Tools for the Analysis of Epidemiological Data


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Documentation for package ‘epiR’ version 2.0.35

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E P R S

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epi.2by2 Summary measures for count data presented in a 2 by 2 table
epi.about The library epiR: summary information
epi.asc Write matrix to an ASCII raster file
epi.betabuster An R version of Wes Johnson and Chun-Lung Su's Betabuster
epi.blcm.paras Number of parameters to be inferred and number of informative priors required for a Bayesian latent class model
epi.bohning Bohning's test for overdispersion of Poisson data
epi.ccc Concordance correlation coefficient
epi.conf Confidence intervals for means, proportions, incidence, and standardised mortality ratios
epi.convgrid Convert British National Grid georeferences to easting and northing coordinates
epi.cp Extract unique covariate patterns from a data set
epi.cpresids Covariate pattern residuals from a logistic regression model
epi.descriptives Descriptive statistics
epi.dgamma Estimate the precision of a [structured] heterogeneity term
epi.directadj Directly adjusted incidence rate estimates
epi.dms Decimal degrees and degrees, minutes and seconds conversion
epi.dsl Mixed-effects meta-analysis of binary outcomes using the DerSimonian and Laird method
epi.edr Estimated dissemination ratio
epi.empbayes Empirical Bayes estimates of observed event counts
epi.epidural Rates of use of epidural anaesthesia in trials of caregiver support
epi.herdtest Estimate the characteristics of diagnostic tests applied at the herd (group) level
epi.incin Laryngeal and lung cancer cases in Lancashire 1974 - 1983
epi.indirectadj Indirectly adjusted incidence risk estimates
epi.insthaz Event instantaneous hazard based on Kaplan-Meier survival estimates
epi.interaction Relative excess risk due to interaction in a case-control study
epi.iv Fixed-effects meta-analysis of binary outcomes using the inverse variance method
epi.kappa Kappa statistic
epi.ltd Lactation to date and standard lactation milk yields
epi.mh Fixed-effects meta-analysis of binary outcomes using the Mantel-Haenszel method
epi.nomogram Post-test probability of disease given sensitivity and specificity of a test
epi.occc Overall concordance correlation coefficient (OCCC)
epi.offset Create offset vector
epi.pooled Estimate herd test characteristics when pooled sampling is used
epi.popsize Estimate population size on the basis of capture-recapture sampling
epi.prcc Partial rank correlation coefficients
epi.prev Estimate true prevalence
epi.psi Proportional similarity index
epi.RtoBUGS R to WinBUGS data conversion
epi.SClip Lip cancer in Scotland 1975 - 1980
epi.smd Fixed-effects meta-analysis of continuous outcomes using the standardised mean difference method
epi.smr Confidence intervals and tests of significance of the standardised mortality [morbidity] ratio
epi.sscc Sample size, power or minimum detectable odds ratio for an unmatched or matched case-control study
epi.ssclus1estb Sample size to estimate a binary outcome using one-stage cluster sampling
epi.ssclus1estc Sample size to estimate a continuous outcome using one-stage cluster sampling
epi.ssclus2estb Number of clusters to be sampled to estimate a binary outcome using two-stage cluster sampling
epi.ssclus2estc Number of clusters to be sampled to estimate a continuous outcome using two-stage cluster sampling
epi.sscohortc Sample size, power or minimum detectable incidence risk ratio for a cohort study using individual count data
epi.sscohortt Sample size, power or minimum detectable incidence rate ratio for a cohort study using person or animal time data
epi.sscompb Sample size, power and minimum detectable risk ratio when comparing binary outcomes
epi.sscompc Sample size, power and minimum detectable difference when comparing continuous outcomes
epi.sscomps Sample size, power and minimum detectable hazard when comparing time to event
epi.ssdetect Sample size to detect an event
epi.ssdxsesp Sample size to estimate the sensitivity or specificity of a diagnostic test
epi.ssdxtest Sample size to validate a diagnostic test in the absence of a gold standard
epi.ssequb Sample size for a parallel equivalence trial, binary outcome
epi.ssequc Sample size for a parallel equivalence trial, continuous outcome
epi.ssninfb Sample size for a non-inferiority trial, binary outcome
epi.ssninfc Sample size for a non-inferiority trial, continuous outcome
epi.sssimpleestb Sample size to estimate a binary outcome using simple random sampling
epi.sssimpleestc Sample size to estimate a continuous outcome using simple random sampling
epi.ssstrataestb Sample size to estimate a binary outcome using stratified random sampling
epi.ssstrataestc Sample size to estimate a continuous outcome using a stratified random sampling design
epi.sssupb Sample size for a parallel superiority trial, binary outcome
epi.sssupc Sample size for a parallel superiority trial, continuous outcome
epi.ssxsectn Sample size, power or minimum detectable prevalence ratio or odds ratio for a cross-sectional study
epi.tests Sensitivity, specificity and predictive value of a diagnostic test

