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Epi (version 2.32)

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

2.32

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

August 23rd, 2018

Functions in Epi (2.32)

Births in Denmark by year and month of birth and sex

The Danish National Diabetes Register.

Fits a regression model to interval censored data.

Population size in Denmark

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

Reorder and combine levels of a factor

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

A case-control study of endometrial cancer

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

Conversion to diabetes

Epidmiological rates for diabetes in Denmark 1996--2015

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

Compute dates/ages for life lines in a Lexis diagram

Compute cumulative sum of estimates.

Plot a Lexis diagram

Compute linear functions of parameters with standard errors and confidence limits

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

Draw life lines in a Lexis diagram.

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

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

Population risk time in Denmark

Draw boxes and arrows for illustration of multistate models.

Bereavement in an elderly cohort

Create a Lexis object

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

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

Salmonella Typhimurium outbreak 1996 in Denmark.

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.

Generate a nested case-control study

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

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

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

Function to expand data for regression analysis of 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.

Compute confidence limits for a difference of two independent proportions.

Mortality in Denmark 1974 ff.

An unmatched case-control study of leprosy incidence

Bladder cancer mortality in Italian males

Convenience versions of grep

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

Births in a London Hospital

Conditional logistic regression

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

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

Function to group a variable in intervals.

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

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

Plot APC-estimates in an APC-frame.

A small occupational cohort

Contrast matrices

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

Fit a floating trend to a factor in generalized linear model

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

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

Male lung cancer incidence in Denmark

Functions to manage and explore the workspace

Plot period and cohort effects in an APC-frame.

Merge a Lexis object with a data frame

Plot estimates with confidence limits (forest plot)

Create percentages in a table

Plot confidence intervals as shaded areas around lines.

Family Object for Poisson Regression

Nice breakpoints

Projection of columns of a matrix.

Diet and heart data

Fits a multiplicative relative risk model to interval censored data.

Function to calculate effects

The time scales of a Lexis object

Calculate floated variances

Fit an addive excess risk model to interval censored data.

Mantel-Haenszel analyses of cohort and case-control studies

transform.Lexis

Transform a Lexis (or stacked.Lexis) objects

A Cohort of Nickel Smelters in South Wales

Fit intensity models to follow-up data in Lexis objects

Time series methods for Lexis objects

Fit a piecewise contsnt intesity model for interval censored data.

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

hivDK: seroconversion in a cohort of Danish men

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

Tables of summary statistics

Plot Equivalence Classes

Is x in the column span of matrix A and what columns are linearly dependent?

Remove transitions from a Lexis object.

Split follow-up time in a Lexis object

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

Plotting Aalen-Johansen curves for competing events

Special functions for use in stat.table

Functions to facilitate analysis of multistate models.

Subsetting Lexis (and stacked.Lexis) objects

Thorotrast Study

Analysis of a two by two table

Summarize transitions and risk time from a Lexis object

Extract time band data from a split Lexis object

Testis cancer incidence in Denmark, 1943--1996

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

Function to compute and draw ROC-curves.