popEpi: Functions for Epidemiological Analysis using Population Data

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Enables computation of epidemiological statistics where e.g. counts or mortality rates of the reference population are used. Currently supported: excess hazard models, rates, mean survival times, relative survival, as well as standardized incidence and mortality ratios (SIRs/SMRs), all of which can be easily adjusted for e.g. age. Fast splitting and aggregation of 'Lexis' objects (from package 'Epi') and other computations achieved using 'data.table'.

Author
Joonas Miettinen [aut, cre], Matti Rantanen [aut], Karri Seppa [ctb]
Date of publication
2016-11-08 18:36:05
Maintainer
Joonas Miettinen <joonas.miettinen@cancer.fi>
License
GPL-3
Version
0.4.1
URLs

View on CRAN

Man pages

adjust
Adjust Estimates by Categorical Variables
aggre
Aggregation of split 'Lexis' data
all_names_present
Check if all names are present in given data
as.aggre
Coercion to Class 'aggre'
as.data.frame.ratetable
Coerce a 'ratetable' Object to Class 'data.frame'
as.data.table.ratetable
Coerce a 'ratetable' Object to Class 'data.table'
as.Date.yrs
Coerce Fractional Year Values to Date Values
cast_simple
Cast 'data.table'/'data.frame' from long format to wide...
cut_bound
Change output values from cut(..., labels = NULL) output
direct_standardization
Direct Adjusting in 'popEpi' Using Weights
fac2num
Convert factor variable to numeric
flexible_argument
Flexible Variable Usage in 'popEpi' Functions
get.yrs
Convert date objects to fractional years
ICSS
Age standardisation weights from the ICSS scheme.
is.Date
Test if object is a 'Date' object
is_leap_year
Detect leap years
Lexis_fpa
Create a Lexis Object with Follow-up Time, Period, and Age...
lexpand
Split case-level observations
lines.sirspline
lines method for sirspline-object
lines.survmean
Graphically Inspect Curves Used in Mean Survival Computation
lines.survtab
'lines' method for survtab objects
longDF2ratetable
*Experimental*: Coerce a long-format 'data.frame' to a...
lower_bound
Return lower_bound value from char string (20,30]
ltable
Tabulate Counts and Other Functions by Multiple Variables...
makeWeightsDT
Make a 'data.table' of Tabulated, Aggregated Values and...
na2zero
Convert NA's to zero in data.table
plot.rate
plot method for rate object
plot.sir
Plot method for sir-object
plot.sirspline
'plot' method for sirspline-object
plot.survmean
Graphically Inspect Curves Used in Mean Survival Computation
plot.survtab
'plot' method for survtab objects
poisson.ci
Get rate and exact Poisson confidence intervals
popEpi
popEpi: Functions for large-scale epidemiological analysis
pophaz
Expected / Population Hazard Data Sets Usage in 'popEpi'
popmort
Population mortality rates in Finland 1951 - 2013 in 101 age...
prepExpo
Prepare Exposure Data for Aggregation
print.aggre
Print an aggre Object
print.rate
Print an rate object
print.survtab
Print a survtab Object
rate
Direct-Standardised Incidence/Mortality Rates
rate_ratio
Confidence intervals for the rate ratios
relpois
Excess hazard Poisson model
relpois_ag
Excess hazard Poisson model
robust_values
Convert values to numeric robustly
rpcurve
Marginal piecewise parametric relative survival curve
RPL
Relative Poisson family object
setaggre
Set 'aggre' attributes to an object by modifying in place
setclass
Set the class of an object (convencience function for...
setcolsnull
Delete 'data.table' columns if there
sibr
sibr - a simulated cohort of Finnish female breast cancer...
sir
Calculate SIR or SMR
sire
sire - a simulated cohort of Finnish female rectal cancer...
sir_exp
Calculate SMR
sir_ratio
Confidence intervals for the ratio of two SIRs/SMRs
sirspline
Estimate splines for SIR or SMR
splitLexisDT
Split case-level observations
splitMulti
Split case-level observations
stdpop101
World standard population by 1 year agegroups from 1 to 101....
stdpop18
Standard populations from 2000: world, europe and nordic.
summary.aggre
Summarize an aggre Object
summary.survtab
Summarize a survtab Object
survmean
Compute Mean Survival Times Using Extrapolation
survtab
Estimate Survival Time Functions
survtab_ag
Estimate Survival Time Functions
try2int
Attempt coercion to integer

