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 as a number of epidemiological datasets.

AuthorBendix Carstensen [aut, cre], Martyn Plummer [aut], Esa Laara [ctb], Michael Hills [ctb]
Date of publication2017-02-23 23:34:30
MaintainerBendix Carstensen <b@bxc.dk>
LicenseGPL-2
Version2.10
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

DMepi: Epidmiological rates for diabetes in Denmark 1996-2015

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

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

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

apc.fit Man page
apc.frame Man page
apc.LCa Man page
apc.lines Man page
apc.plot Man page
Aplot Man page
as.Date.cal.yr Man page
bdendo Man page
bdendo11 Man page
B.dk Man page
births Man page
blcaIT Man page
boxarr Man page
boxes Man page
boxes.Lexis Man page
boxes.matrix Man page
boxes.MS Man page
breaks Man page
brv Man page
cal.yr Man page
cbind.Lexis Man page
ccwc Man page
ci.cum Man page
ci.exp Man page
ci.lin Man page
ci.mat Man page
ci.pd Man page
ci.pred Man page
clear Man page
clogistic Man page
contr.2nd Man page
contr.cum Man page
contr.diff Man page
contr.orth Man page
count Man page
countLexis Man page
cp.lines Man page
Cplot Man page
cp.matlines Man page
cp.matpoints Man page
cp.points Man page
cutLexis Man page
dbox Man page
detrend Man page
diet Man page
DMconv Man page
DMepi Man page
DMlate Man page
DMrand Man page
dur Man page
effx Man page
effx.match Man page
entry Man page
erl Man page
erl1 Man page
etm Man page
etm.Lexis Man page
ewrates Man page
exit Man page
factorize Man page
factorize.Lexis Man page
fillarr Man page
fit.add Man page
fit.mult Man page
float Man page
ftrend Man page
gen.exp Man page
gmortDK Man page
hivDK Man page
Icens Man page
LCa.fit Man page
lep Man page
levels.Lexis Man page
Lexis Man page
[.Lexis Man page
Lexis.diagram Man page
Lexis.lines Man page
Life.lines Man page
lines.apc Man page
linesEst Man page
lines.Lexis Man page
lines.pState Man page
lls Man page
lungDK Man page
mcutLexis Man page
M.dk Man page
merge.data.frame Man page
merge.Lexis Man page
mh Man page
mortDK Man page
msdata Man page
msdata.Lexis Man page
N2Y Man page
NArray Man page
ncut Man page
N.dk Man page
nice Man page
nickel Man page
Ns Man page
nState Man page
occup Man page
pc.lines Man page
pc.matlines Man page
pc.matpoints Man page
pc.points Man page
pctab Man page
percent Man page
plot.apc Man page
plotEst Man page
plot.LCa Man page
plot.Lexis Man page
plot.pState Man page
pointsEst Man page
points.Lexis Man page
Pplot Man page
predict.LCa Man page
print.floated Man page
print.Icens Man page
print.LCa Man page
print.stat.table Man page
pState Man page
PY.ann Man page
PY.ann.Lexis Man page
rateplot Man page
ratio Man page
rbind.Lexis Man page
Relevel Man page
Relevel.factor Man page
Relevel.Lexis Man page
rm.tr Man page
ROC Man page
show.apc.LCa Man page
simLexis Man page
splitLexis Man page
stack.Lexis Man page
stat.table Man page
status Man page
S.typh Man page
subset.Lexis Man page
subset.stacked.Lexis Man page
summary.LCa Man page
surv1 Man page
surv2 Man page
tbox Man page
Termplot Man page
testisDK Man page
thoro Man page
timeBand Man page
timeScales Man page
tmat Man page
tmat.Lexis Man page
transform.Lexis Man page
transform.stacked.Lexis Man page
twoby2 Man page
Wald Man page
Y.dk Man page
yll Man page
ZArray Man page

Files

Epi
Epi/inst
Epi/inst/CITATION
Epi/inst/doc
Epi/inst/doc/Follow-up.pdf
Epi/inst/doc/index.html
Epi/inst/doc/yll.pdf
Epi/inst/doc/yll.R
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/inst/doc/yll.rnw
Epi/src
Epi/src/chinv2.c
Epi/src/chsolve2.c
Epi/src/cholesky2.c
Epi/src/clogit.c
Epi/src/init.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/DMepi.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/mcutLexis.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/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/vignettes/yll.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/mcutLexis.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/DMepi.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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