Package: asbio 1.13-1

asbio: A Collection of Statistical Tools for Biologists

Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.

Authors:Ken Aho [aut, cre]

asbio_1.13-1.tar.gz
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asbio_1.13-1.tgz(r-4.6-any)asbio_1.13-1.tgz(r-4.5-any)
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asbio_1.13.tgz(r-4.5-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
asbio/json (API)

# Install 'asbio' in R:
install.packages('asbio', repos = c('https://kenaho1.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • agrostis - Agrostis variabilis cover measurements
  • aids - Aids and veterans dataset
  • alfalfa.split.plot - An agricultural split plot design
  • anolis - Anolis lizard contingency table data
  • anscombe - Anscombe's quartet
  • ant.dew - Ant honeydew data
  • asthma - Asthma repeated measures dataset from Littell et al.
  • baby.walk - Baby walking times experimental data
  • bats - Bat forearm length as a function of bat age
  • BCI.count - Barro Colorado Island Tree Counts
  • BCI.plant - Tree presence/absence data from Barro Colorado island
  • bear - Grizzly bear litter sizes
  • beetle - Wood boring beetle data
  • bighorn.sel - Datasets for resource use and availability
  • bighornAZ.sel - Datasets for resource use and availability
  • bombus - Bombus pollen data.
  • bone - Bone development data
  • bromus - Bromus tectorum dataset
  • C.isotope - Atmospheric carbon and D14C measurements
  • caribou - Caribou count data
  • case0902 - Dataset of mammal traits from Ramsey and Schaefer
  • case1202 - Dataset of salary attributes for male and female workers from Ramsey and Schafer
  • chronic - Chronic ailment counts for urban and rural women in Australia
  • cliff.env - Environmental data for the community dataset cliff.sp
  • cliff.sp - Yellowstone NP cliff community data
  • concrete - Concrete strength dataset for data mining
  • corn - Corn yield data
  • crab.weight - Crab gill and body weight data
  • crabs - Agresti crabs dataset
  • cuckoo - Tippett cuckoo egg data
  • death.penalty - Florida state death penalty data
  • deer - Maternal deer data
  • deer.296 - Mule deer telemetry data
  • depression - Hamilton depression scores before and after drug treatment
  • dO2 - Dissolved levels in locations above and below a town
  • drugs - Contingency data for high school marijuana, alcohol, and cigarette use
  • e.cancer - Esophageal cancer data modified slightly to create a balanced three-way factorial design
  • elk.sel - Datasets for resource use and availability
  • enzyme - Enzymatic rate data for the phospholipase protein ExoU
  • exercise.repeated - Repeated measures data for an exercise experiment.
  • facebook - Facebook performance metrics for data mining and machine learning
  • Fbird - Frigatebird drumming frequency data
  • fire - Fire data from Yellowstone National Park
  • fly.sex - Fly sex and longevity
  • frog - Australian frog calls following fire
  • fruit - Fruit weight data from Littell et al.
  • garments - Garment Latin square data from Littell et al.
  • Glucose2 - Glucose Levels Following Alcohol Ingestion
  • goat.sel - Datasets for resource use and availability
  • goats - Mountain goat data from Yellowstone National Park
  • grass - Agricultural factorial design
  • heart - Heart rate data from Milliken and Johnson
  • ipomopsis - Ipomopsis fruit yield data
  • juniper.sel - Datasets for resource use and availability
  • K - Soil potassium analyses from 8 laboratories
  • larrea - Creosote bush counts
  • life.exp - Mouse life expectancy data
  • magnets - Magnet pain relief data
  • montane.island - Mountain island biogeographic data
  • moose.sel - Datasets for resource use and availability
  • mosquito - Mosquito wing length data
  • mule.sel - Datasets for resource use and availability
  • myeloma - Patient responses to myeloma drug treatments
  • PCB - PCBs and herring egg thickness
  • pika - Nitrogen content of soils under pika haypiles
  • plantTraits - Plant traits for 136 species
  • PM2.5 - PM 2.5 pollutant data from Pocatello Idaho
  • polyamine - Polyamine data from Hollander and Wolfe
  • portneuf - Portneuf River longitudinal N and P data
  • potash - Potash/cotton strength data
  • potato - Fisher's Rothamsted potato data
  • prostate - Prostate cancer data
  • quail.sel - Datasets for resource use and availability
  • Rabino_CO2 - CSIRO d13C-CO2 data from Rubino et al., A revised 1000 year atmospheric 13C-CO2 record from Law Dome and South Pole, Antarctica
  • Rabino_del13C - CSIRO d13C-CO2 data from Rubino et al., A revised 1000 year atmospheric 13C-CO2 record from Law Dome and South Pole, Antarctica
  • rat - Rat glycogen data from Sokal and Rohlf
  • refinery - Refinery CO dataset
  • rmvm - A multivariate normal dataset for data mining
  • savage - Mammalian BMR and biomass data from Savage et al.
  • sc.twin - Matched pairs schizophrenia data
  • sedum.ts - CO2 exchange time series data
  • Semiconductor - Split plot computer chip data from Littell et al.
  • SexDeterm - Fern environmental sex determination data
  • shad - American gizzard shad data
  • simberloff - Compilations of genus and species counts from Simberloff
  • SM.temp.moist - Alpine soil temperature and moisture time series
  • snore - Snoring and heart disease contingency data
  • so2.us.cities - SO2 data for 32 US cities with respect to 6 explanatory variables
  • starkey - DEM data from the Starkey experimental forest in NE Oregon
  • suess - Del14C in the atmosphere from 1700-1950
  • trag - Salsify height dataset
  • veneer - Veneer data from Littell et al.
  • vs - Scandinavian site by species community matrix
  • wash.rich - Species richness and environmental variables from Mt Washburn
  • webs - Spider web length data
  • wheat - Agricultural randomized block design
  • whickham - Whickham contingency table data for smokers and survivorship
  • wildebeest - Wildebeest carcass categorical data
  • wine - White wine quality data for data mining
  • world.co2 - World CO2 levels, by country, from 1980 to 2006
  • world.emissions - Greenhouse gas emissions from Our World in Data
  • world.pop - Population levels in various countries from 1980-2006

