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popEpi (version 0.2.1)

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

1,841

Version

0.2.1

License

GPL-3

Issues

39

Pull Requests

0

Stars

8

Forks

7

Maintainer

Joonas Miettinen

Last Published

September 29th, 2015

Functions in popEpi (0.2.1)

is.Date

Test if object is a Date object
fac2num

Convert factor variable to numeric
RPL

Relative Poisson family object
all_names_present

Check if all names are present in given data
as.pe.Lexis

Add class 'pe' to a Lexis object.
na2zero

Convert NA's to zero in data.table
plot.sir

Plot method for sir-object
shift.var

Shifts a variable to create lag or lead values
setclass

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

Return lower_bound value from char string (20,30]
poisson.ci

Get rate and exact Poisson confidence intervals
splitLexisDT

Split case-level observations
lines.survtab

lines method for survtab objects
sire

sire - a simulated cohort of Finnish female rectal cancer patients
as.data.frame.ratetable

Coerce a ratetable object to data.frame
try2int

Attempts to convert a numeric object to integer, but won't if loss of information is imminent
ltable

Tabulate counts and other functions with multiple factors into a long-format table
print.sirspline

Print method for sirspline objects
longDF2ratetable

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

Tabulate counts and other functions with multiple factors into a long-format table
cut_bound

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

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

Add class 'pe' to a data.table object.
as.pe.list

Add class 'pe' to a list object.
is_leap_year

Detect leap years
ICSS

Age standardization weights from the ICSS scheme.
plot.pe

Plot methods for popEpi objects
get.yrs

Convert date objects to fractional years
plot.sirspline

Plot method for sirspline-object
lexpand

Split case-level observations
plot.survtab

plot method for survtab objects
rpcurve

Marginal piecewise parametric relative survival curve
sibr

sibr - a simulated cohort of Finnish female breast cancer patients
setcolsnull

Delete data.table columns if there
splitMulti

Split case-level observations
survtab

Survival tables
relpois

Excess hazard Poisson model
as.data.table.ratetable

Coerce a ratetable object to data.table
popEpi

popEpi: Functions for large-scale epidemiological analysis
print.sir

Print method for sir objects
popmort

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

Estimate splines for SIR or SMR
robust_values

Convert values to numeric robustly
sir

Calculate SIR or SMR
survmean

Compute mean survival times using extrapolation