A B C D E F G H I L M N O P R S T U W Y Z misc
Epi-package | Epi: Functions for manipulation and statistical analysis of epidemiological data |
AaJ.Lexis | The Aalen-Johansen estimator of state probabilities from a multistate 'Lexis' object. |
absorbing | Time series and other methods for Lexis objects |
addCov.Lexis | Add covariates (typically clinical measurements) taken at known times to a Lexis object. |
addDrug.Lexis | Expand a Lexis object with information of drug exposure based on purchase dates and -amounts |
after | Time series and other methods for Lexis objects |
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.dk | Births in Denmark by year and month of birth and sex |
bdendo | A case-control study of endometrial cancer |
bdendo11 | A case-control study of endometrial cancer |
before | Time series and other methods for Lexis objects |
births | Births in a London Hospital |
blcaIT | Bladder cancer mortality in Italian males |
bootLexis | Create a bootstrap sample of persons (as identified by 'lex.id') from a Lexis object |
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. |
BrCa | Clinical status, relapse, metastasis and death in 2982 women with breast cancer. |
breaks | Extract time band data from a split Lexis object |
brv | Bereavement in an elderly cohort |
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.Crisk | Compute cumulative risks and expected sojourn times from models for cause-specific rates. |
ci.cum | Compute cumulative sum of estimates. |
ci.eta | Linear predictor ('eta') from a formula, coefficients, vcov and a prediction frame. |
ci.exp | Compute linear functions of parameters with standard errors and confidence limits, optionally transforming to a different scale. |
ci.lin | Compute linear functions of parameters with standard errors and confidence limits, optionally transforming to a different scale. |
ci.mat | Compute linear functions of parameters with standard errors and confidence limits, optionally transforming to a different scale. |
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, optionally transforming to a different scale. |
ci.ratio | Compute linear functions of parameters with standard errors and confidence limits, optionally transforming to a different scale. |
ci.surv | Compute cumulative sum of estimates. |
clear | Functions to manage and explore the workspace |
clogistic | Conditional logistic regression |
coarse.Lexis | Expand a Lexis object with information of drug exposure based on purchase dates and -amounts |
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. |
coxph.Lexis | Fit intensity models to follow-up data in Lexis objects |
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.matshade | 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. |
dbox | Draw boxes and arrows for illustration of multistate models. |
decurve | Projection of a model matrix on the orthogonal complement of a trend or curvature. |
detrend | Projection of a model matrix on the orthogonal complement of a trend or curvature. |
diet | Diet and heart data |
DMconv | Conversion to diabetes |
DMepi | Epidemiological rates for diabetes in Denmark 1996-2015 |
DMlate | The Danish National Diabetes Register. |
DMrand | The Danish National Diabetes Register. |
dur | Time series and other methods for Lexis objects |
effx | Function to calculate effects |
effx.match | Function to calculate effects for individually matched case-control studies |
entry | Time series and other methods for Lexis objects |
Epi | Epi: Functions for manipulation and statistical analysis of epidemiological data |
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' or 'etm'. |
etm.Lexis | Create a data structures suitable for use with packages 'mstate' or 'etm'. |
ewrates | Rates of lung and nasal cancer mortality, and total mortality. |
exit | Time series and other methods for Lexis objects |
expand.data | Function to expand data for regression analysis of interval censored data. |
factorize | Transform a Lexis (or stacked.Lexis) object |
factorize.Lexis | Transform a Lexis (or stacked.Lexis) object |
fgrep | Convenience versions of grep |
fillarr | Draw boxes and arrows for illustration of multistate models. |
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 |
ftrend | Fit a floating trend to a factor in generalized linear model |
gam.Lexis | Fit intensity models to follow-up data in Lexis objects |
gen.exp | Generate covariates for drug-exposure follow-up from drug purchase records. |
glm.Lexis | Fit intensity models to follow-up data in Lexis objects |
