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Epi (version 2.50)

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

9,144

Version

2.50

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

May 27th, 2024

Functions in Epi (2.50)

Epidemiological rates for diabetes in Denmark 1996--2015

Epi: Functions for manipulation and statistical analysis of epidemiological data

Conversion to diabetes

Births in Denmark by year and month of birth and sex

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

Fits a regression model to interval censored data.

Create a Lexis object of follow-up

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

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

Population size in Denmark

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

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

The Danish National Diabetes Register.

Mortality in Denmark 1974 ff.

Draw life lines in a Lexis diagram.

Compute dates/ages for life lines in a Lexis diagram

Function to compute and draw ROC-curves.

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

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

Plot a Lexis diagram

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.

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

Reorder and combine levels of a factor

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.

Population risk time in Denmark

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

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

Salmonella Typhimurium outbreak 1996 in Denmark.

A case-control study of endometrial cancer

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

Births in a London Hospital

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

Bereavement in an elderly cohort

Bladder cancer mortality in Italian males

Compute cumulative sum of estimates.

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

Draw boxes and arrows for illustration of multistate models.

Generate a nested case-control study

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

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.

Conditional logistic regression

Contrast matrices

Compute confidence limits for a difference of two independent proportions.

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

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

Diet and heart data

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

Function to calculate effects

Fit an additive excess risk model to interval censored data.

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

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

Fits a multiplicative relative risk model to interval censored data.

Calculate floated variances

Fit a piecewise contsnt intesity model for 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

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

Male lung cancer incidence in Denmark

Plot columns of a matrix as stacked areas.

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

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?

Create a basis of harmonic functions.

Convenience versions of grep

An unmatched case-control study of leprosy incidence

Plot APC-estimates in an APC-frame.

hivDK: seroconversion in a cohort of Danish men

Nice breakpoints

Mantel-Haenszel analyses of cohort and case-control studies

Function to group a variable in intervals.

Merge a Lexis object with a data frame

A small occupational cohort

Functions to manage and explore the workspace

Fit intensity models to follow-up data in Lexis objects

A Cohort of Nickel Smelters in South Wales

Plot confidence intervals as shaded areas around lines.

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

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

Diabetes prevance as of 2010-01-01 in Denmark

Plot period and cohort effects in an APC-frame.

Plotting Aalen-Johansen curves for competing events

Plot estimates with confidence limits (forest plot)

Create percentages in a table

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

Plot Equivalence Classes

Projection of columns of a matrix.

Family Object for Poisson Regression

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

Split follow-up time in a Lexis object

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

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

Functions to facilitate analysis of multistate models.

Tables of summary statistics

Remove transitions from a Lexis object.

Special functions for use in stat.table

Remove Lexis attributes from a Lexis object.

Summarize transitions and risk time from a Lexis object

transform.Lexis

Transform a Lexis (or stacked.Lexis) object

The time scales of a Lexis object

Combining a Lexis objects with data frames or other Lexis objects

Analysis of a two by two table

Time series and other methods for Lexis objects

Testis cancer incidence in Denmark, 1943--1996

Clinical trial: Steno2 baseline and follow-up.

Extract time band data from a split Lexis object

Subsetting Lexis (and stacked.Lexis) objects

Thorotrast Study