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Epi (version 2.30)

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

6,284

Version

2.30

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

May 15th, 2018

Functions in Epi (2.30)

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.

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

Mortality in Denmark 1974 ff.

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

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

Fit a floating trend to a factor in generalized linear model

Fit a piecewise contsnt intesity model for interval censored data.

Conditional logistic regression

Reorder and combine levels of a factor

Contrast matrices

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

Fit an addive excess risk model to interval censored data.

Nice breakpoints

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

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

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

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

Compute confidence limits for a difference of two independent proportions.

Bladder cancer mortality in Italian males

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

A case-control study of endometrial cancer

Convenience versions of grep

Tables of summary statistics

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

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

Bereavement in an elderly cohort

Function to calculate effects for individually matched case-control studies

Male lung cancer incidence in Denmark

Extract time band data from a split Lexis object

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

Generate a nested case-control study

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

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

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

Plot confidence intervals as shaded areas around lines.

hivDK: seroconversion in a cohort of Danish men

Special functions for use in stat.table

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

Create percentages in a table

Births in a London Hospital

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

An unmatched case-control study of leprosy incidence

Fits a multiplicative relative risk model to interval censored data.

Functions to manage and explore the workspace

A small occupational cohort

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

Combining a Lexis objects with data frames or other Lexis objects

Plot estimates with confidence limits (forest plot)

Calculate floated variances

Compute cumulative sum of estimates.

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

Mantel-Haenszel analyses of cohort and case-control studies

Merge a Lexis object with a data frame

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

Compute linear functions of parameters with standard errors and confidence limits

Split follow-up time in a Lexis object

Plotting Aalen-Johansen curves for competing events

transform.Lexis

Transform a Lexis (or stacked.Lexis) objects

Plot Equivalence Classes

Analysis of a two by two table

Function to calculate effects

The time scales of a Lexis object

Remove transitions from a Lexis object.

Diet and heart data

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

Projection of columns of a matrix.

Function to group a variable in intervals.

Plot APC-estimates in an APC-frame.

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

A Cohort of Nickel Smelters in South Wales

Plot period and cohort effects in an APC-frame.

Functions to facilitate analysis of multistate models.

Time series methods for Lexis objects

Thorotrast Study

Subsetting Lexis (and stacked.Lexis) objects

Summarize transitions and risk time from a Lexis object

Testis cancer incidence in Denmark, 1943--1996

Conversion to diabetes

Epidmiological rates for diabetes in Denmark 1996--2015

Population size in Denmark

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

Births in Denmark by year and month of birth and sex

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

The Danish National Diabetes Register.

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

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

Create a Lexis object

Compute dates/ages for life lines in a Lexis diagram

Fits a regression model to interval censored data.

Function to compute and draw ROC-curves.

Draw boxes and arrows for illustration of multistate models.

Population risk time in Denmark

Plot a Lexis diagram

Salmonella Typhimurium outbreak 1996 in Denmark.

Draw life lines in a Lexis diagram.