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Epi (version 2.16)

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

2.16

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

June 30th, 2017

Functions in Epi (2.16)

Draw life lines in a Lexis diagram.

Compute dates/ages for life lines in a Lexis diagram

Births in Denmark by year and month of birth and sex

Conversion to diabetes

Create a Lexis object

Plot a Lexis diagram

Epidmiological rates for diabetes in Denmark 1996--2015

The Danish National Diabetes Register.

Fits a regression model to interval censored data.

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

Function to compute and draw ROC-curves.

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

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

Births in a London Hospital

Bladder cancer mortality in Italian males

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

Generate a nested case-control study

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

Fit an addive excess risk model to interval censored data.

Fits a multiplicative relative risk model to interval censored data.

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

hivDK: seroconversion in a cohort of Danish men

Mortality in Denmark 1974 ff.

Population size in Denmark

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

Reorder and combine levels of a factor

Salmonella Typhimurium outbreak 1996 in Denmark.

A case-control study of endometrial cancer

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

Draw boxes and arrows for illustration of multistate models.

Bereavement in an elderly cohort

Compute confidence limits for a difference of two independent proportions.

Conditional logistic regression

Plot period and cohort effects in an APC-frame.

Create percentages in a table

Time series methods for Lexis objects

Tables of summary statistics

Fit a floating trend to a factor in generalized linear model

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

Merge a Lexis object with a data frame

merge.data.frame

Merge data frame with a Lexis object

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

Contrast matrices

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

Calculate floated variances

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

Split follow-up time in a Lexis object

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

An unmatched case-control study of leprosy incidence

Convenience versions of grep

Functions to facilitate analysis of multistate models.

transform.Lexis

Transform a Lexis (or stacked.Lexis) objects

Analysis of a two by two table

Testis cancer incidence in Denmark, 1943--1996

Thorotrast Study

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

Diet and heart data

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 group a variable in intervals.

Nice breakpoints

Remove transitions from a Lexis object.

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.

Population risk time in Denmark

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

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

Compute cumulative sum of estimates.

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

Male lung cancer incidence in Denmark

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

Mantel-Haenszel analyses of cohort and case-control studies

Compute linear functions of parameters with standard errors and confidence limits

Function to calculate effects

Function to calculate effects for individually matched case-control studies

Plot APC-estimates in an APC-frame.

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

Plotting Aalen-Johansen curves for competing events

Plot estimates with confidence limits (forest plot)

Extract time band data from a split Lexis object

The time scales of a Lexis object

Functions to manage and explore the workspace

A Cohort of Nickel Smelters in South Wales

A small occupational cohort

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

Special functions for use in stat.table

Subsetting Lexis (and stacked.Lexis) objects

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

Projection of columns of a matrix.

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

Fit a piecewise contsnt intesity model for interval censored data.

Summarize transitions and risk time from a Lexis object

Plot Equivalence Classes