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Epi (version 2.55)

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

6,284

Version

2.55

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

September 10th, 2024

Functions in Epi (2.55)

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.

Compute dates/ages for life lines in a Lexis diagram

Plot a Lexis diagram

Draw life lines in a Lexis diagram.

Function to compute and draw ROC-curves.

Population size in Denmark

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

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

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

Reorder and combine levels of a factor

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.

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

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

Population risk time in Denmark

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.

Bereavement in an elderly cohort

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

Births in a London Hospital

Generate a nested case-control study

Compute cumulative sum of estimates.

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

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

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

Bladder cancer mortality in Italian males

Draw boxes and arrows for illustration of multistate models.

Contrast matrices

Conditional logistic regression

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 for individually matched case-control studies

Function to calculate effects

Diet and heart data

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

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

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

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

Fit a floating trend to a factor in generalized linear model

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

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

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

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

Fit an additive excess risk model to interval censored data.

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

Fits a multiplicative relative risk model to interval censored data.

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.

Fit a piecewise contsnt intesity model for interval censored data.

Convenience versions of grep

Plot columns of a matrix as stacked areas.

Function to group a variable in intervals.

hivDK: seroconversion in a cohort of Danish men

Male lung cancer incidence in Denmark

Nice breakpoints for axes on plots

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

Functions to manage and explore the workspace

An unmatched case-control study of leprosy incidence

A Cohort of Nickel Smelters in South Wales

Family Object for Poisson Regression

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

Plot confidence intervals as shaded areas around lines.

Create a basis of harmonic functions.

Diabetes prevance as of 2010-01-01 in Denmark

Mantel-Haenszel analyses of cohort and case-control studies

Fit intensity models to follow-up data in Lexis objects

Plot estimates with confidence limits (forest plot)

Projection of columns of a matrix.

Plot period and cohort effects in an APC-frame.

A small occupational cohort

Combining a Lexis objects with data frames or other Lexis objects

Plot Equivalence Classes

Testis cancer incidence in Denmark, 1943--1996

Create percentages in a table

Time series and other methods for Lexis objects

Tables of summary statistics

Plot APC-estimates in an APC-frame.

Summarize transitions and risk time from a Lexis object

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

Subsetting Lexis (and stacked.Lexis) objects

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

Remove transitions from a Lexis object.

Thorotrast Study

transform.Lexis

Transform a Lexis (or stacked.Lexis) object

Analysis of a two by two table

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

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

Plotting Aalen-Johansen curves for competing events

Merge a Lexis object with a data frame

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

Split follow-up time in a Lexis object

Functions to facilitate analysis of multistate models.

Extract time band data from a split Lexis object

The time scales of a Lexis object

Remove Lexis attributes from a Lexis object.

Special functions for use in stat.table

Clinical trial: Steno2 baseline and follow-up.

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

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.

The Danish National Diabetes Register.

Epidemiological rates for diabetes in Denmark 1996--2015

Create a Lexis object of follow-up

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.