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Epi (version 2.47)

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

License

GPL-2

Maintainer

Bendix Carstensen

Last Published

June 26th, 2022

Functions in Epi (2.47)

The Danish National Diabetes Register.

Epi: Functions for manipulation and statistical analysis of epidemiological data

Epidemiological rates for diabetes in Denmark 1996--2015

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

Create a Lexis object of follow-up

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

Births in Denmark by year and month of birth and sex

Fits a regression model to interval censored data.

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

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

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.

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

Plot a Lexis diagram

Conversion to diabetes

Mortality in Denmark 1974 ff.

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

Population size in Denmark

Draw life lines in a Lexis diagram.

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

Compute dates/ages for life lines in a Lexis diagram

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.

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

A case-control study of endometrial cancer

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

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

Generate a nested case-control study

Bereavement in an elderly cohort

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.

Compute cumulative sum of estimates.

Draw boxes and arrows for illustration of multistate models.

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

Bladder cancer mortality in Italian males

Births in a London Hospital

Contrast matrices

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

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

Compute confidence limits for a difference of two independent proportions.

Conditional logistic regression

Function to calculate effects

Diet and heart data

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

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

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

Function to calculate effects for individually matched case-control studies

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

Fit an addive excess risk model to interval censored data.

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

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

Functions to manage and explore the workspace

Plot columns of a matrix as stacked areas.

Male lung cancer incidence in Denmark

Plot confidence intervals as shaded areas around lines.

Fit a floating trend to a factor in generalized linear model

Fit a piecewise contsnt intesity model for interval censored data.

Mantel-Haenszel analyses of cohort and case-control studies

Convenience versions of grep

Nice breakpoints

Fit intensity models to follow-up data in Lexis objects

Create percentages in a table

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

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

Function to group a variable in intervals.

Plot APC-estimates in an APC-frame.

A small occupational cohort

An unmatched case-control study of leprosy incidence

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

A Cohort of Nickel Smelters in South Wales

Plot estimates with confidence limits (forest plot)

Plot Equivalence Classes

Plot period and cohort effects in an APC-frame.

Plotting Aalen-Johansen curves for competing events

Remove transitions from a Lexis object.

Combining a Lexis objects with data frames or other Lexis objects

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

transform.Lexis

Transform a Lexis (or stacked.Lexis) object

Analysis of a two by two table

Time series and other methods for Lexis objects

Fits a multiplicative relative risk model to interval censored data.

Tables of summary statistics

Calculate floated variances

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

Create a basis of harmonic functions.

Diabetes prevance as of 2010-01-01 in Denmark

Family Object for Poisson Regression

Extract time band data from a split Lexis object

The time scales of a Lexis object

Special functions for use in stat.table

Subsetting Lexis (and stacked.Lexis) objects

hivDK: seroconversion in a cohort of Danish men

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

Clinical trial: Steno2 baseline and follow-up.

Summarize transitions and risk time from a Lexis object

Testis cancer incidence in Denmark, 1943--1996

Thorotrast Study

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

Merge a Lexis object with a data frame

Projection of columns of a matrix.

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.