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Epi (version 2.56)

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

11,182

Version

2.56

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

October 1st, 2024

Functions in Epi (2.56)

Compute dates/ages for life lines in a Lexis diagram

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

Population size in Denmark

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

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.

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

Plot a Lexis diagram

Function to compute and draw ROC-curves.

Draw life lines in a Lexis diagram.

Reorder and combine levels of a factor

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.

A case-control study of endometrial cancer

Salmonella Typhimurium outbreak 1996 in Denmark.

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

Population risk time in Denmark

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

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

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

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

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

Bereavement in an elderly cohort

Generate a nested case-control study

Births in a London Hospital

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

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

Compute cumulative sum of estimates.

Draw boxes and arrows for illustration of multistate models.

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

Bladder cancer mortality in Italian males

Conditional logistic regression

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

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

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

Compute confidence limits for a difference of two independent proportions.

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

Function to calculate effects

Diet and heart data

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.

Fit a piecewise contsnt intesity model for interval censored data.

Contrast matrices

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

Fit a floating trend to a factor in generalized linear model

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

Calculate floated variances

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

Fits a multiplicative relative risk model to interval censored data.

Functions to manage and explore the workspace

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

hivDK: seroconversion in a cohort of Danish men

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

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

Fit an additive excess risk model to interval censored data.

Create a basis of harmonic functions.

Plot APC-estimates in an APC-frame.

Male lung cancer incidence in Denmark

An unmatched case-control study of leprosy incidence

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

Convenience versions of grep

Function to group a variable in intervals.

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

Nice breakpoints for axes on plots

A Cohort of Nickel Smelters in South Wales

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

Plot estimates with confidence limits (forest plot)

Fit intensity models to follow-up data in Lexis objects

Mantel-Haenszel analyses of cohort and case-control studies

Merge a Lexis object with a data frame

Create percentages in a table

Plot Equivalence Classes

Diabetes prevance as of 2010-01-01 in Denmark

Family Object for Poisson Regression

Plot columns of a matrix as stacked areas.

A small occupational cohort

Plot confidence intervals as shaded areas around lines.

Plot period and cohort effects in an APC-frame.

Time series and other methods for Lexis objects

Tables of summary statistics

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

Plotting Aalen-Johansen curves for competing events

Combining a Lexis objects with data frames or other Lexis objects

Split follow-up time in a Lexis object

The time scales of a Lexis object

Extract time band data from a split Lexis object

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

Testis cancer incidence in Denmark, 1943--1996

Thorotrast Study

Remove transitions from a Lexis object.

Subsetting Lexis (and stacked.Lexis) objects

Functions to facilitate analysis of multistate models.

Summarize transitions and risk time from a Lexis object

Projection of columns of a matrix.

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

transform.Lexis

Transform a Lexis (or stacked.Lexis) object

Analysis of a two by two table

Special functions for use in stat.table

Remove Lexis attributes from a Lexis object.

Clinical trial: Steno2 baseline and follow-up.

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

Conversion to diabetes

Epi: Functions for manipulation and statistical analysis of epidemiological data

Births in Denmark by year and month of birth and sex

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

Epidemiological rates for diabetes in Denmark 1996--2015

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

The Danish National Diabetes Register.

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

Fits a regression model to interval censored data.

Create a Lexis object of follow-up