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Epi (version 2.59)

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, rate estimation and simulation for multistate data - the Lexis suite of functions, which includes interfaces to 'mstate', 'etm' and 'cmprsk' packages. 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

7,473

Version

2.59

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

January 13th, 2025

Functions in Epi (2.59)

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

Births in Denmark by year and month of birth and sex

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

Create a Lexis object of follow-up

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

Conversion to diabetes

Epidemiological rates for diabetes in Denmark 1996--2015

Compute dates/ages for life lines in a Lexis diagram

The Danish National Diabetes Register.

Convert a Lexis obejct to a data set suitable for input to the msm:msm function.

Epi: Functions for manipulation and statistical analysis of epidemiological data

Plot a Lexis diagram

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

Expand a Lexis object with information of drug exposure based on purchase dates and -amounts

Population risk time in Denmark

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.

Draw life lines in a Lexis diagram.

Mortality in Denmark 1974 ff.

Population size in Denmark

Reorder and combine levels of a factor

Salmonella Typhimurium outbreak 1996 in Denmark.

Fits a regression model to interval censored data.

A case-control study of endometrial cancer

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

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.

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

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

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

Generate a nested case-control study

Compute cumulative risks and expected sojourn times from models for cause-specific rates.

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

Compute cumulative sum of estimates.

Bereavement in an elderly cohort

Linear predictor (eta) from a formula, coefficients, vcov and a prediction frame.

Draw boxes and arrows for illustration of multistate models.

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

Births in a London Hospital

Bladder cancer mortality in Italian males

Conditional logistic regression

Contrast matrices

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

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

Diet and heart data

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

Function to calculate effects

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.

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

Calculate floated variances

Compute confidence limits for a difference of two independent proportions.

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

Fit a floating trend to a factor in generalized linear model

Fit a piecewise contsnt intesity model for interval censored data.

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

Convenience versions of grep

Fit an additive excess risk model to interval censored data.

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

Fits a multiplicative relative risk model to interval censored data.

hivDK: seroconversion in a cohort of Danish men

Functions to manage and explore the workspace

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

Male lung cancer incidence in Denmark

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

Draw a box with text explaining the numbers in and between boxes from boxes.MS and boxes.Lexis

Plot APC-estimates in an APC-frame.

An unmatched case-control study of leprosy incidence

Plot columns of a matrix as stacked areas.

Nice breakpoints for axes on plots

A Cohort of Nickel Smelters in South Wales

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

Function to group a variable in intervals.

Plot confidence intervals as shaded areas around lines.

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

Merge a Lexis object with a data frame

Plotting Aalen-Johansen curves for competing events

Mantel-Haenszel analyses of cohort and case-control studies

A small occupational cohort

Plot period and cohort effects in an APC-frame.

Generate paths travelled through a Lexis multistate model data frame.

Create a basis of harmonic functions.

Fit intensity models to follow-up data in Lexis objects

Create percentages in a table

Plot Equivalence Classes

Plot estimates with confidence limits (forest plot)

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

Family Object for Poisson Regression

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

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

Remove transitions from a Lexis object.

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

Diabetes prevance as of 2010-01-01 in Denmark

Projection of columns of a matrix.

Split follow-up time in a Lexis object

Functions to facilitate analysis of multistate models.

Summarize transitions and risk time from a Lexis object

Testis cancer incidence in Denmark, 1943--1996

The time scales of a Lexis object

Combining a Lexis objects with data frames or other Lexis objects

Remove Lexis attributes from a Lexis object.

Clinical trial: Steno2 baseline and follow-up.

Thorotrast Study

Subsetting Lexis (and stacked.Lexis) objects

Extract time band data from a split Lexis object

Analysis of a two by two table

transform.Lexis

Transform a Lexis (or stacked.Lexis) object

Time series and other methods for Lexis objects

Tables of summary statistics

Special functions for use in stat.table

The Aalen-Johansen estimator of state probabilities from a multistate Lexis object.

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