalized linear model

Compute dates/ages for life lines in a Lexis diagram

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

Draw boxes and arrows for illustration of multistate models.

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

An unmatched case-control study of leprosy incidence

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

Plot a Lexis diagram

Function to group a variable in intervals.

Special functions for use in stat.table

Nice breakpoints

Tables of summary statistics

Function to calculate effects for individually matched case-control studies

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

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

Population size in Denmark

Create percentages in a table

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

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

Combining a Lexis objects with data frames or other Lexis objects

Generate a nested case-control study

Compute cumulative sum of estimates.

The Danish National Diabetes Register.

hivDK: seroconversion in a cohort of Danish men

Function to calculate effects

Fits a regression model to interval censored data.

Functions to manage and explore the workspace

Male lung cancer incidence in Denmark

Functions to facilitate analysis of multistate models.

Time series methods for Lexis objects

Subsetting Lexis (and stacked.Lexis) objects

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.

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

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

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

A case-control study of endometrial cancer

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

Fits a multiplicative relative risk model to interval censored data.

Calculate floated variances

Mortality in Denmark 1974 ff.

merge.data.frame

Merge data frame with a Lexis object

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

A Cohort of Nickel Smelters in South Wales

Remove transitions from a Lexis object.

Reorder and combine levels of a factor

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

A small occupational cohort

Salmonella Typhimurium outbreak 1996 in Denmark.

Function to compute and draw ROC-curves.

Plot period and cohort effects in an APC-frame.

Testis cancer incidence in Denmark, 1943--1996

Extract time band data from a split Lexis object

Compute linear functions of parameters with standard errors and confidence limits

Compute confidence limits for a difference of two independent proportions.

Create a Lexis object

Draw life lines in a Lexis diagram.

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

Fit an addive excess risk model to interval censored data.

Conditional logistic regression

Contrast matrices

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

Births in Denmark by year and month of birth and sex

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

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

Population risk time in Denmark

Analysis of a two by two table