gmortDK | Population mortality rates for Denmark in 5-years age groups. |
harm | Create a basis of harmonic functions. |
hivDK | hivDK: seroconversion in a cohort of Danish men |
Icens | Fits a regression model to interval censored data. |
id.span | Is 'x' in the column span of matrix 'A' and what columns are linearly dependent? |
idSpan | Is 'x' in the column span of matrix 'A' and what columns are linearly dependent? |
in.span | Is 'x' in the column span of matrix 'A' and what columns are linearly dependent? |
inSpan | Is 'x' in the column span of matrix 'A' and what columns are linearly dependent? |
LCa.fit | Fit Lee-Carter-type models for rates to arbitrarily shaped observations of rates in a Lexis diagram. |
legendbox | Draw a box with text explaining the numbers in and between boxes from 'boxes.MS' and 'boxes.Lexis' |
lep | An unmatched case-control study of leprosy incidence |
levels.Lexis | Transform a Lexis (or stacked.Lexis) object |
Lexis | Create a Lexis object of follow-up |
Lexis.diagram | Plot a Lexis diagram |
Lexis.lines | Draw life lines in a Lexis diagram. |
Lexis2msm | Convert a Lexis obejct to a data set suitable for input to the 'msm:msm' function. |
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.dk | Mortality in Denmark 1974 ff. |
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 events |
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' or 'etm'. |
msdata.Lexis | Create a data structures suitable for use with packages 'mstate' or 'etm'. |
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 |
nid | Create a bootstrap sample of persons (as identified by 'lex.id') from a Lexis object |
nid.Lexis | Create a bootstrap sample of persons (as identified by 'lex.id') from a Lexis object |
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. |
occup | A small occupational cohort |
order.Lexis | Transform a Lexis (or stacked.Lexis) object |
orderLexis | Transform a Lexis (or stacked.Lexis) object |
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.matshade | 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) |
poisreg | Family Object for Poisson Regression |
Pplot | Functions to plot rates from a table classified by age and calendar time (period) |
pr | Diabetes prevance as of 2010-01-01 in Denmark |
preceding | Time series and other methods for Lexis objects |
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.Lexis | Create a Lexis object of follow-up |
print.mh | Mantel-Haenszel analyses of cohort and case-control studies |
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 |
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 |
rcutLexis | A function to cut follow-up at intermediate event times. |
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) object |
rm.tr | Remove transitions from a Lexis object. |
ROC | Function to compute and draw ROC-curves. |
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. |
sortLexis | Transform a Lexis (or stacked.Lexis) object |
splitLexis | Split follow-up time in a Lexis object |
st2alb | Clinical trial: Steno2 baseline and follow-up. |
st2clin | Clinical trial: Steno2 baseline and follow-up. |
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 and other methods for Lexis objects |
steno2 | Clinical trial: Steno2 baseline and follow-up. |
subset.Lexis | Subsetting Lexis (and stacked.Lexis) objects |
subset.stacked.Lexis | Subsetting Lexis (and stacked.Lexis) objects |
succeeding | Time series and other methods for Lexis objects |
summary.Icens | Fits a regression model to interval censored data. |
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. |
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 |
thinCol | Is 'x' in the column span of matrix 'A' and what columns are linearly dependent? |
thoro | Thorotrast Study |
timeBand | Extract time band data from a split Lexis object |
timeScales | The time scales of a Lexis object |
timeSince | 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) object |
transform.stacked.Lexis | Transform a Lexis (or stacked.Lexis) object |
transient | Time series and other methods for Lexis objects |
tsNA20 | The time scales of a Lexis object |
twoby2 | Analysis of a two by two table |
unLexis | Remove Lexis attributes from a 'Lexis' object. |
Wald | Compute linear functions of parameters with standard errors and confidence limits, optionally transforming to a different scale. |
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. |
ZArray | Set up an array of NAs, solely from the list of dimnames |
[.Lexis | Subsetting Lexis (and stacked.Lexis) objects |