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Epi (version 2.53)

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

2.53

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

July 18th, 2024

Functions in Epi (2.53)

Epi: Functions for manipulation and statistical analysis of epidemiological data

Create a Lexis object of follow-up

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

Births in Denmark by year and month of birth and sex

Conversion to diabetes

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

Epidemiological rates for diabetes in Denmark 1996--2015

Fits a regression model to interval censored data.

The Danish National Diabetes Register.

Plot a Lexis diagram

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

Draw life lines in a Lexis diagram.

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.

Reorder and combine levels of a factor

Population size in Denmark

Salmonella Typhimurium outbreak 1996 in Denmark.

Mortality in Denmark 1974 ff.

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.

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

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

A case-control study of endometrial cancer

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.

Compute dates/ages for life lines in a Lexis diagram

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

Draw boxes and arrows for illustration of multistate models.

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

Generate a nested case-control study

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

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

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

Compute cumulative sum of estimates.

Births in a London Hospital

Function to calculate effects for individually matched case-control studies

Function to calculate effects

Bereavement in an elderly cohort

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

Compute confidence limits for a difference of two independent proportions.

Bladder cancer mortality in Italian males

Conditional logistic regression

Contrast matrices

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

Fit a piecewise contsnt intesity model for interval censored data.

Fits a multiplicative relative risk model to interval censored data.

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

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

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

Calculate floated variances

hivDK: seroconversion in a cohort of Danish men

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

Functions to manage and explore the workspace

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

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

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?

Fit an additive excess risk model to interval censored data.

Create a basis of harmonic functions.

Mantel-Haenszel analyses of cohort and case-control studies

Male lung cancer incidence in Denmark

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

Merge a Lexis object with a data frame

Family Object for Poisson Regression

Diabetes prevance as of 2010-01-01 in Denmark

Fit intensity models to follow-up data in Lexis objects

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

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

Remove transitions from a Lexis object.

Plot columns of a matrix as stacked areas.

Combining a Lexis objects with data frames or other Lexis objects

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

Special functions for use in stat.table

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

Diet and heart data

Convenience versions of grep

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

Plot APC-estimates in an APC-frame.

Clinical trial: Steno2 baseline and follow-up.

Function to group a variable in intervals.

Plotting Aalen-Johansen curves for competing events

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

Fit a floating trend to a factor in generalized linear model

Plot period and cohort effects in an APC-frame.

A small occupational cohort

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

Plot confidence intervals as shaded areas around lines.

Create percentages in a table

Split follow-up time in a Lexis object

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

Functions to facilitate analysis of multistate models.

An unmatched case-control study of leprosy incidence

Nice breakpoints

Plot estimates with confidence limits (forest plot)

A Cohort of Nickel Smelters in South Wales

Plot Equivalence Classes

Time series and other methods for Lexis objects

Projection of columns of a matrix.

Subsetting Lexis (and stacked.Lexis) objects

Summarize transitions and risk time from a Lexis object

transform.Lexis

Transform a Lexis (or stacked.Lexis) object

Tables of summary statistics

Extract time band data from a split Lexis object

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

Testis cancer incidence in Denmark, 1943--1996

Thorotrast Study

The time scales of a Lexis object

Remove Lexis attributes from a Lexis object.

Analysis of a two by two table