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Epi (version 2.47.1)

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

2.47.1

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

April 25th, 2023

Functions in Epi (2.47.1)

Epidemiological rates for diabetes in Denmark 1996--2015

Epi: Functions for manipulation and statistical analysis of epidemiological data

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.

The Danish National Diabetes Register.

Fits a regression model to interval censored data.

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

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

Create a Lexis object of follow-up

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

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

Mortality in Denmark 1974 ff.

Population size in Denmark

Compute dates/ages for life lines in a Lexis diagram

Draw life lines in a Lexis diagram.

Function to compute and draw ROC-curves.

Plot a Lexis diagram

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

Reorder and combine levels of a factor

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

A case-control study of endometrial cancer

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

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

Salmonella Typhimurium outbreak 1996 in Denmark.

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

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

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

Bereavement in an elderly cohort

Births in a London Hospital

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

Compute cumulative sum of estimates.

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

Generate a nested case-control study

Draw boxes and arrows for illustration of multistate models.

Bladder cancer mortality in Italian males

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

Diet and heart data

Function to calculate effects for individually matched case-control studies

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

Compute confidence limits for a difference of two independent proportions.

Function to calculate effects

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

Conditional logistic regression

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

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

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 floating trend to a factor in generalized linear model

Calculate floated variances

Fits a multiplicative relative risk model to interval censored data.

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

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

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

Contrast matrices

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

Plot columns of a matrix as stacked areas.

Fit an addive excess risk model to interval censored data.

An unmatched case-control study of leprosy incidence

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

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

hivDK: seroconversion in a cohort of Danish men

Create a basis of harmonic functions.

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

A small occupational cohort

Fit a piecewise contsnt intesity model for interval censored data.

Plot period and cohort effects in an APC-frame.

Function to group a variable in intervals.

Functions to manage and explore the workspace

A Cohort of Nickel Smelters in South Wales

Nice breakpoints

Plot confidence intervals as shaded areas around lines.

Mantel-Haenszel analyses of cohort and case-control studies

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

Fit intensity models to follow-up data in Lexis objects

Plotting Aalen-Johansen curves for competing events

Family Object for Poisson Regression

Diabetes prevance as of 2010-01-01 in Denmark

Male lung cancer incidence in Denmark

Projection of columns of a matrix.

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

Create percentages in a table

Convenience versions of grep

Clinical trial: Steno2 baseline and follow-up.

Combining a Lexis objects with data frames or other Lexis objects

Split follow-up time in a Lexis object

Functions to facilitate analysis of multistate models.

Special functions for use in stat.table

Plot APC-estimates in an APC-frame.

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

Merge a Lexis object with a data frame

Subsetting Lexis (and stacked.Lexis) objects

Plot estimates with confidence limits (forest plot)

transform.Lexis

Transform a Lexis (or stacked.Lexis) object

Analysis of a two by two table

Tables of summary statistics

Remove transitions from a Lexis object.

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

Time series and other methods for Lexis objects

Plot Equivalence Classes

Extract time band data from a split Lexis object

The time scales of a Lexis object

Summarize transitions and risk time from a Lexis object

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

Testis cancer incidence in Denmark, 1943--1996

Thorotrast Study