Files in this package

popEpi
popEpi/inst
popEpi/inst/doc
popEpi/inst/doc/survtab_examples.html
popEpi/inst/doc/sir.R
popEpi/inst/doc/survtab_examples.R
popEpi/inst/doc/sir.html
popEpi/tests
popEpi/tests/testthat.R
popEpi/tests/testthat
popEpi/tests/testthat/test_utils.R
popEpi/tests/testthat/test_aggre.R
popEpi/tests/testthat/test_splitMulti.R
popEpi/tests/testthat/test_survtab_observed.R
popEpi/tests/testthat/test_survtab_bad_surv_ints.R
popEpi/tests/testthat/test_mean_survival.R
popEpi/tests/testthat/test_lexpand.R
popEpi/tests/testthat/test_relpois_mean_curve.R
popEpi/tests/testthat/test_survtab_usage.R
popEpi/tests/testthat/test_rate.R
popEpi/tests/testthat/test_survtab_relative.R
popEpi/tests/testthat/test_splitLexisDT.R
popEpi/tests/testthat/test_sir.R
popEpi/tests/testthat/test_weighter.R
popEpi/tests/testthat/test_expo.R
popEpi/NAMESPACE
popEpi/NEWS
popEpi/NEWS.md
popEpi/data
popEpi/data/stdpop18.rdata
popEpi/data/sibr.rdata
popEpi/data/popmort.rdata
popEpi/data/ICSS.rdata
popEpi/data/stdpop101.rdata
popEpi/data/sire.rdata
popEpi/R
popEpi/R/survival_utility_functions.R
popEpi/R/evaluation.R
popEpi/R/incidence_rates.R
popEpi/R/lexpand2.R
popEpi/R/relative_poisson_net_survival.R
popEpi/R/weighted_table.R
popEpi/R/ltable.R
popEpi/R/direct_adjusting.R
popEpi/R/relative_poisson.R
popEpi/R/data_document.R
popEpi/R/sir.R
popEpi/R/splitting_utility_functions.R
popEpi/R/splitLexisDT.R
popEpi/R/popEpi_package.r
popEpi/R/splitMulti.R
popEpi/R/aggregating.R
popEpi/R/mean_survival.R
popEpi/R/S3_definitions.R
popEpi/R/prevalence.R
popEpi/R/flexyargs.R
popEpi/R/incidence_rates_utils.R
popEpi/R/pophaz.R
popEpi/R/utility_functions.R
popEpi/R/lifetime_function.R
popEpi/R/fractional_years.R
popEpi/R/startup_message.R
popEpi/R/survival_lexis.R
popEpi/R/survival_aggregated.R
popEpi/R/lexpand.R
popEpi/R/sir_utils.R
popEpi/README.md
popEpi/MD5
popEpi/build
popEpi/build/vignette.rds
popEpi/DESCRIPTION
popEpi/man
popEpi/man/stdpop18.Rd
popEpi/man/sire.Rd
popEpi/man/survtab.Rd
popEpi/man/as.aggre.Rd
popEpi/man/direct_standardization.Rd
popEpi/man/survmean.Rd
popEpi/man/as.data.frame.ratetable.Rd
popEpi/man/poisson.ci.Rd
popEpi/man/setaggre.Rd
popEpi/man/lines.survtab.Rd
popEpi/man/popEpi.Rd
popEpi/man/summary.aggre.Rd
popEpi/man/cut_bound.Rd
popEpi/man/rpcurve.Rd
popEpi/man/all_names_present.Rd
popEpi/man/setcolsnull.Rd
popEpi/man/fac2num.Rd
popEpi/man/longDF2ratetable.Rd
popEpi/man/flexible_argument.Rd
popEpi/man/plot.sirspline.Rd
popEpi/man/rate.Rd
popEpi/man/robust_values.Rd
popEpi/man/stdpop101.Rd
popEpi/man/sirspline.Rd
popEpi/man/ICSS.Rd
popEpi/man/lines.survmean.Rd
popEpi/man/makeWeightsDT.Rd
popEpi/man/relpois.Rd
popEpi/man/as.Date.yrs.Rd
popEpi/man/adjust.Rd
popEpi/man/print.survtab.Rd
popEpi/man/lower_bound.Rd
popEpi/man/sir.Rd
popEpi/man/plot.rate.Rd
popEpi/man/sibr.Rd
popEpi/man/cast_simple.Rd
popEpi/man/lexpand.Rd
popEpi/man/summary.survtab.Rd
popEpi/man/plot.survmean.Rd
popEpi/man/ltable.Rd
popEpi/man/survtab_ag.Rd
popEpi/man/popmort.Rd
popEpi/man/get.yrs.Rd
popEpi/man/splitLexisDT.Rd
popEpi/man/as.data.table.ratetable.Rd
popEpi/man/print.rate.Rd
popEpi/man/sir_exp.Rd
popEpi/man/rate_ratio.Rd
popEpi/man/is.Date.Rd
popEpi/man/prepExpo.Rd
popEpi/man/plot.survtab.Rd
popEpi/man/Lexis_fpa.Rd
popEpi/man/na2zero.Rd
popEpi/man/sir_ratio.Rd
popEpi/man/print.aggre.Rd
popEpi/man/try2int.Rd
popEpi/man/relpois_ag.Rd
popEpi/man/splitMulti.Rd
popEpi/man/pophaz.Rd
popEpi/man/aggre.Rd
popEpi/man/RPL.Rd
popEpi/man/setclass.Rd
popEpi/man/lines.sirspline.Rd
popEpi/man/plot.sir.Rd
popEpi/man/is_leap_year.Rd