Epi: A Package for Statistical Analysis in Epidemiology

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.

AuthorBendix Carstensen [aut, cre], Martyn Plummer [aut], Esa Laara [ctb], Michael Hills [ctb]
Date of publication2016-10-04 14:35:49
MaintainerBendix Carstensen <bxc@steno.dk>
LicenseGPL-2
Version2.7
http://BendixCarstensen.com/Epi/

View on CRAN

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

Files in this package

Epi
Epi/inst
Epi/inst/CITATION
Epi/inst/doc
Epi/inst/doc/Follow-up.pdf
Epi/inst/doc/index.html
Epi/inst/doc/Follow-up.rnw
Epi/inst/doc/Follow-up.R
Epi/inst/doc/simLexis.pdf
Epi/inst/doc/simLexis.R
Epi/inst/doc/simLexis.rnw
Epi/src
Epi/src/chinv2.c
Epi/src/chsolve2.c
Epi/src/cholesky2.c
Epi/src/clogit.c
Epi/NAMESPACE
Epi/data
Epi/data/lungDK.rda
Epi/data/diet.rda
Epi/data/lep.rda
Epi/data/hivDK.rda
Epi/data/testisDK.rda
Epi/data/S.typh.rda
Epi/data/ewrates.rda
Epi/data/blcaIT.rda
Epi/data/mortDK.rda
Epi/data/births.rda
Epi/data/bdendo11.rda
Epi/data/M.dk.rda
Epi/data/N.dk.rda
Epi/data/bdendo.rda
Epi/data/thoro.rda
Epi/data/occup.rda
Epi/data/brv.rda
Epi/data/Y.dk.rda
Epi/data/DMrand.rda
Epi/data/gmortDK.rda
Epi/data/B.dk.rda
Epi/data/nickel.rda
Epi/data/DMconv.rda
Epi/data/DMlate.rda
Epi/R
Epi/R/expand.data.r
Epi/R/clear.R Epi/R/clogistic.R Epi/R/detrend.R Epi/R/lexis.R
Epi/R/ncut.r
Epi/R/Life.lines.R Epi/R/twoby2.R Epi/R/rateplot.R Epi/R/cal.yr.R Epi/R/splitLexis.R
Epi/R/effx.r
Epi/R/N2Y.r
Epi/R/contr.orth.R Epi/R/stattable.R Epi/R/factorize.R Epi/R/apc.fit.R Epi/R/ROC.R Epi/R/ci.mat.R
Epi/R/effx.match.r
Epi/R/apc.frame.R
Epi/R/Ns.r
Epi/R/Termplot.R Epi/R/foreign.R Epi/R/contr.diff.R Epi/R/ci.cum.R Epi/R/plotEst.R
Epi/R/crr.Lexis.r
Epi/R/float.R Epi/R/cutLexis.R Epi/R/contr.2nd.R Epi/R/boxes.MS.R Epi/R/erl.R Epi/R/ccwc.R
Epi/R/summary.Lexis.r
Epi/R/gen.exp.R Epi/R/Icens.R Epi/R/pctab.R Epi/R/simLexis.R Epi/R/apc.LCa.R Epi/R/Lexis.lines.R Epi/R/Pplot.R Epi/R/lls.R Epi/R/mh.R Epi/R/LCa.fit.R Epi/R/fit.baseline.R
Epi/R/print.Icens.r
Epi/R/NArray.R Epi/R/print.floated.R Epi/R/ftrend.R Epi/R/Relevel.R Epi/R/contr.cum.R Epi/R/ci.lin.R
Epi/R/fit.mult.r
Epi/R/Wald.R
Epi/R/plotevent.r
Epi/R/ci.pd.R Epi/R/Cplot.R Epi/R/rm.tr.R
Epi/R/fit.add.r
Epi/R/as.Date.cal.yr.R
Epi/R/projection.ip.r
Epi/R/Lexis.diagram.R Epi/R/zzz.R Epi/R/apc.plot.R Epi/R/Aplot.R Epi/R/stack.Lexis.R
Epi/R/summary.Icens.r
Epi/vignettes
Epi/vignettes/index.html
Epi/vignettes/Follow-up.rnw
Epi/vignettes/simLexis.rnw
Epi/MD5
Epi/build
Epi/build/vignette.rds
Epi/DESCRIPTION
Epi/man
Epi/man/Lexis.lines.Rd Epi/man/cutLexis.Rd Epi/man/bdendo.Rd Epi/man/ci.cum.Rd Epi/man/blcaIT.Rd Epi/man/N.dk.Rd Epi/man/lls.Rd Epi/man/time.scales.Rd Epi/man/pc.lines.Rd Epi/man/Lexis.Rd Epi/man/DMlate.Rd Epi/man/mh.Rd Epi/man/Y.dk.Rd Epi/man/effx.Rd Epi/man/lines.apc.Rd Epi/man/testisDK.Rd Epi/man/stack.Lexis.Rd Epi/man/fit.mult.Rd Epi/man/hivDK.Rd Epi/man/boxes.MS.Rd Epi/man/plotEst.Rd Epi/man/rm.tr.Rd Epi/man/foreign.Lexis.Rd Epi/man/splitLexis.Rd Epi/man/cal.yr.Rd Epi/man/nickel.Rd Epi/man/time.band.Rd Epi/man/Termplot.Rd Epi/man/diet.Rd Epi/man/ci.pd.Rd Epi/man/subset.Lexis.Rd Epi/man/ewrates.Rd Epi/man/start.Lexis.Rd Epi/man/merge.Lexis.Rd Epi/man/simLexis.Rd Epi/man/stattable.funs.Rd Epi/man/thoro.Rd Epi/man/lungDK.Rd Epi/man/births.Rd Epi/man/transform.Lexis.Rd Epi/man/B.dk.Rd
Epi/man/crr.Lexis.rd
Epi/man/nice.Rd Epi/man/occup.Rd
Epi/man/projection.ip.rd
Epi/man/S.typh.Rd Epi/man/erl.Rd Epi/man/pctab.Rd Epi/man/effx.match.Rd Epi/man/stattable.Rd Epi/man/brv.Rd Epi/man/rbind.Lexis.Rd Epi/man/detrend.Rd Epi/man/bdendo11.Rd Epi/man/ftrend.Rd Epi/man/ROC.Rd Epi/man/Icens.Rd Epi/man/Lexis.diagram.Rd Epi/man/apc.LCa.Rd Epi/man/fit.add.Rd Epi/man/N2Y.Rd
Epi/man/plotevent.rd
Epi/man/Life.lines.Rd Epi/man/float.Rd Epi/man/gmortDK.Rd Epi/man/M.dk.Rd Epi/man/apc.fit.Rd Epi/man/twoby2.Rd Epi/man/Ns.Rd Epi/man/apc.frame.Rd Epi/man/mortDK.Rd Epi/man/NArray.Rd Epi/man/rateplot.Rd Epi/man/contr.cum.Rd
Epi/man/summary.Lexis.rd
Epi/man/DMconv.Rd Epi/man/merge.data.frame.Rd Epi/man/Relevel.Rd Epi/man/ci.lin.Rd
Epi/man/fit.baseline.rd
Epi/man/plot.apc.Rd Epi/man/lep.Rd Epi/man/ccwc.Rd Epi/man/clogistic.Rd Epi/man/ncut.Rd
Epi/man/expand.data.rd
Epi/man/plot.Lexis.Rd Epi/man/gen.exp.Rd Epi/man/LCa.fit.Rd
Epi/CHANGES

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