Package: popEpi 0.4.12

Joonas Miettinen

popEpi: Functions for Epidemiological Analysis using Population Data

Enables computation of epidemiological statistics, including those where counts or mortality rates of the reference population are used. Currently supported: excess hazard models (Dickman, Sloggett, Hills, and Hakulinen (2012) <doi:10.1002/sim.1597>), rates, mean survival times, relative/net survival (in particular the Ederer II (Ederer and Heise (1959)) and Pohar Perme (Pohar Perme, Stare, and Esteve (2012) <doi:10.1111/j.1541-0420.2011.01640.x>) estimators), and standardized incidence and mortality ratios, all of which can be easily adjusted for by covariates such as age. Fast splitting and aggregation of 'Lexis' objects (from package 'Epi') and other computations achieved using 'data.table'.

Authors:Joonas Miettinen [cre, aut], Matti Rantanen [aut], Karri Seppa [ctb]

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popEpi.pdf |popEpi.html✨
popEpi/json (API)
NEWS

# Install 'popEpi' in R:
install.packages('popEpi', repos = c('https://epiverse-connect.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/finnishcancerregistry/popepi/issues

Datasets:
  • ICSS - Age standardisation weights from the ICSS scheme.
  • meanpop_fi - Mean population counts in Finland year, sex, and age group.
  • popmort - Population mortality rates in Finland 1951 - 2013 in 101 age groups and by gender. This is an example of a population hazard table as used in 'popEpi'; for the general help page, see 'pophaz'.
  • sibr - Sibr - a simulated cohort of Finnish female breast cancer patients
  • sire - Sire - a simulated cohort of Finnish female rectal cancer patients
  • stdpop101 - World standard population by 1 year age groups from 1 to 101. Sums to 100 000.
  • stdpop18 - Standard populations from 2000: world, Europe and Nordic.

On CRAN:

adjust-estimatesage-adjustingdirect-adjustingepidemiologyindirect-adjustingsurvival

7.16 score 8 stars 96 scripts 1.6k downloads 2 mentions 50 exports 31 dependencies

Last updated 5 months agofrom:9041b96e37. Checks:OK: 3 NOTE: 2 ERROR: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 10 2024
R-4.5-winNOTEOct 10 2024
R-4.5-linuxNOTEOct 10 2024
R-4.4-winOKOct 10 2024
R-4.4-macOKOct 10 2024
R-4.3-winERROROct 10 2024
R-4.3-macERROROct 10 2024

Exports:adjustaggreall_names_presentarray_to_long_dfarray_to_long_dtarray_to_ratetableas.aggrecast_simplecut_boundexpr.by.cjfac2numget.yrsis_leap_yearis.DateLexis_fpalexpandlong_df_to_arraylong_df_to_ratetablelong_dt_to_arraylong_dt_to_ratetablelower_boundltablena2zeropoisson.ciprepExporaterate_ratioratetable_to_arrayratetable_to_long_dfratetable_to_long_dtrelpoisrelpois_agrobust_valuesrpcurveRPLsetaggresetcolsnullsirsir_agsir_expsir_lexsir_ratiosirsplinesplitLexisDTsplitMultiSurvsurvmeansurvtabsurvtab_agtry2int

Dependencies:clicmprskdata.tabledplyrEpietmfansigenericsgluelatticelifecyclemagrittrMASSMatrixmgcvnlmenumDerivpillarpkgconfigplyrR6RcppRcppArmadillorlangsurvivaltibbletidyselectutf8vctrswithrzoo

SMR Vignette

Matti Rantanen

Rendered fromsir.Rmdusingknitr::rmarkdownon Oct 10 2024.

Last update: 2022-09-14
Started: 2015-09-23

Examples of using survtab

Joonas Miettinen

Rendered fromsurvtab_examples.Rmdusingknitr::rmarkdownon Oct 10 2024.

