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Epi (version 2.19)

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

2.19

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

August 9th, 2017

Functions in Epi (2.19)

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.

Births in Denmark by year and month of birth and sex

Conversion to diabetes

Create a Lexis object

Plot a Lexis diagram

Draw life lines in a Lexis diagram.

Compute dates/ages for life lines in a Lexis diagram

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

Function to compute and draw ROC-curves.

Reorder and combine levels of a factor

Salmonella Typhimurium outbreak 1996 in Denmark.

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

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

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

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

Generate a nested case-control study

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

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

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

A case-control study of endometrial cancer

Fit a floating trend to a factor in generalized linear model

A small occupational cohort

Plot period and cohort effects in an APC-frame.

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

Mortality in Denmark 1974 ff.

Population size in Denmark

Draw boxes and arrows for illustration of multistate models.

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

Compute confidence limits for a difference of two independent proportions.

Conditional logistic regression

Fits a multiplicative relative risk model to interval censored data.

Plotting Aalen-Johansen curves for competing events

Testis cancer incidence in Denmark, 1943--1996

Thorotrast Study

Bereavement in an elderly cohort

Contrast matrices

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

Bladder cancer mortality in Italian males

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

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

Diet and heart data

Function to calculate effects

Convenience versions of grep

Plot APC-estimates in an APC-frame.

Calculate floated variances

Functions to manage and explore the workspace

Male lung cancer incidence in Denmark

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

Merge a Lexis object with a data frame

Plot estimates with confidence limits (forest plot)

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

Function to group a variable in intervals.

Combining a Lexis objects with data frames or other Lexis objects

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.

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

Nice breakpoints

A Cohort of Nickel Smelters in South Wales

Create percentages in a table

Plot Equivalence Classes

Subsetting Lexis (and stacked.Lexis) objects

Summarize transitions and risk time from a Lexis object

Extract time band data from a split Lexis object

Remove transitions from a Lexis object.

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

Split follow-up time in a Lexis object

The time scales of a Lexis object

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.

Tables of summary statistics

Special functions for use in stat.table

Compute cumulative sum of estimates.

Compute linear functions of parameters with standard errors and confidence limits

Fit an addive excess risk model to interval censored data.

Fit a piecewise contsnt intesity model for interval censored data.

hivDK: seroconversion in a cohort of Danish men

An unmatched case-control study of leprosy incidence

merge.data.frame

Merge data frame with a Lexis object

Mantel-Haenszel analyses of cohort and case-control studies

Projection of columns of a matrix.

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

Functions to facilitate analysis of multistate models.

Time series methods for Lexis objects

transform.Lexis

Transform a Lexis (or stacked.Lexis) objects

Analysis of a two by two table