popEpi: Functions for Epidemiological Analysis using Population Data

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'.

AuthorJoonas Miettinen [aut, cre], Matti Rantanen [aut], Karri Seppa [ctb]
Date of publication2016-11-08 18:36:05
MaintainerJoonas Miettinen <joonas.miettinen@cancer.fi>
LicenseGPL-3
Version0.4.1
https://github.com/WetRobot/popEpi

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.