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Epi (version 2.40)

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

21,467

Version

2.40

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

November 25th, 2019

Functions in Epi (2.40)

Births in Denmark by year and month of birth and sex

Conversion to diabetes

Create a Lexis object

Epi: Functions for manipulation and statistical analysis of epidemiological data

Fits a regression model to interval censored data.

The Danish National Diabetes Register.

Epidemiological rates for diabetes in Denmark 1996--2015

Plot a Lexis diagram

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

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

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

Salmonella Typhimurium outbreak 1996 in Denmark.

Reorder and combine levels of a factor

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

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

A case-control study of endometrial cancer

Births in a London Hospital

Compute dates/ages for life lines in a Lexis diagram

Draw life lines in a Lexis diagram.

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

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

Contrast matrices

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

Compute confidence limits for a difference of two independent proportions.

Conditional logistic regression

Population size in Denmark

Mortality in Denmark 1974 ff.

Function to compute and draw ROC-curves.

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

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

Bladder cancer mortality in Italian males

Draw boxes and arrows for illustration of multistate models.

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

Bereavement in an elderly cohort

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

Create a basis of harmonic functions.

Function to calculate effects for individually matched case-control studies

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

Diet and heart data

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

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

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

Function to calculate effects

Generate a nested case-control study

An unmatched case-control study of leprosy incidence

Fit a piecewise contsnt intesity model for interval censored data.

Fit an addive excess risk model to 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 cumulative sum of estimates.

Population risk time in Denmark

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

hivDK: seroconversion in a cohort of Danish men

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

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

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

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

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

Merge a Lexis object with a data frame

Plot confidence intervals as shaded areas around lines.

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

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

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

Fit a floating trend to a factor in generalized linear model

Time series and other methods for Lexis objects

Male lung cancer incidence in Denmark

Convenience versions of grep

Plot columns of a matrix as stacked areas.

A small occupational cohort

Compact printing of Lexis object

Fits a multiplicative relative risk model to interval censored data.

Diabetes prevance as of 2010-01-01 in Denmark

Calculate floated variances

Functions to manage and explore the workspace

A Cohort of Nickel Smelters in South Wales

Plot APC-estimates in an APC-frame.

Plot period and cohort effects in an APC-frame.

Tables of summary statistics

Function to group a variable in intervals.

Mantel-Haenszel analyses of cohort and case-control studies

The time scales of a Lexis object

Special functions for use in stat.table

Subsetting Lexis (and stacked.Lexis) objects

Projection of columns of a matrix.

Plotting Aalen-Johansen curves for competing events

Thorotrast Study

Nice breakpoints

Extract time band data from a split Lexis object

Analysis of a two by two table

Plot estimates with confidence limits (forest plot)

Create percentages in a table

Plot Equivalence Classes

Fit intensity models to follow-up data in Lexis objects

Family Object for Poisson Regression

transform.Lexis

Transform a Lexis (or stacked.Lexis) object

Split follow-up time in a Lexis object

Remove transitions from a Lexis object.

Summarize transitions and risk time from a Lexis object

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

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

Testis cancer incidence in Denmark, 1943--1996

Functions to facilitate analysis of multistate models.