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

7.86 score 5 stars 3 packages 352 scripts 3.8k downloads 11 mentions 276 exports 15 dependencies

Last updated from:e52cad0a4b. Checks:8 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK280
source / vignettesOK261
linux-release-x86_64OK274
macos-release-arm64OK192
macos-oldrel-arm64OK181
windows-develOK180
windows-releaseOK210
windows-oldrelOK150
wasm-releaseFAIL119

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Dependencies:cachemdeSolvedigestfastmapgWidgets2gWidgets2tcltklatticememoisemultcompViewmvtnormpixmapplotrixrlangscatterplot3dtkrplot

simpson
Rendered fromsimpson.Rnwusingutils::Sweave

Last update: 2024-01-20
Started: 2023-08-20

Dichotomous key for Type I, II, and III SS
Rendered fromtypeISS_key.Rnwusingutils::Sweave

Last update: 2023-08-20
Started: 2023-08-20

Random and mixed effect covariance structures
Rendered fromranefCov.Rnwusingutils::Sweave

Last update: 2023-08-20
Started: 2023-08-20

Readme and manuals

Help Manual

Help pageTopics
Agrostis variabilis cover measurementsagrostis
Aids and veterans datasetaids
An agricultural split plot designalfalfa.split.plot
Functions for calculating alpha diversity.alpha.div Simp.index SW.index
Animation demonstrations of confidence intervals.anm.ci anm.ci.tck
Animated demonstration of frequentist binomial convergence of probability using a coin flip.anm.coin anm.coin.tck
Animated demonstration of density for a continuous pdfanm.cont.pdf see.pdf.conc.tck
Animated depiction of six-sided die throws.anm.die anm.die.tck
Animated depiction of experimental designsanm.ExpDesign anm.ExpDesign.tck ExpDesign
Animated depictions of population growthanm.exp.growth anm.exp.growth.tck anm.geo.growth anm.geo.growth.tck anm.log.growth anm.log.growth.tck
Animated plots of log-likelihood functionsanm.loglik anm.loglik.tck loglik.binom.plot loglik.custom.plot loglik.exp.plot loglik.norm.plot loglik.plot loglik.pois.plot
Animated plot of least squares function.anm.ls anm.ls.tck
Animated plot of the least squares function.anm.ls.reg anm.ls.reg.tck
Animated depictions of Lotka-Volterra competition and exploitation modelsanm.LVc.tck anm.LVcomp anm.LVe.tck anm.LVexp
Animation of Markov Chain Monte Carlo walks in bivariate normal spaceanm.mc.bvn anm.mc.bvn.tck anm.mc.norm
Animated demonstration of randomized sampling designsanm.samp.design anm.samp.design.tck samp.design
Anolis lizard contingency table dataanolis
Anscombe's quartetanscombe
Ant honeydew dataant.dew
Agresti-Pendergrast testAP.test
Asthma repeated measures dataset from Littell et al. (2002)asthma
Area under a receiver operating characteristic (ROC) curveauc
Baby walking times experimental datababy.walk
Bat forearm length as a function of bat agebats
Bayesian graphical summaries for discrete or categorical data.Bayes.disc Bayes.disc.tck
Bayesian linear models with uniform priorsbayes.lm print.blm
Barro Colorado Island Tree CountsBCI.count
Tree presence/absence data from Barro Colorado islandBCI.plant
Brunner-Dette-Munk testBDM.2way BDM.test print.BDM
Grizzly bear litter sizesbear
Wood boring beetle databeetle
Determine agreement of two classificationsbest.agreement print.max_agree
Conversion between binary digits and decimal numbersbin2dec dec2bin dec2bin.twos
Bombus pollen data.bombus
Bone development databone
Pulldown menus for 'asbio' interactive graphical functionsbook.menu
Bootstrap CI of M-estimators differences of two samplesboot.ci.M print.bci
A simple function for bootstrappingbootstrap print.bootstrap
Angle of azimuth to a boundary.bound.angle
Barplots with error bars (including interval plots)bplot
Bromus tectorum datasetbromus
Bivariate boxplotsbv.boxplot
Make plots of bivariate normal distributionsbvn.plot
