Epi: A Package for Statistical Analysis in Epidemiology
Version 2.6

Functions for demographic and epidemiological analysis in the Lexis diagram, i.e. register and cohort follow-up data, in particular representation, manipulation and simulation of multistate data - the Lexis suite of functions, which includes interfaces to 'mstate', 'etm' and 'cmprsk' packages. Also 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 some epidemiological datasets.

Browse man pages Browse package API and functions Browse package files

AuthorBendix Carstensen [aut, cre], Martyn Plummer [aut], Esa Laara [ctb], Michael Hills [ctb]
Date of publication2016-10-02 09:22:48
MaintainerBendix Carstensen <bxc@steno.dk>
LicenseGPL-2
Version2.6
URL http://BendixCarstensen.com/Epi/
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("Epi", repos="http://R-Forge.R-project.org")

Man pages

apc.fit: Fit an Age-Period-Cohort model to tabular data.
apc.frame: Produce an empty frame for display of parameter-estimates...
apc.LCa: Fit Age-Period-Cohort models and Lee-Carter models with...
bdendo: A case-control study of endometrial cancer
bdendo11: A 1:1 subset of the endometrial cancer case-control study
B.dk: Births in Denmark by year and month of birth and sex
births: Births in a London Hospital
blcaIT: Bladder cancer mortality in Italian males
boxes.MS: Draw boxes and arrows for illustration of multistate models.
brv: Bereavement in an elderly cohort
cal.yr: Functions to convert character, factor and various date...
ccwc: Generate a nested case-control study
ci.cum: Compute cumulative sum of estimates.
ci.lin: Compute linear functions of parameters with standard errors...
ci.pd: Compute confidence limits for a difference of two independent...
clogistic: Conditional logistic regression
contr.cum: Contrast matrices
cutLexis: Cut follow-up at a specified date for each person.
detrend: Projection of a model matrix on to the orthogonal complement...
diet: Diet and heart data
DMconv: Conversion to diabetes
DMlate: The Danish National Diabetes Register.
effx: Function to calculate effects
effx.match: Function to calculate effects for individually matched...
erl: Compute survival functions from rates and expected residual...
ewrates: Rates of lung and nasal cancer mortality, and total...
fit.add: Fit an addive excess risk model to interval censored data.
fit.mult: Fits a multiplicative relative risk model to interval...
float: Calculate floated variances
foreign.Lexis: Create a data structures suitable for use with packages...
ftrend: Fit a floating trend to a factor in generalized linear model
gen.exp: Generate covariates for drug-exposure follow-up from drug...
gmortDK: Population mortality rates for Denmark in 5-years age groups.
hivDK: hivDK: seroconversion in a cohort of Danish men
Icens: Fits a regression model to interval censored data.
LCa.fit: Fit Lee-Carter-type models for rates to arbitrarily shaped...
lep: An unmatched case-control study of leprosy incidence
Lexis: Create a Lexis object
Lexis.diagram: Plot a Lexis diagram
Lexis.lines: Draw life lines in a Lexis diagram.
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
lungDK: Male lung cancer incidence in Denmark
M.dk: Mortality in Denmark 1974 ff.
merge.data.frame: Merge data frame with a Lexis object
merge.Lexis: Merge a Lexis object with a data frame
mh: Mantel-Haenszel analyses of cohort and case-control studies
mortDK: Population mortality rates for Denmark in 1-year age-classes.
N2Y: Create risk time ("Person-Years") in Lexis triangles from...
NArray: Set up an array of NAs, solely from the list of dimnames
ncut: Function to group a variable in intervals.
N.dk: Population size in Denmark
nice: Nice breakpoints
nickel: A Cohort of Nickel Smelters in South Wales
Ns: Natural splines - (cubic splines linear beyond outermost...
occup: A small occupational cohort
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
plotEst: Plot estimates with confidence limits (forest plot)
plot.Lexis: Lexis diagrams
rateplot: Functions to plot rates from a table classified by age and...
rbind.Lexis: Combining a Lexis objects with data frames or other Lexis...
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...
splitLexis: Split follow-up time in a Lexis object
stack.Lexis: Functions to facilitate analysis of multistate models.
start.Lexis: Time series methods for Lexis objects
stattable: Tables of summary statistics
stattable.funs: Special functions for use in stat.table
S.typh: Salmonella Typhimurium outbreak 1996 in Denmark.
subset.Lexis: Subsetting Lexis (and stacked.Lexis) objects
Termplot: A wrapper for 'termplot' that optionally (but by default)...
testisDK: Testis cancer incidence in Denmark, 1943-1996
thoro: Thorotrast Study
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) objects
twoby2: Analysis of a two by two table
Y.dk: Population risk time in Denmark

