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'.

Install the latest version of this package by entering the following in R:
install.packages("popEpi")
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

Functions

adjust Man page
aggre Man page
all_names_present Man page
as.aggre Man page
as.aggre.data.frame Man page
as.aggre.data.table Man page
as.aggre.default Man page
as.data.frame.ratetable Man page
as.data.table.ratetable Man page
as.Date.yrs Man page
cast_simple Man page
cut_bound Man page
direct_adjusting Man page
direct_standardization Man page
expr.by.cj Man page
fac2num Man page
flexible_argument Man page
get.yrs Man page
ICSS Man page
is.Date Man page
is_leap_year Man page
Lexis_fpa Man page
lexpand Man page
lines.sirspline Man page
lines.survmean Man page
lines.survtab Man page
longDF2ratetable Man page
lower_bound Man page
ltable Man page
makeWeightsDT Man page
na2zero Man page
plot.rate Man page
plot.sir Man page
plot.sirspline Man page
plot.survmean Man page
plot.survtab Man page
poisson.ci Man page
popEpi Man page
popEpi-package Man page
pophaz Man page
popmort Man page
prepExpo Man page
print.aggre Man page
print.rate Man page
print.survtab Man page
rate Man page
rate_ratio Man page
relpois Man page
relpois_ag Man page
robust_values Man page
rpcurve Man page
RPL Man page
setaggre Man page
setclass Man page
setcolsnull Man page
sibr Man page
sir Man page
sir_ag Man page
sire Man page
sir_exp Man page
sir_lex Man page
sir_ratio Man page
sirspline Man page
splitLexisDT Man page
splitMulti Man page
stdpop101 Man page
stdpop18 Man page
summary.aggre Man page
summary.survtab Man page
survmean Man page
survtab Man page
survtab_ag Man page
try2int Man page

Files

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

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

Please suggest features or report bugs with the GitHub issue tracker.

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