R: Tools for the Analysis of Epidemiological Data

# Tools for the Analysis of Epidemiological Data

## Documentation for package ‘epiR’ version 2.0.95

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

## Help Pages

E P R S

## -- E --

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.evalue | Compute E-value for risk, rate, odds and hazard ratio estimates
epi.fpos | Calculate the expected number of false positive and false negative test results
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.mbf | Minimum Bayes Factor using the Goodman or Sellke et al. method.
epi.mh | Fixed-effects meta-analysis of binary outcomes using the Mantel-Haenszel method
epi.nomogram | Post-test probability of an outcome given diagnostic test sensitivity and specificity
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 and the expected number of false positives
epi.psi | Proportional similarity index
epi.realrisk | An R version of the Winton Centre's RealRisk calculator
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 statistical 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 and power when comparing binary outcomes
epi.sscompc | Sample size and power when comparing continuous outcomes
epi.sscomps | Sample size and power 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 or equality trial, binary outcome
epi.ssequc | Sample size for a parallel equivalence or equality 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

## -- P --

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

## -- R --

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 the 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

## -- S --

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