Atmospheric carbon and D14C measurementsC.isotope
Caribou count datacaribou
Dataset of mammal traits from Ramsey and Schaefer (1997)case0902
Dataset of salary attributes for male and female workers from Ramsey and Schafer (1997)case1202
Chi plots for diagnosing multivariate independence.chi.plot
Chronic ailment counts for urban and rural women in Australiachronic
Bootstrap confidence intervalsci.boot print.ciboot
Confidence interval for the product of two proportionsci.impt
Confidence interval for the medianci.median
One sided confidence interval for mu.ci.mu.oneside
Z and t confidence intervals for mu.ci.mu.t ci.mu.z print.ci
Confidence interval estimation for the binomial parameter pi using five popular methods.ci.p
Confidence intervals for the ratio of binomial and multinomial proportionsci.prat
Confidence intervals for ratios of proportions when the denominator is knownci.prat.ak
Confidence interval for sigma squared.ci.sigma
Confidence intervals for stratified random samples.ci.strat
Environmental data for the community dataset cliff.spcliff.env
Yellowstone NP cliff community datacliff.sp
Concrete strength dataset for data miningconcrete
Calculation and display of concordant and discordant pairsConDis.matrix
Corn yield datacorn
crab gill and body weight datacrab.weight
Agresti crabs datasetcrabs
Tippett cuckoo egg datacuckoo
Mahalanobis distance for two sites using a pooled covariance matrixD.sq
Florida state death penalty datadeath.penalty
Maternal deer datadeer
Mule deer telemetry datadeer.296
Hamilton depression scores before and after drug treatmentdepression
Doornik-Hansen test for multivariate normality.DH.test
Dissolved levels in locations above and below a towndO2
Contingency data for high school marijuana, alcohol, and cigarette usedrugs
Esophageal cancer data modified slightly to create a balanced three-way factorial designe.cancer
Efficiency of a randomized block design compared to a CRDeff.rbd
Enzymatic rate data for the phospholipase protein ExoUenzyme
May's effective specialization indexES.May
Repeated measures data for an exercise experiment.exercise.repeated
Facebook performance metrics for data mining and machine learningfacebook
Frigatebird drumming frequency dataFbird
Fire data from Yellowstone National Parkfire
Fly sex and longevityfly.sex
Australian frog calls following firefrog
Fruit weight data from Littell et al. (2002)fruit
Geometric meanG.mean
Likelihood ratio test for tabular datag.test
Garment Latin square data from Littell et al. (2002)garments
Glucose Levels Following Alcohol IngestionGlucose2
Mountain goat data from Yellowstone National Parkgoats
Agricultural factorial designgrass
Harmonic meanH.mean
Heart rate data from Milliken and Johnson (2009)heart
Hodges-Lehman estimator of locationHL.mean
Huber M-estimator of locationhuber.mu
Huber M-estimator iterative least squares algorithmhuber.NR
Huber one step M-estimatorhuber.one.step
Visual illusions illustrating human perception errors.illusions
Ipomopsis fruit yield dataipomopsis
Calculates joint confidence intervals for parameters in linear models using a Bonferroni procedure.joint.ci.bonf
Soil potassium analyses from 8 laboratoriesK
Calculates kappa statistic and other classification error statisticsKappa
Kaplan-Meier survivorship.km
Kullback test for equal covariance matrices.Kullback print.kback
Creosote bush countslarrea
Mouse life expectancy datalife.exp
AIC, AICc, BIC, Mallow's Cp, and PRESS evaluation of linear modelslm.select
Magnet pain relief datamagnets
Simple functions for MCMC demonstrationsmat.pow MC Rf
Monte Carlo hypothesis testing for two samples.MC.test
Gibbs sampling of normal hierarchical modelsmcmc.norm.hier norm.hier.summary
Maximum likelihood algorithm for determining the binomial dispersal coefficientML.k
Sample modeMode
