Package: evidence 0.8.10

evidence: Analysis of Scientific Evidence Using Bayesian and Likelihood Methods

Bayesian (and some likelihoodist) functions as alternatives to hypothesis-testing functions in R base using a user interface patterned after those of R's hypothesis testing functions. See McElreath (2016, ISBN: 978-1-4822-5344-3), Gelman and Hill (2007, ISBN: 0-521-68689-X) (new edition in preparation) and Albert (2009, ISBN: 978-0-387-71384-7) for good introductions to Bayesian analysis and Pawitan (2002, ISBN: 0-19-850765-8) for the Likelihood approach. The functions in the package also make extensive use of graphical displays for data exploration and model comparison.

Authors:Robert van Hulst

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evidence.pdf |evidence.html✨
evidence/json (API)
NEWS

# Install 'evidence' in R:
install.packages('evidence', repos = c('https://rvhulst.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/rvhulst/evidence/issues

Datasets:
  • AOV1 - Made-up data for a balanced one-way anova.
  • AOV2 - Made-up data for an unbalanced one-way anova.
  • Aspirin - A contingency table for heart attacks and aspirin use.
  • BirdsCS - Simulated clutch size data for birds with different nesting locations.
  • Clin - Made-up data to illustrate Simpson's paradox.
  • Fat - Human body fat and several covariates for calculating it.
  • Glasses - A contingency table of 16 British youths categorized as juvenile delinquents or not, and as wearing glasses or not.
  • HSCrab - Morphology of horseshoe crabs.
  • SRb94 - Data of the growth of tissue cultures on five different media.
  • Smoking - Mortality due to heart infarct in smokers and non-smokers.
  • Snoring - Data on the incidence of hypertension and three indicator variables.
  • bodytemp - Data on body temperature, heart rate, and gender of 130 human subjects.
  • budworm - Mortality data of moth larvae due to increasing doses of insecticide.
  • crickets - Made-up data that are not unlike the actual data collected by Nespolo et al.(2003).
  • darwin - Charles Darwin's (1876) data on the fecundity of selfed and crossed corn plants.
  • fev - Data on lung capacity of 654 children and adolescents.
  • lightspeed - Simon Newcomb's measurements of the speed of light
  • rats - Carcinogenesis data on rats exposed to a carcinogen.
  • weightgain - Weight gain in rats

On CRAN:

1.63 score 43 scripts 219 downloads 29 exports 115 dependencies

Last updated 7 years agofrom:673a9d9fd2. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 02 2024
R-4.5-winNOTENov 02 2024
R-4.5-linuxNOTENov 02 2024
R-4.4-winNOTENov 02 2024
R-4.4-macNOTENov 02 2024
R-4.3-winNOTENov 02 2024
R-4.3-macNOTENov 02 2024

Exports:B1NmeanB1NsirB1propB1propSimB2NsirB2propsBft2x2BiasVarTObinPriorsPlotBnNsirBregbfBt.testCTAHPDcrdL1propL2proplooicplotmeansplotMedDiagnnineplotNPVoverdispersionCheckp2BFp2minppPPVsigtestCIsn2ft2x2SSQsumchart

Dependencies:abindbackportsbase64encbayesplotBHbootbslibcachemcallrcheckmateclicolorspacecolourpickercommonmarkcpp11crayoncrosstalkdescdigestdistributionaldplyrDTdygraphsevaluatefansifarverfastmapfontawesomefsgenericsggplot2ggridgesgluegridExtragtablegtoolshighrhtmltoolshtmlwidgetshttpuvigraphinlineisobandjquerylibjsonliteknitrlabelingLaplacesDemonlaterlatticelazyevalLearnBayeslifecyclelme4loomagrittrmarkdownMASSMatrixmatrixStatsmemoisemgcvmimeminiUIminqamunsellnlmenloptrnumDerivpillarpkgbuildpkgconfigplyrposteriorprocessxpromisespsQuickJSRR6rappdirsRColorBrewerRcppRcppEigenRcppParallelreshape2rlangrmarkdownrstanrstanarmrstantoolssassscalesshinyshinyjsshinystanshinythemessourcetoolsStanHeadersstringistringrsurvivaltensorAthreejstibbletidyselecttinytexutf8vctrsviridisLitewithrxfunxtablextsyamlzoo

