A Package for Statistical Analysis in Epidemiology


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Documentation for package ‘Epi’ version 2.19

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A B C D E F G H I L M N O P R S T W Y Z misc

-- A --

addCov.Lexis Add covariates (typically clinical measurements) taken at known times to a Lexis object.
apc.fit Fit an Age-Period-Cohort model to tabular data.
apc.frame Produce an empty frame for display of parameter-estimates from Age-Period-Cohort-models.
apc.LCa Fit Age-Period-Cohort models and Lee-Carter models with effects modeled by natural splines.
apc.lines Plot APC-estimates in an APC-frame.
apc.plot Plot the estimates from a fitted Age-Period-Cohort model
Aplot Functions to plot rates from a table classified by age and calendar time (period)
as.Date.cal.yr Functions to convert character, factor and various date objects into a number, and vice versa.

-- B --

B.dk Births in Denmark by year and month of birth and sex
bdendo A case-control study of endometrial cancer
bdendo11 A 1:1 subset of the endometrial cancer case-control study
births Births in a London Hospital
blcaIT Bladder cancer mortality in Italian males
boxarr Draw boxes and arrows for illustration of multistate models.
boxes Draw boxes and arrows for illustration of multistate models.
boxes.Lexis Draw boxes and arrows for illustration of multistate models.
boxes.matrix Draw boxes and arrows for illustration of multistate models.
boxes.MS Draw boxes and arrows for illustration of multistate models.
breaks Extract time band data from a split Lexis object
brv Bereavement in an elderly cohort

-- C --

cal.yr Functions to convert character, factor and various date objects into a number, and vice versa.
cbind.Lexis Combining a Lexis objects with data frames or other Lexis objects
ccwc Generate a nested case-control study
ci.cum Compute cumulative sum of estimates.
ci.exp Compute linear functions of parameters with standard errors and confidence limits
ci.lin Compute linear functions of parameters with standard errors and confidence limits
ci.mat Compute linear functions of parameters with standard errors and confidence limits
ci.pd Compute confidence limits for a difference of two independent proportions.
ci.pred Compute linear functions of parameters with standard errors and confidence limits
ci.ratio Compute linear functions of parameters with standard errors and confidence limits
clear Functions to manage and explore the workspace
clogistic Conditional logistic regression
contr.2nd Contrast matrices
contr.cum Contrast matrices
contr.diff Contrast matrices
contr.orth Contrast matrices
count Special functions for use in stat.table
countLexis Cut follow-up at a specified date for each person.
cp.lines Plot period and cohort effects in an APC-frame.
cp.matlines Plot period and cohort effects in an APC-frame.
cp.matpoints Plot period and cohort effects in an APC-frame.
cp.points Plot period and cohort effects in an APC-frame.
Cplot Functions to plot rates from a table classified by age and calendar time (period)
crr.Lexis Fit a competing risks regression model (Fine-Gray model) using a Lexis object)
cutLexis Cut follow-up at a specified date for each person.

-- D --

dbox Draw boxes and arrows for illustration of multistate models.
detrend Projection of a model matrix on to the orthogonal complement of a trend.
diet Diet and heart data
DMconv Conversion to diabetes
DMepi Epidmiological rates for diabetes in Denmark 1996-2015
DMlate The Danish National Diabetes Register.
DMrand The Danish National Diabetes Register.
dur Time series methods for Lexis objects

-- E --

effx Function to calculate effects
effx.match Function to calculate effects for individually matched case-control studies
entry Time series methods for Lexis objects
erl Compute survival functions from rates and expected residual lifetime in an illness-death model as well as years of life lost to disease.
erl1 Compute survival functions from rates and expected residual lifetime in an illness-death model as well as years of life lost to disease.
etm Create a data structures suitable for use with packages mstate, etm.
etm.Lexis Create a data structures suitable for use with packages mstate, etm.
ewrates Rates of lung and nasal cancer mortality, and total mortality.
exit Time series methods for Lexis objects
expand.data Function to expand data for regression analysis of interval censored data.

-- F --

factorize Transform a Lexis (or stacked.Lexis) objects
factorize.Lexis Transform a Lexis (or stacked.Lexis) objects
fgrep Convenience versions of grep
fillarr Draw boxes and arrows for illustration of multistate models.
fit.add Fit an addive 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
ftrend Fit a floating trend to a factor in generalized linear model

-- G --

gen.exp Generate covariates for drug-exposure follow-up from drug purchase records.
gmortDK Population mortality rates for Denmark in 5-years age groups.

-- H --

hivDK hivDK: seroconversion in a cohort of Danish men

-- I --

Icens Fits a regression model to interval censored data.

-- L --

LCa.fit Fit Lee-Carter-type models for rates to arbitrarily shaped observations of rates in a Lexis diagram.
lep An unmatched case-control study of leprosy incidence
levels.Lexis Transform a Lexis (or stacked.Lexis) objects
Lexis Create a Lexis object
Lexis.diagram Plot a Lexis diagram
Lexis.lines Draw life lines in a Lexis diagram.
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.
lines.Lexis Lexis diagrams
lines.pState Simulate a Lexis object representing follow-up in a multistate model.
linesEst Plot estimates with confidence limits (forest plot)
lls Functions to manage and explore the workspace
lungDK Male lung cancer incidence in Denmark

-- M --

M.dk Mortality in Denmark 1974 ff.
mcutLexis Cut follow-up at multiple event dates and keep track of order of events
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.
msdata Create a data structures suitable for use with packages mstate, etm.
msdata.Lexis Create a data structures suitable for use with packages mstate, etm.