Last update: 2019-09-04
Started: 2015-09-23

Readme and manuals

Help Manual

Help pageTopics
Adjust Estimates by Categorical Variablesadjust
Aggregation of split 'Lexis' dataaggre
Check if all names are present in given dataall_names_present
`array`s, `data.frame`s and `ratetable`sarray_df_ratetable_utils array_to_long_df array_to_long_dt array_to_ratetable long_df_to_array long_df_to_ratetable long_dt_to_array long_dt_to_ratetable ratetable_to_array ratetable_to_long_df ratetable_to_long_dt
Coercion to Class 'aggre'as.aggre as.aggre.data.frame as.aggre.data.table as.aggre.default
Coerce Fractional Year Values to Date Valuesas.Date.yrs
Cast 'data.table'/'data.frame' from long format to wide formatcast_simple
Change output values from cut(..., labels = NULL) outputcut_bound
Direct Adjusting in 'popEpi' Using Weightsdirect_adjusting direct_standardization
Convert factor variable to numericfac2num
Flexible Variable Usage in 'popEpi' Functionsflexible_argument
Convert date objects to fractional yearsget.yrs
Age standardisation weights from the ICSS scheme.ICSS
Detect leap yearsis_leap_year
Test if object is a 'Date' objectis.Date
Create a Lexis Object with Follow-up Time, Period, and Age Time ScalesLexis_fpa
Split case-level observationslexpand
lines method for sirspline-objectlines.sirspline
Graphically Inspect Curves Used in Mean Survival Computationlines.survmean
'lines' method for survtab objectslines.survtab
Return lower_bound value from char string (20,30]lower_bound
Tabulate Counts and Other Functions by Multiple Variables into a Long-Format Tableexpr.by.cj ltable
Mean population counts in Finland year, sex, and age group.meanpop_fi
Convert NA's to zero in data.tablena2zero
plot method for rate objectplot.rate
Plot method for sir-objectplot.sir
'plot' method for sirspline-objectplot.sirspline
Graphically Inspect Curves Used in Mean Survival Computationplot.survmean
'plot' method for survtab objectsplot.survtab
Get rate and exact Poisson confidence intervalspoisson.ci
Expected / Population Hazard Data Sets Usage in 'popEpi'pophaz
Population mortality rates in Finland 1951 - 2013 in 101 age groups and by gender. This is an example of a population hazard table as used in 'popEpi'; for the general help page, see 'pophaz'.popmort
Prepare Exposure Data for AggregationprepExpo
Print an 'aggre' Objectprint.aggre
Print an rate objectprint.rate
Print a survtab Objectprint.survtab
Direct-Standardised Incidence/Mortality Ratesrate
Confidence intervals for the rate ratiosrate_ratio
Excess hazard Poisson modelrelpois
Excess hazard Poisson modelrelpois_ag
Convert values to numeric robustlyrobust_values
Marginal piecewise parametric relative survival curverpcurve
Relative Poisson family objectRPL
Set 'aggre' attributes to an object by modifying in placesetaggre
Set the class of an object (convenience function for 'setattr(obj, "class", CLASS)'); can add instead of replacesetclass
Delete 'data.table' columns if theresetcolsnull
sibr - a simulated cohort of Finnish female breast cancer patientssibr
Calculate SIR or SMRsir
Calculate SMRsir_ag sir_exp sir_lex
Confidence intervals for the ratio of two SIRs/SMRssir_ratio
sire - a simulated cohort of Finnish female rectal cancer patientssire
Estimate splines for SIR or SMRsirspline
Split case-level observationssplitLexisDT
Split case-level observationssplitMulti
World standard population by 1 year age groups from 1 to 101. Sums to 100 000.stdpop101
Standard populations from 2000: world, Europe and Nordic.stdpop18
Summarize an 'aggre' Objectsummary.aggre
Summarize a survtab Objectsummary.survtab
Survival ObjectsSurv
Compute Mean Survival Times Using Extrapolationsurvmean
Estimate Survival Time Functionssurvtab
Estimate Survival Time Functionssurvtab_ag
Attempt coercion to integertry2int