Readme and manuals

Help Manual

Help pageTopics
evidence: Functions and Data for Bayesian and Likelihood Analysisevidence-package evidence
Made-up data for a balanced one-way anova.AOV1
Made-up data for an unbalanced one-way anova.AOV2
A contingency table for heart attacks and aspirin use.Aspirin
Bayesian analysis of one sample from a Normal distribution with imprecise priors.B1Nmean
Bayesian analysis of a Normal sample using a SIR prior.B1Nsir
Bayesian analysis of the binomial parameter for one sample.B1prop
simulates Bayesian updating of the binomial parameter pi.B1propSim
Bayesian analysis of the means of two Normal samples using SIR priors.B2Nsir
Bayesian analysis of the binomial parameters for two samples.B2props
Bayesian analysis of a 2 x 2 contingency table.Bft2x2
a simple example of the bias-variance trade-off.BiasVarTO
function to plot diverse Beta distributions for use as Binomial priorsbinPriorsPlot
Simulated clutch size data for birds with different nesting locations.BirdsCS
Bayesian analysis of n >= 2 Normal means with standard improper reference priors.BnNsir
Data on body temperature, heart rate, and gender of 130 human subjects.bodytemp
Bayesian regression model comparison with Bayes factors.Bregbf
Bayesian t-test using reference priors.Bt.test
Mortality data of moth larvae due to increasing doses of insecticide.budworm
Made-up data to illustrate Simpson's paradox.Clin
Made-up data that are not unlike the actual data collected by Nespolo et al.(2003).crickets
Contingency Table Analysis in different waysCTA
Charles Darwin's (1876) data on the fecundity of selfed and crossed corn plants.darwin
Human body fat and several covariates for calculating it.Fat
Data on lung capacity of 654 children and adolescents.fev
A contingency table of 16 British youths categorized as juvenile delinquents or not, and as wearing glasses or not.Glasses
generates the 100 * (1 - alpha)% most probable interval of a distribution of empirical valuesHPDcrd
Morphology of horseshoe crabs.HSCrab
Likelihood analysis of the binomial parameter for one sample.L1prop
Likelihood analysis of the binomial parameters for two samples.L2prop
Simon Newcomb's measurements of the speed of lightlightspeed
A dot plot is produced for several related models showing for each model its LOOIC-value with its credible interval.looicplot
Plots a simple strip chart of the observations with group means and grand mean.meansplot
Computes the posterior probability of having a certain disease from prevalence, sensitivity, and specificity data.MedDiagn
produces a Normality plot for the argument surrounded by eight other Normality plots for Normal distributions having the same mean and standard deviation as the argumentnineplot
computes the Negative Predictive Value.NPV
A robust comparison of the location and the scale of the input vector.overdispersionCheck
Conversion of a frequentist p-value to the lower bound of the Bayes factor against the null hypothesis assuming equal odds of the null and the alternativep2BF
Conversion of a frequentist p-value to a lower bound of the posterior probability that the null hypothesis is true assuming equal odds of the null and the alternativep2minpp
calculates the positive predictive value (PPV) of a diagnostic test.PPV
Carcinogenesis data on rats exposed to a carcinogen.rats
Universal Fisherian significance test with confidence interval.sigtestCI
Mortality due to heart infarct in smokers and non-smokers.Smoking
Conversion of 2 props input to 2x2 contingency tablesn2ft2x2
Data on the incidence of hypertension and three indicator variables.Snoring
Data of the growth of tissue cultures on five different media.SRb94
A support function that calculates the sum of squares of a data vector.SSQ
Plotting routine for dataframes of looic values.sumchart
weight gain in ratsweightgain