Modified Levene's testmodlevene.test print.mltest
Mountain island biogeographic datamontane.island
Datasets for resource use and availabilitybighorn.sel bighornAZ.sel elk.sel goat.sel juniper.sel moose.sel mule.sel quail.sel
Mosquito wing length datamosquito
Mack-Skillings testMS.test
Patient responses to myeloma drug treatmentsmyeloma
Nearest neighbor boundary coordinatesnear.bound
One sample t-testone.sample.t
One sample z-testone.sample.z print.oneSamp
Paik diagramspaik
Conducts pairwise post hoc and planned comparisons associated with an ANOVAbonf.cont bonfCI dunnettCI lsdCI pairw.anova print.pairw scheffe.cont scheffeCI tukeyCI
Multiple pairwise comparison procedure to accompany a Friedman test.FR.multi.comp pairw.fried
Multiple pairwise comparison procedure to accompany a Kruskal-Wallis testKW.multi.comp pairw.kw
Welch tests controlled for simultaneous inferencepairw.oneway
Functions for customizing correlation matricespanel.cor.res panel.lm
Partial correlations of determination in multiple regressionpartial.R2
Partial residual plots for interpretation of multiple regression.partial.resid.plot
PCBs and herring egg thicknessPCB
Permutation test for two and three way factorial designsperm.fact.test
Nitrogen content of soils under pika haypilespika
Plant traits for 136 speciesplantTraits
Plots confidence intervals and/or bars with letters indicating significant differences for objects from class pairwplot.pairw
Creates plots for one way ANCOVAsplotAncova
Plots a simple linear regression along with confidence and prediction intervals.plotCI.reg
PM 2.5 pollutant data from Pocatello IdahoPM2.5
Polyamine data from Hollander and Wolfe (1999)polyamine
Portneuf River longitudinal N and P dataportneuf
Potash/cotton strength datapotash
Fisher's Rothamsted potato datapotato
Power analysis for a one sample z-testpower.z.test
prediction sum of squarespress
Preston diversity analysisPreston.dist
Prostate cancer dataprostate
Perpendicularityprint.prp.index prp
Jacknife pseudo-valuespseudo.v
Normal quantile plots for single or multiple factor levelsqq.Plot
Biweight midvariance, and biweight midcorrelation.r.bw
Visualize the sampling distribution of Pearson's product moment correlationr.dist see.r.dist.tck
R hat MCMC convergence statisticR.hat
Percentage bend correlationr.pb
CSIRO d13C-CO2 data from Rubino et al., A revised 1000 year atmospheric 13C-CO2 record from Law Dome and South Pole, AntarcticaRabino_CO2 Rabino_del13C
Rat glycogen data from Sokal and Rohlf (2012)rat
Refinery CO datasetrefinery
Random draws from a scaled inverse chi-square distributionrinvchisq
A multivariate normal dataset for data miningrmvm
Animated and/or snapshot representations of a statistic's sampling distributiondirty.dist samp.dist samp.dist.method.tck samp.dist.n samp.dist.snap samp.dist.snap.tck1 samp.dist.snap.tck2 samp.dist.tck
Animated representation of sampling distribution basicssamp.dist.mech samp.dist.mech.tck
Mammalian BMR and biomass data from Savage et al. (2004)savage
Matched pairs schizophrenia datasc.twin
Jackknife standard error from a set of pseudovaluesse.jack se.jack1
CO2 exchange time series datasedum.ts
Interactive depiction of precision and accuracysee.accPrec.tck
Visualize ANCOVA mechanicssee.ancova.tck
Interactive depiction of the ANOVA mechanismsee.anova.tck
Depict the effect of range on correlationsee.cor.range.tck
Visualize exponential power functionssee.exppower.tck
Visualize the Hardy Weinberg equilibriumsee.HW see.HW.tck
ANOVA linear modelssee.lma.tck
Regression linear model derivation from linear algebrapm1 see.lmr.tck
Unbalanced and balanced linear modelspm see.lmu.tck
Interactive worksheet for logical and fallacious argumentssee.logic
Visualization of the M-estimation functionsee.M
