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Epi (version 2.34)

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

11,182

Version

2.34

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

February 10th, 2019

Functions in Epi (2.34)

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

Plot a Lexis diagram

Draw life lines in a Lexis diagram.

Compute dates/ages for life lines in a Lexis diagram

Mortality in Denmark 1974 ff.

Births in Denmark by year and month of birth and sex

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

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

Population risk time in Denmark

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

Population size in Denmark

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

Contrast matrices

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

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

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

The Danish National Diabetes Register.

Fits a regression model to interval censored data.

Conversion to diabetes

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

Epidemiological rates for diabetes in Denmark 1996--2015

Compute confidence limits for a difference of two independent proportions.

Bladder cancer mortality in Italian males

Conditional logistic regression

Salmonella Typhimurium outbreak 1996 in Denmark.

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

Function to compute and draw ROC-curves.

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.

Reorder and combine levels of a factor

Fits a multiplicative relative risk model to interval censored data.

Calculate floated variances

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

Draw boxes and arrows for illustration of multistate models.

Mantel-Haenszel analyses of cohort and case-control studies

Fit intensity models to follow-up data in Lexis objects

Bereavement in an elderly cohort

Diet and heart data

Function to calculate effects

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

Births in a London Hospital

A case-control study of endometrial cancer

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

Fit an addive excess risk model to interval censored data.

Generate a nested case-control study

hivDK: seroconversion in a cohort of Danish men

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

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

Fit a piecewise contsnt intesity model for interval censored data.

Compute cumulative sum of estimates.

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

Merge a Lexis object with a data frame

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

Compute linear functions of parameters with standard errors and confidence limits, optionally transforming to a different scale.

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

Nice breakpoints

A Cohort of Nickel Smelters in South Wales

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

Projection of columns of a matrix.

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

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

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

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

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

Male lung cancer incidence in Denmark

Fit a floating trend to a factor in generalized linear model

An unmatched case-control study of leprosy incidence

Function to group a variable in intervals.

Plot confidence intervals as shaded areas around lines.

Plot estimates with confidence limits (forest plot)

Plot Equivalence Classes

Convenience versions of grep

Subsetting Lexis (and stacked.Lexis) objects

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

Create percentages in a table

Plotting Aalen-Johansen curves for competing events

Summarize transitions and risk time from a Lexis object

Plot APC-estimates in an APC-frame.

Functions to facilitate analysis of multistate models.

Functions to manage and explore the workspace

Family Object for Poisson Regression

Diabetes prevance as of 2010-01-01 in Denmark

A small occupational cohort

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

Split follow-up time in a Lexis object

Plot period and cohort effects in an APC-frame.

Time series and other methods for Lexis objects

Tables of summary statistics

Special functions for use in stat.table

transform.Lexis

Transform a Lexis (or stacked.Lexis) object

Analysis of a two by two table

Testis cancer incidence in Denmark, 1943--1996

Thorotrast Study

Combining a Lexis objects with data frames or other Lexis objects

Remove transitions from a Lexis object.

Extract time band data from a split Lexis object

The time scales of a Lexis object

Create a Lexis object