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print.epi.2by2 Summary measures for count data presented in a 2 by 2 table
print.epi.occc Overall concordance correlation coefficient (OCCC)
print.epi.tests Sensitivity, specificity and predictive value of a diagnostic test

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rsu.adjrisk Adjusted risk values
rsu.dxtest Sensitivity and specificity of diagnostic tests interpreted in series or parallel
rsu.epinf Effective probability of disease
rsu.pfree.equ Equilibrium probability of disease freedom assuming representative or risk based sampling
rsu.pfree.rs Calculate Probability of freedom for given population sensitivity and probability of introduction
rsu.pstar Design prevalence back calculation
rsu.sep Probability that the prevalence of disease in a population is less than or equal to a specified design prevalence
rsu.sep.cens Surveillance system sensitivity assuming data from a population census
rsu.sep.pass Surveillance system sensitivity assuming passive surveillance and representative sampling within clusters
rsu.sep.rb Surveillance system sensitivity assuming risk-based sampling and varying unit sensitivity
rsu.sep.rb1rf Surveillance system sensitivity assuming risk-based sampling on one risk factor
rsu.sep.rb2rf Surveillance system sensitivity assuming risk-based sampling on two risk factors
rsu.sep.rb2st Surveillance system sensitivity assuming risk based, two-stage sampling
rsu.sep.rbvarse Surveillance system sensitivity assuming risk based sampling and varying unit sensitivity
rsu.sep.rs Surveillance system sensitivity assuming representative sampling
rsu.sep.rs2st Surveillance system sensitivity assuming representative two-stage sampling
rsu.sep.rsfreecalc Surveillance system sensitivity for detection of disease assuming representative sampling and imperfect test sensitivity and specificity.
rsu.sep.rsmult Surveillance system sensitivity by combining multiple surveillance components
rsu.sep.rspool Surveillance system sensitivity assuming representative sampling, imperfect pooled sensitivity and perfect pooled specificity
rsu.sep.rsvarse Surveillance system sensitivity assuming representative sampling and varying unit sensitivity
rsu.spp.rs Surveillance system specificity assuming representative sampling
rsu.sspfree.rs Sample size to achieve a desired probability of disease freedom assuming representative sampling
rsu.sssep.rb2st1rf Sample size to achieve a desired surveillance system sensitivity assuming risk-based 2-stage sampling on one risk factor at the cluster level
rsu.sssep.rb2st2rf Sample size to achieve a desired surveillance system sensitivity assuming risk-based 2-stage sampling on two risk factors at either the cluster level, unit level, or both
rsu.sssep.rbmrg Sample size to achieve a desired surveillance system sensitivity assuming risk-based sampling and multiple sensitivity values within risk groups
rsu.sssep.rbsrg Sample size to achieve a desired surveillance system sensitivity assuming risk-based sampling and a single sensitivity value for each risk group
rsu.sssep.rs Sample size to achieve a desired surveillance system sensitivity assuming representative sampling
rsu.sssep.rs2st Sample size to achieve a desired surveillance system sensitivity assuming two-stage sampling
rsu.sssep.rsfreecalc Sample size to achieve a desired surveillance system sensitivity to detect disease at a specified design prevalence assuming representative sampling, imperfect unit sensitivity and specificity
rsu.sssep.rspool Sample size to achieve a desired surveillance system sensitivity using pooled samples assuming representative sampling

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summary.epi.2by2 Summary measures for count data presented in a 2 by 2 table
summary.epi.occc Overall concordance correlation coefficient (OCCC)
summary.epi.tests Sensitivity, specificity and predictive value of a diagnostic test