Functions

Files

Epi/CHANGES
Epi/DESCRIPTION
Epi/NAMESPACE
Epi/R
Epi/R/Aplot.R
Epi/R/Cplot.R
Epi/R/Icens.R
Epi/R/LCa.fit.R
Epi/R/Lexis.diagram.R
Epi/R/Lexis.lines.R
Epi/R/Life.lines.R
Epi/R/N2Y.r
Epi/R/NArray.R
Epi/R/Ns.r
Epi/R/Pplot.R
Epi/R/ROC.R
Epi/R/Relevel.R
Epi/R/Termplot.R
Epi/R/Wald.R
Epi/R/apc.LCa.R
Epi/R/apc.fit.R
Epi/R/apc.frame.R
Epi/R/apc.plot.R
Epi/R/as.Date.cal.yr.R
Epi/R/boxes.MS.R
Epi/R/cal.yr.R
Epi/R/ccwc.R
Epi/R/ci.cum.R
Epi/R/ci.lin.R
Epi/R/ci.mat.R
Epi/R/ci.pd.R
Epi/R/clear.R
Epi/R/clogistic.R
Epi/R/contr.2nd.R
Epi/R/contr.cum.R
Epi/R/contr.diff.R
Epi/R/contr.orth.R
Epi/R/crr.Lexis.r
Epi/R/cutLexis.R
Epi/R/detrend.R
Epi/R/effx.match.r
Epi/R/effx.r
Epi/R/erl.R
Epi/R/expand.data.r
Epi/R/factorize.R
Epi/R/fit.add.r
Epi/R/fit.baseline.R
Epi/R/fit.mult.r
Epi/R/float.R
Epi/R/foreign.R
Epi/R/ftrend.R
Epi/R/gen.exp.R
Epi/R/lexis.R
Epi/R/lls.R
Epi/R/mh.R
Epi/R/ncut.r
Epi/R/pctab.R
Epi/R/plotEst.R
Epi/R/plotevent.r
Epi/R/print.Icens.r
Epi/R/print.floated.R
Epi/R/projection.ip.r
Epi/R/rateplot.R
Epi/R/rm.tr.R
Epi/R/simLexis.R
Epi/R/splitLexis.R
Epi/R/stack.Lexis.R
Epi/R/stattable.R
Epi/R/summary.Icens.r
Epi/R/summary.Lexis.r
Epi/R/twoby2.R
Epi/R/zzz.R
Epi/build
Epi/build/vignette.rds
Epi/data
Epi/data/B.dk.rda
Epi/data/DMconv.rda
Epi/data/DMlate.rda
Epi/data/DMrand.rda
Epi/data/M.dk.rda
Epi/data/N.dk.rda
Epi/data/S.typh.rda
Epi/data/Y.dk.rda
Epi/data/bdendo.rda
Epi/data/bdendo11.rda
Epi/data/births.rda
Epi/data/blcaIT.rda
Epi/data/brv.rda
Epi/data/diet.rda
Epi/data/ewrates.rda
Epi/data/gmortDK.rda
Epi/data/hivDK.rda
Epi/data/lep.rda
Epi/data/lungDK.rda
Epi/data/mortDK.rda
Epi/data/nickel.rda
Epi/data/occup.rda
Epi/data/testisDK.rda
Epi/data/thoro.rda
Epi/inst
Epi/inst/CITATION
Epi/inst/doc
Epi/inst/doc/Follow-up.R
Epi/inst/doc/Follow-up.pdf
Epi/inst/doc/Follow-up.rnw
Epi/inst/doc/index.html
Epi/inst/doc/simLexis.R
Epi/inst/doc/simLexis.pdf
Epi/inst/doc/simLexis.rnw
Epi/man
Epi/man/B.dk.Rd
