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Epi (version 2.43)

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

2.43

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

January 27th, 2021

Functions in Epi (2.43)

Epi: Functions for manipulation and statistical analysis of epidemiological data

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

Epidemiological rates for diabetes in Denmark 1996--2015

Create a Lexis object

Births in Denmark by year and month of birth and sex

Conversion to diabetes

Fits a regression model to interval censored data.

The Danish National Diabetes Register.

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

Population size in Denmark

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

Mortality in Denmark 1974 ff.

Plot a Lexis diagram

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

Reorder and combine levels of a factor

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

Function to compute and draw ROC-curves.

Population risk time in Denmark

Salmonella Typhimurium outbreak 1996 in Denmark.

Draw life lines in a Lexis diagram.

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.

Bladder cancer mortality in Italian males

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

Draw boxes and arrows for illustration of multistate models.

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

Births in a London Hospital

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

A case-control study of endometrial cancer

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

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

Compute dates/ages for life lines in a Lexis diagram

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

Compute confidence limits for a difference of two independent proportions.

Compute cumulative risk and/or expected sojourn time from competing risks models.

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

Compute cumulative sum of estimates.

Generate a nested case-control study

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

hivDK: seroconversion in a cohort of Danish men

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

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

Conditional logistic regression

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

Contrast matrices

Bereavement in an elderly cohort

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

Create a basis of harmonic functions.

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

Fit an addive excess risk model to interval censored data.

Function to calculate effects

Functions to manage and explore the workspace

Fit a floating trend to a factor in generalized linear model

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

Function to calculate effects for individually matched case-control studies

Diet and heart data

Mantel-Haenszel analyses of cohort and case-control studies

Male lung cancer incidence in Denmark

Fit intensity models to follow-up data in Lexis objects

Plot columns of a matrix as stacked areas.

Plot confidence intervals as shaded areas around lines.

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

Function to group a variable in intervals.

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

Merge a Lexis object with a data frame

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

Remove transitions from a Lexis object.

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

Convenience versions of grep

An unmatched case-control study of leprosy incidence

Fits a multiplicative relative risk model to interval censored data.

Fit a piecewise contsnt intesity model for interval censored data.

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

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

Calculate floated variances

Plot APC-estimates in an APC-frame.

Family Object for Poisson Regression

Diabetes prevance as of 2010-01-01 in Denmark

Nice breakpoints

Subsetting Lexis (and stacked.Lexis) objects

A small occupational cohort

A Cohort of Nickel Smelters in South Wales

Summarize transitions and risk time from a Lexis object

Compact printing of Lexis object

Projection of columns of a matrix.

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

Plot period and cohort effects in an APC-frame.

Functions to facilitate analysis of multistate models.

Plotting Aalen-Johansen curves for competing events

Split follow-up time in a Lexis object

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

Create percentages in a table

A function to cut follow-up at intermediate event times.

Plot estimates with confidence limits (forest plot)

Combining a Lexis objects with data frames or other Lexis objects

Time series and other methods for Lexis objects

Special functions for use in stat.table

Clinical trial: Steno2 baseline and follow-up.

Plot Equivalence Classes

Testis cancer incidence in Denmark, 1943--1996

Tables of summary statistics

Thorotrast Study

The time scales of a Lexis object

Extract time band data from a split Lexis object

transform.Lexis

Transform a Lexis (or stacked.Lexis) object

Analysis of a two by two table