Functions for Epidemiological Analysis using Population Data


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Documentation for package ‘popEpi’ version 0.4.12

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