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Epi (version 2.58)

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

2.58

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

November 25th, 2024

Functions in Epi (2.58)

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

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

Mortality in Denmark 1974 ff.

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

Draw life lines in a Lexis diagram.

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.

Compute dates/ages for life lines in a Lexis diagram

Population size in Denmark

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.

Salmonella Typhimurium outbreak 1996 in Denmark.

A case-control study of endometrial cancer

Population risk time in Denmark

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

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

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

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

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

Draw boxes and arrows for illustration of multistate models.

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

Births in a London Hospital

Bladder cancer mortality in Italian males

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

Compute cumulative sum of estimates.

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

Bereavement in an elderly cohort

Generate a nested case-control study

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

Diet and heart data

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

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

Conditional logistic regression

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

Function to calculate effects

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

Contrast matrices

Compute confidence limits for a difference of two independent proportions.

Function to calculate effects for individually matched case-control studies

Calculate floated variances

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

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

Fits a multiplicative relative risk model to interval censored data.

Fit a piecewise contsnt intesity model for interval censored data.

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

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

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

Fit a floating trend to a factor in generalized linear model

Fit an additive excess risk model to interval censored data.

An unmatched case-control study of leprosy incidence

Male lung cancer incidence in Denmark

hivDK: seroconversion in a cohort of Danish men

Functions to manage and explore the workspace

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

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

Mantel-Haenszel analyses of cohort and case-control studies

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

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

Fit intensity models to follow-up data in Lexis objects

Convenience versions of grep

Merge a Lexis object with a data frame

Plot columns of a matrix as stacked areas.

Plot confidence intervals as shaded areas around lines.

Create a basis of harmonic functions.

Create percentages in a table

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

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

Plot estimates with confidence limits (forest plot)

Plot Equivalence Classes

Function to group a variable in intervals.

Family Object for Poisson Regression

A small occupational cohort

Diabetes prevance as of 2010-01-01 in Denmark

Plotting Aalen-Johansen curves for competing events

Plot period and cohort effects in an APC-frame.

Combining a Lexis objects with data frames or other Lexis objects

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

Subsetting Lexis (and stacked.Lexis) objects

Split follow-up time in a Lexis object

Functions to facilitate analysis of multistate models.

Special functions for use in stat.table

Time series and other methods for Lexis objects

Tables of summary statistics

Extract time band data from a split Lexis object

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)

Clinical trial: Steno2 baseline and follow-up.

The time scales of a Lexis object

A Cohort of Nickel Smelters in South Wales

Remove Lexis attributes from a Lexis object.

Plot APC-estimates in an APC-frame.

Nice breakpoints for axes on plots

Remove transitions from a Lexis object.

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

transform.Lexis

Transform a Lexis (or stacked.Lexis) object

Analysis of a two by two table

Testis cancer incidence in Denmark, 1943--1996

Thorotrast Study

Epidemiological rates for diabetes in Denmark 1996--2015

Epi: Functions for manipulation and statistical analysis of epidemiological data

Conversion to diabetes

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

The Danish National Diabetes Register.

Births in Denmark by year and month of birth and sex

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

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

Create a Lexis object of follow-up

Fits a regression model to interval censored data.