Epi2.56 package

Statistical Analysis in Epidemiology

AaJ.Lexis

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

addCov.Lexis

Add covariates (typically clinical measurements) taken at known times ...

addDrug.Lexis

Expand a Lexis object with information of drug exposure based on purch...

apc.fit

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

apc.frame

Produce an empty frame for display of parameter-estimates from Age-Per...

apc.LCa

Fit Age-Period-Cohort models and Lee-Carter models with effects modele...

bootLexis

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

boxes.MS

Draw boxes and arrows for illustration of multistate models.

cal.yr

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

ccwc

Generate a nested case-control study

ci.Crisk

Compute cumulative risks and expected sojourn times from models for ca...

ci.cum

Compute cumulative sum of estimates.

ci.eta

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

ci.lin

Compute linear functions of parameters with standard errors and confid...

ci.pd

Compute confidence limits for a difference of two independent proporti...

clogistic

Conditional logistic regression

contr.cum

Contrast matrices

crr.Lexis

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

cutLexis

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

detrend

Projection of a model matrix on the orthogonal complement of a trend o...

effx.match

Function to calculate effects for individually matched case-control st...

effx

Function to calculate effects

Epi

Epi: Functions for manipulation and statistical analysis of epidemiolo...

erl

Compute survival functions from rates and expected residual lifetime i...

expand.data

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

fit.add

Fit an additive excess risk model to interval censored data.

fit.baseline

Fit a piecewise contsnt intesity model for interval censored data.

fit.mult

Fits a multiplicative relative risk model to interval censored data.

float

Calculate floated variances

foreign.Lexis

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

ftrend

Fit a floating trend to a factor in generalized linear model

gen.exp

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

harm

Create a basis of harmonic functions.

Icens

Fits a regression model to interval censored data.

in.span

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

LCa.fit

Fit Lee-Carter-type models for rates to arbitrarily shaped observation...

legendbox

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

Lexis.diagram

Plot a Lexis diagram

Lexis.lines

Draw life lines in a Lexis diagram.

Lexis

Create a Lexis object of follow-up

Lexis2msm

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

lgrep

Convenience versions of grep

Life.lines

Compute dates/ages for life lines in a Lexis diagram

lines.apc

Plot APC-estimates in an APC-frame.

lls

Functions to manage and explore the workspace

mat2pol

Plot columns of a matrix as stacked areas.

matshade

Plot confidence intervals as shaded areas around lines.

mcutLexis

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

merge.Lexis

Merge a Lexis object with a data frame

mh

Mantel-Haenszel analyses of cohort and case-control studies

mod.Lexis

Fit intensity models to follow-up data in Lexis objects

N2Y

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

NArray

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

ncut

Function to group a variable in intervals.

nice

Nice breakpoints for axes on plots

Ns

Natural splines - (cubic splines linear beyond outermost knots) with c...

pc.lines

Plot period and cohort effects in an APC-frame.

pctab

Create percentages in a table

plot.apc

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

plot.Lexis

Lexis diagrams

plotCIF

Plotting Aalen-Johansen curves for competing events

plotEst

Plot estimates with confidence limits (forest plot)

plotevent

Plot Equivalence Classes

poisreg

Family Object for Poisson Regression

projection.ip

Projection of columns of a matrix.

rateplot

Functions to plot rates from a table classified by age and calendar ti...

rbind.Lexis

Combining a Lexis objects with data frames or other Lexis objects

rcutLexis

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

Relevel

Reorder and combine levels of a factor

rm.tr

Remove transitions from a Lexis object.

ROC

Function to compute and draw ROC-curves.

simLexis

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

splitLexis

Split follow-up time in a Lexis object

stack.Lexis

Functions to facilitate analysis of multistate models.

start.Lexis

Time series and other methods for Lexis objects

stattable.funs

Special functions for use in stat.table

stattable

Tables of summary statistics

subset.Lexis

Subsetting Lexis (and stacked.Lexis) objects

summary.Lexis

Summarize transitions and risk time from a Lexis object

Termplot

A wrapper for termplot that optionally (but by default) exponentiate...

time.band

Extract time band data from a split Lexis object

time.scales

The time scales of a Lexis object

transform.Lexis

Transform a Lexis (or stacked.Lexis) object

twoby2

Analysis of a two by two table

unLexis

Remove Lexis attributes from a Lexis object.

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.