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Epi (version 2.48)

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

8,952

Version

2.48

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

March 31st, 2024

Functions in Epi (2.48)

Compute dates/ages for life lines in a Lexis diagram

Draw life lines in a Lexis diagram.

Plot a Lexis diagram

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

A case-control study of endometrial cancer

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

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

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.

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

Bereavement in an elderly cohort

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

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

Compute cumulative sum of estimates.

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

Population size in Denmark

Mortality in Denmark 1974 ff.

Generate a nested case-control study

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

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

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

Contrast matrices

Function to compute and draw ROC-curves.

Draw boxes and arrows for illustration of multistate models.

Reorder and combine levels of a factor

Diet and heart data

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

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

Function to calculate effects

Compute confidence limits for a difference of two independent proportions.

Conditional logistic regression

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

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

Fit an additive excess risk model to interval censored data.

Salmonella Typhimurium outbreak 1996 in Denmark.

Fit a piecewise contsnt intesity model for interval censored data.

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

An unmatched case-control study of leprosy incidence

Convenience versions of grep

Fits a multiplicative relative risk model to interval censored data.

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

Calculate floated variances

Births in a London Hospital

Bladder cancer mortality in Italian males

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.

A Cohort of Nickel Smelters in South Wales

Plotting Aalen-Johansen curves for competing events

A small occupational cohort

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

Male lung cancer incidence in Denmark

Thorotrast Study

Extract time band data from a split Lexis object

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

Function to group a variable in intervals.

Plot APC-estimates in an APC-frame.

Nice breakpoints

Functions to manage and explore the workspace

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

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.

Fit a floating trend to a factor in generalized linear model

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

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

hivDK: seroconversion in a cohort of Danish men

Create a basis of harmonic functions.

Family Object for Poisson Regression

Plot Equivalence Classes

Tables of summary statistics

Plot period and cohort effects in an APC-frame.

Special functions for use in stat.table

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

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

Merge a Lexis object with a data frame

Mantel-Haenszel analyses of cohort and case-control studies

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

Summarize transitions and risk time from a Lexis object

Split follow-up time in a Lexis object

Create percentages in a table

Plot confidence intervals as shaded areas around lines.

Testis cancer incidence in Denmark, 1943--1996

Clinical trial: Steno2 baseline and follow-up.

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

Diabetes prevance as of 2010-01-01 in Denmark

Projection of columns of a matrix.

Subsetting Lexis (and stacked.Lexis) objects

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

Remove transitions from a Lexis object.

The time scales of a Lexis object

Functions to facilitate analysis of multistate models.

Time series and other methods for Lexis objects

Remove Lexis attributes from a Lexis object.

Analysis of a two by two table

transform.Lexis

Transform a Lexis (or stacked.Lexis) object

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

Epi: Functions for manipulation and statistical analysis of epidemiological data

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

Epidemiological rates for diabetes in Denmark 1996--2015

The Danish National Diabetes Register.

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

Create a Lexis object of follow-up

Conversion to diabetes

Fits a regression model to interval censored data.

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