Depiction of the effect of random level selection on inferences concerning fixed effectssee.mixedII
Interactive depiction of the multinomial distributionsee.mnom.tck
Interactive visualization of least squares regression.see.adddel see.move
Visualize important non-linear functionssee.nlm
Visualize pdfssee.beta.tck see.betacdf.tck see.bin.tck see.bincdf.tck see.chi.tck see.chicdf.tck see.disc.unif.tck see.disc.unifcdf.tck see.exp.tck see.expcdf.tck see.F.tck see.Fcdf.tck see.gam.tck see.gamcdf.tck see.geo.tck see.geocdf.tck see.hyper.tck see.hypercdf.tck see.lnorm.tck see.lnormcdf.tck see.logis.tck see.logiscdf.tck see.nbin.tck see.nbincdf.tck see.norm.tck see.normcdf.tck see.pdfdriver see.pdfdriver.tck see.pois.tck see.poiscdf.tck see.t.tck see.tcdf.tck see.unif.tck see.unifcdf.tck see.weib.tck see.weibcdf.tck
Interactive depiction of type I and type II error and powersee.power see.power.tck
Visualize random effects modelr.eff see.rEffect.tck
Demonstration of regression mechanicssee.regression.tck
Interactive depiction of ROC curvessee.roc.tck
Interactive smoother demonstrationssee.smooth.tck
Visualize t-testssee.ttest.tck
Interactive depiction of type I and II errorsee.typeI_II
Interactive self-testing questionsselftest.ANOVAmixed.tck1 selftest.ANOVAsiminf.tck1 selftest.ANVOVA_design.tck selftest.ANVOVA_design_review.tck selftest.bayes4.tck selftest.bayes5.tck selftest.codettest.tck selftest.comb.tck selftest.conf.tck1 selftest.corr.tck1 selftest.H0.tck selftest.jack.tck selftest.ML_OLS.tck selftest.nonparametric6.tck selftest.pdfs.tck selftest.prob.tck selftest.regapproaches.tck1 selftest.regapproaches.tck2 selftest.regapproaches.tck3 selftest.regapproaches.tck4 selftest.regchar.tck1 selftest.regdiag.tck1 selftest.regdiag.tck2 selftest.regdiag.tck3 selftest.regGLM.tck1 selftest.sampd.tck1 selftest.science.tck1 selftest.se.tck1 selftest.stats.tck selftest.stats.tck1 selftest.ttest.tck selftest.typeIISS.tck1
Split plot computer chip data from Littell et al. (2006)Semiconductor
Fern environmental sex determination dataSexDeterm
American gizzard shad datashad
Shading functions for interpretation of pdf probabilities.shade shade.bin shade.chi shade.F shade.norm shade.poi shade.t shade.wei
GUI display of probabilityshade.bin.tck shade.chi.tck shade.F.tck shade.norm.tck shade.poi.tck shade.t.tck
Compilations of genus and species counts from Simberloff (1970)simberloff
Sample skewness and kurtosiskurt skew
Alpine soil temperature and moisture time seriesSM.temp.moist
Snoring and heart disease contingency datasnore
SO2 data for 32 US cities with respect to 6 explanatory variablesso2.us.cities
Variance and standard error estimators for the sampling distribution of the sample meanstan.error stan.error.sq
DEM data from the Starkey experimental forest in NE Oregonstarkey
del14C in the atmosphere from 1700-1950suess
Salsify height datasettrag
Transition matrix analysisanm.TM.tck anm.transM transM
Trim datatrim.me
Robust test for random factors using trimmed means.trim.ranef.test
Robust one way trimmed means test.trim.test
Tukey's test of additivity.print.addtest tukey.add.test
Veneer data from Littell et al. (2002)veneer
Venn probability diagrams for an event with two outcomesVenn Venn.tck
Scandinavian site by species community matrixvarespec vs
Species richness and environmental variables from Mt Washburnwash.rich
Spider web length datawebs
Agricultural randomized block designwheat
Whickham contingency table data for smokers and survivorshipwhickham
Wildebeest carcass categorical datawildebeest
Winsorize datawin
White wine quality data for data miningwine
World CO2 levels, by country, from 1980 to 2006world.co2
Greenhouse gas emissions from Our World in Dataworld.emissions
Population levels in various countries from 1980-2006world.pop