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popEpi (version 0.3.0)

Functions for Epidemiological Analysis using Population Data

Description

Enables computation of various epidemiological statistics where the use of population data such as population counts and hazards is required. Relatively high computation speed achieved by using data.table.

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Install

install.packages('popEpi')

Monthly Downloads

3,282

Version

0.3.0

License

GPL-3

Issues

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Repository

https://github.com/WetRobot/popEpi

Maintainer

Joonas Miettinen

Last Published

March 31st, 2016

Functions in popEpi (0.3.0)

sire - a simulated cohort of Finnish female rectal cancer patients

Coerce Fractional Year Values to Date Values

Graphically Inspect Curves Used in Mean Survival Computation

Convert NA's to zero in data.table

Print an aggre Object

Coercion to Class aggre

World standard population by 1 year agegroups from 1 to 101. Sums to 100 000.

Marginal piecewise parametric relative survival curve

Return lower_bound value from char string (20,30]

Convert date objects to fractional years

Summaryize an aggre Object

longDF2ratetable

Experimental: Coerce a long-format data.frame to a ratetable object

all_names_present

Check if all names are present in given data

Estimate Survival Time Functions

Make a data.table of Tabulated, Aggregated Values and Weights

Change output values from cut(..., labels = NULL) output

Plot method for sir-object

Convert values to numeric robustly

Split case-level observations

Adjust Estimates by Categorical Variables

direct_standardization

Direct Adjusting in popEpi Using Weights

Print method for sir objects

Shift a variable to create lag or lead values

Aggregation of split Lexis data

lines method for survtab objects

Relative Poisson family object

as.data.frame.ratetable

Coerce a ratetable Object to Class data.frame

Print a survtab Object

Excess hazard Poisson model

Age standardisation weights from the ICSS scheme.

flexible_argument

Flexible Variable Usage in popEpi Functions

Graphically Inspect Curves Used in Mean Survival Computation

lines.sirspline

lines method for sirspline-object

Delete data.table columns if there

Test if object is a Date object

popEpi: Functions for large-scale epidemiological analysis

Detect leap years

Tabulate Counts and Other Functions by Multiple Variables into a Long-Format Table

Split case-level observations

Compute Mean Survival Times Using Extrapolation

Prepare Exposure Data for Aggregation

Cast data.table/data.frame from long format to wide format

Set 'aggre' attributes to an object by modifying in place

plot method for sirspline-object

Standard populations from 2000: world, europe and nordic.

Expected / Population Hazard Data Sets Usage in popEpi

print.sirspline

Print method for sirspline objects

Set the class of an object (convencience function for setattr(obj, "class", CLASS)); can add instead of replace

Split case-level observations

Direct-Standardised Incidence/Mortality Rates

as.data.table.ratetable

Coerce a ratetable Object to Class data.table

Population mortality rates in Finland 1951 - 2013 in 101 age groups and by gender

plot method for survtab objects

Calculate SIR or SMR

Get rate and exact Poisson confidence intervals

Convert factor variable to numeric

Excess hazard Poisson model

summary.survtab

Summarize a survtab Object

Estimate splines for SIR or SMR

sibr - a simulated cohort of Finnish female breast cancer patients

Attempt coercion to integer