Functions for Epidemiological Analysis using Population Data

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Documentation for package ‘popEpi’ version 0.4.11

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help 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
array_df_ratetable_utils	'array's, 'data.frame's and 'ratetable's
array_to_long_df	'array's, 'data.frame's and 'ratetable's
array_to_long_dt	'array's, 'data.frame's and 'ratetable's
array_to_ratetable	'array's, 'data.frame's and 'ratetable's
as.aggre	Coercion to Class 'aggre'
as.aggre.data.frame	Coercion to Class 'aggre'
as.aggre.data.table	Coercion to Class 'aggre'
as.aggre.default	Coercion to Class 'aggre'
as.Date.yrs	Coerce Fractional Year Values to Date Values
cast_simple	Cast 'data.table'/'data.frame' from long format to wide format
cut_bound	Change output values from cut(..., labels = NULL) output
direct_adjusting	Direct Adjusting in 'popEpi' Using Weights
direct_standardization	Direct Adjusting in 'popEpi' Using Weights
expr.by.cj	Tabulate Counts and Other Functions by Multiple Variables into a Long-Format Table
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 Time Scales
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
long_df_to_array	'array's, 'data.frame's and 'ratetable's
long_df_to_ratetable	'array's, 'data.frame's and 'ratetable's
long_dt_to_array	'array's, 'data.frame's and 'ratetable's
long_dt_to_ratetable	'array's, 'data.frame's and 'ratetable's
lower_bound	Return lower_bound value from char string (20,30]
ltable	Tabulate Counts and Other Functions by Multiple Variables into a Long-Format Table
meanpop_fi	Mean population counts in Finland year, sex, and age group.
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
pophaz	Expected / Population Hazard Data Sets Usage in 'popEpi'
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'.
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
ratetable_to_array	'array's, 'data.frame's and 'ratetable's
ratetable_to_long_df	'array's, 'data.frame's and 'ratetable's
ratetable_to_long_dt	'array's, 'data.frame's and 'ratetable's
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 (convenience function for 'setattr(obj, "class", CLASS)'); can add instead of replace
setcolsnull	Delete 'data.table' columns if there
sibr	sibr - a simulated cohort of Finnish female breast cancer patients
sir	Calculate SIR or SMR
sire	sire - a simulated cohort of Finnish female rectal cancer patients
sirspline	Estimate splines for SIR or SMR
sir_ag	Calculate SMR
sir_exp	Calculate SMR
sir_lex	Calculate SMR
sir_ratio	Confidence intervals for the ratio of two SIRs/SMRs
splitLexisDT	Split case-level observations
splitMulti	Split case-level observations
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.
summary.aggre	Summarize an 'aggre' Object
summary.survtab	Summarize a survtab Object
Surv	Survival Objects
survmean	Compute Mean Survival Times Using Extrapolation
survtab	Estimate Survival Time Functions
survtab_ag	Estimate Survival Time Functions
try2int	Attempt coercion to integer