-- N --

N.dk Population size in Denmark
N2Y Create risk time ("Person-Years") in Lexis triangles from population count data.
NArray Set up an array of NAs, solely from the list of dimnames
ncut Function to group a variable in intervals.
ngrep Convenience versions of grep
nice Nice breakpoints
nickel A Cohort of Nickel Smelters in South Wales
Ns Natural splines - (cubic splines linear beyond outermost knots) with convenient specification of knots and possibility of centering, detrending and clamping.
nState Simulate a Lexis object representing follow-up in a multistate model.

-- O --

occup A small occupational cohort
order.Lexis Transform a Lexis (or stacked.Lexis) objects

-- P --

pc.lines Plot period and cohort effects in an APC-frame.
pc.matlines Plot period and cohort effects in an APC-frame.
pc.matpoints Plot period and cohort effects in an APC-frame.
pc.points Plot period and cohort effects in an APC-frame.
pctab Create percentages in a table
percent Special functions for use in stat.table
plot.apc Plot the estimates from a fitted Age-Period-Cohort model
plot.LCa Fit Lee-Carter-type models for rates to arbitrarily shaped observations of rates in a Lexis diagram.
plot.Lexis Lexis diagrams
plot.pState Simulate a Lexis object representing follow-up in a multistate model.
plotCIF Plotting Aalen-Johansen curves for competing events
plotEst Plot estimates with confidence limits (forest plot)
plotevent Plot Equivalence Classes
points.Lexis Lexis diagrams
pointsEst Plot estimates with confidence limits (forest plot)
Pplot Functions to plot rates from a table classified by age and calendar time (period)
predict.LCa Fit Lee-Carter-type models for rates to arbitrarily shaped observations of rates in a Lexis diagram.
print.floated Calculate floated variances
print.Icens Fits a regression model to interval censored data.
print.LCa Fit Lee-Carter-type models for rates to arbitrarily shaped observations of rates in a Lexis diagram.
print.stat.table Tables of summary statistics
print.summary.Lexis Summarize transitions and risk time from a Lexis object
projection.ip Projection of columns of a matrix.
pState Simulate a Lexis object representing follow-up in a multistate model.
PY.ann Lexis diagrams
PY.ann.Lexis Lexis diagrams

-- R --

rateplot Functions to plot rates from a table classified by age and calendar time (period)
ratio Special functions for use in stat.table
rbind.Lexis Combining a Lexis objects with data frames or other Lexis objects
Relevel Reorder and combine levels of a factor
Relevel.factor Reorder and combine levels of a factor
Relevel.Lexis Transform a Lexis (or stacked.Lexis) objects
rm.tr Remove transitions from a Lexis object.
ROC Function to compute and draw ROC-curves.

-- S --

S.typh Salmonella Typhimurium outbreak 1996 in Denmark.
show.apc.LCa Fit Age-Period-Cohort models and Lee-Carter models with effects modeled by natural splines.
simLexis Simulate a Lexis object representing follow-up in a multistate model.
sort.Lexis Transform a Lexis (or stacked.Lexis) objects
splitLexis Split follow-up time in a Lexis object
stack.Lexis Functions to facilitate analysis of multistate models.
stackedCIF Plotting Aalen-Johansen curves for competing events
stat.table Tables of summary statistics
status Time series methods for Lexis objects
subset.Lexis Subsetting Lexis (and stacked.Lexis) objects
subset.stacked.Lexis Subsetting Lexis (and stacked.Lexis) objects
summary.LCa Fit Lee-Carter-type models for rates to arbitrarily shaped observations of rates in a Lexis diagram.
summary.Lexis Summarize transitions and risk time from a Lexis object
surv1 Compute survival functions from rates and expected residual lifetime in an illness-death model as well as years of life lost to disease.
surv2 Compute survival functions from rates and expected residual lifetime in an illness-death model as well as years of life lost to disease.

-- T --

tbox Draw boxes and arrows for illustration of multistate models.
Termplot 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.
testisDK Testis cancer incidence in Denmark, 1943-1996
thoro Thorotrast Study
timeBand Extract time band data from a split Lexis object
timeScales The time scales of a Lexis object
tmat Functions to facilitate analysis of multistate models.
tmat.Lexis Functions to facilitate analysis of multistate models.
transform.Lexis Transform a Lexis (or stacked.Lexis) objects
transform.stacked.Lexis Transform a Lexis (or stacked.Lexis) objects
twoby2 Analysis of a two by two table

-- W --

Wald Compute linear functions of parameters with standard errors and confidence limits

-- Y --

Y.dk Population risk time in Denmark
yll Compute survival functions from rates and expected residual lifetime in an illness-death model as well as years of life lost to disease.

-- Z --

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

-- misc --

[.Lexis Subsetting Lexis (and stacked.Lexis) objects