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Epi (version 2.44)

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

8,038

Version

2.44

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

February 27th, 2021

Functions in Epi (2.44)

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

Epi: Functions for manipulation and statistical analysis of epidemiological data

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

Births in Denmark by year and month of birth and sex

Fits a regression model to interval censored data.

Conversion to diabetes

The Danish National Diabetes Register.

Plot a Lexis diagram

Create a Lexis object

Reorder and combine levels of a factor

Epidemiological rates for diabetes in Denmark 1996--2015

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

Population size in Denmark

Salmonella Typhimurium outbreak 1996 in Denmark.

Mortality in Denmark 1974 ff.

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

Bereavement in an elderly cohort

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

Draw life lines in a Lexis diagram.

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

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

Compute dates/ages for life lines in a Lexis diagram

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

A case-control study of endometrial cancer

Births in a London Hospital

Function to compute and draw ROC-curves.

Bladder cancer mortality in Italian males

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

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

Generate a nested case-control study

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

Compute cumulative sum of estimates.

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

Draw boxes and arrows for illustration of multistate models.

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

Function to calculate effects for individually matched case-control studies

Diet and heart data

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

Fit an addive excess risk model to interval censored data.

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

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

Contrast matrices

Fit a piecewise contsnt intesity model for interval censored data.

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

Fits a multiplicative relative risk model to interval censored data.

Function to calculate effects

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

Compact printing of Lexis object

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

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

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

Create a basis of harmonic functions.

Functions to manage and explore the workspace

Calculate floated variances

Compute confidence limits for a difference of two independent proportions.

Conditional logistic regression

hivDK: seroconversion in a cohort of Danish men

Plot APC-estimates in an APC-frame.

Convenience versions of grep

Mantel-Haenszel analyses of cohort and case-control studies

Merge a Lexis object with a data frame

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

Plot period and cohort effects in an APC-frame.

Create percentages in a table

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

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

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

Projection of columns of a matrix.

Split follow-up time in a Lexis object

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

Diabetes prevance as of 2010-01-01 in Denmark

An unmatched case-control study of leprosy incidence

A Cohort of Nickel Smelters in South Wales

Male lung cancer incidence in Denmark

Plot columns of a matrix as stacked areas.

Fit intensity models to follow-up data in Lexis objects

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

Tables of summary statistics

The time scales of a Lexis object

transform.Lexis

Transform a Lexis (or stacked.Lexis) object

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

A small occupational cohort

Family Object for Poisson Regression

Fit a floating trend to a factor in generalized linear model

Plot Equivalence Classes

Special functions for use in stat.table

Plot confidence intervals as shaded areas around lines.

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

Analysis of a two by two table

Function to group a variable in intervals.

Plotting Aalen-Johansen curves for competing events

Nice breakpoints

Plot estimates with confidence limits (forest plot)

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

Clinical trial: Steno2 baseline and follow-up.

Remove transitions from a Lexis object.

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

Thorotrast Study

Functions to facilitate analysis of multistate models.

Subsetting Lexis (and stacked.Lexis) objects

Extract time band data from a split Lexis object

Summarize transitions and risk time from a Lexis object

Time series and other methods for Lexis objects

Testis cancer incidence in Denmark, 1943--1996