# Functions for Epidemiological Analysis using Population Data

## Documentation for package ‘popEpi’ version 0.4.9

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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
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 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