Epi/man/DMconv.Rd
Epi/man/DMlate.Rd
Epi/man/Icens.Rd
Epi/man/LCa.fit.Rd
Epi/man/Lexis.Rd
Epi/man/Lexis.diagram.Rd
Epi/man/Lexis.lines.Rd
Epi/man/Life.lines.Rd
Epi/man/M.dk.Rd
Epi/man/N.dk.Rd
Epi/man/N2Y.Rd
Epi/man/NArray.Rd
Epi/man/Ns.Rd
Epi/man/ROC.Rd
Epi/man/Relevel.Rd
Epi/man/S.typh.Rd
Epi/man/Termplot.Rd
Epi/man/Y.dk.Rd
Epi/man/apc.LCa.Rd
Epi/man/apc.fit.Rd
Epi/man/apc.frame.Rd
Epi/man/bdendo.Rd
Epi/man/bdendo11.Rd
Epi/man/births.Rd
Epi/man/blcaIT.Rd
Epi/man/boxes.MS.Rd
Epi/man/brv.Rd
Epi/man/cal.yr.Rd
Epi/man/ccwc.Rd
Epi/man/ci.cum.Rd
Epi/man/ci.lin.Rd
Epi/man/ci.pd.Rd
Epi/man/clogistic.Rd
Epi/man/contr.cum.Rd
Epi/man/crr.Lexis.rd
Epi/man/cutLexis.Rd
Epi/man/detrend.Rd
Epi/man/diet.Rd
Epi/man/effx.Rd
Epi/man/effx.match.Rd
Epi/man/erl.Rd
Epi/man/ewrates.Rd
Epi/man/expand.data.rd
Epi/man/fit.add.Rd
Epi/man/fit.baseline.rd
Epi/man/fit.mult.Rd
Epi/man/float.Rd
Epi/man/foreign.Lexis.Rd
Epi/man/ftrend.Rd
Epi/man/gen.exp.Rd
Epi/man/gmortDK.Rd
Epi/man/hivDK.Rd
Epi/man/lep.Rd
Epi/man/lines.apc.Rd
Epi/man/lls.Rd
Epi/man/lungDK.Rd
Epi/man/merge.Lexis.Rd
Epi/man/merge.data.frame.Rd
Epi/man/mh.Rd
Epi/man/mortDK.Rd
Epi/man/ncut.Rd
Epi/man/nice.Rd
Epi/man/nickel.Rd
Epi/man/occup.Rd
Epi/man/pc.lines.Rd
Epi/man/pctab.Rd
Epi/man/plot.Lexis.Rd
Epi/man/plot.apc.Rd
Epi/man/plotEst.Rd
Epi/man/plotevent.rd
Epi/man/projection.ip.rd
Epi/man/rateplot.Rd
Epi/man/rbind.Lexis.Rd
Epi/man/rm.tr.Rd
Epi/man/simLexis.Rd
Epi/man/splitLexis.Rd
Epi/man/stack.Lexis.Rd
Epi/man/start.Lexis.Rd
Epi/man/stattable.Rd
Epi/man/stattable.funs.Rd
Epi/man/subset.Lexis.Rd
Epi/man/summary.Lexis.rd
Epi/man/testisDK.Rd
Epi/man/thoro.Rd
Epi/man/time.band.Rd
Epi/man/time.scales.Rd
Epi/man/transform.Lexis.Rd
Epi/man/twoby2.Rd
Epi/src
Epi/src/chinv2.c
Epi/src/cholesky2.c
Epi/src/chsolve2.c
Epi/src/clogit.c
Epi/vignettes
Epi/vignettes/Follow-up.rnw
Epi/vignettes/index.html
Epi/vignettes/simLexis.rnw
Epi documentation built on Oct. 3, 2016, 12:14 a.m.