A Collection of Statistical Tools for Biologists
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Documentation for package ‘asbio’ version 1.9-7
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A B C D E F G H I J K L M N O P Q R S T V W
-- A --
| agrostis | Agrostis variabilis cover measurements |
| aids | Aids and veterans dataset |
| alfalfa.split.plot | An agricultural split plot design |
| alpha.div | Functions for calculating alpha diversity. |
| anm.ci | Animation demonstrations of confidence intervals. |
| anm.ci.tck | Animation demonstrations of confidence intervals. |
| anm.coin | Animated demonstration of frequentist binomial convergence of probability using a coin flip. |
| anm.coin.tck | Animated demonstration of frequentist binomial convergence of probability using a coin flip. |
| anm.cont.pdf | Animated demonstration of density for a continuous pdf |
| anm.die | Animated depiction of six-sided die throws. |
| anm.die.tck | Animated depiction of six-sided die throws. |
| anm.exp.growth | Animated depictions of population growth |
| anm.exp.growth.tck | Animated depictions of population growth |
| anm.ExpDesign | Animated depiction of experimental designs |
| anm.ExpDesign.tck | Animated depiction of experimental designs |
| anm.geo.growth | Animated depictions of population growth |
| anm.geo.growth.tck | Animated depictions of population growth |
| anm.log.growth | Animated depictions of population growth |
| anm.log.growth.tck | Animated depictions of population growth |
| anm.loglik | Animated plots of log-likelihood functions |
| anm.loglik.tck | Animated plots of log-likelihood functions |
| anm.ls | Animated plot of least squares function. |
| anm.ls.reg | Animated plot of the least squares function. |
| anm.ls.reg.tck | Animated plot of the least squares function. |
| anm.ls.tck | Animated plot of least squares function. |
| anm.LVc.tck | Animated depictions of Lotka-Volterra competition and exploitation models |
| anm.LVcomp | Animated depictions of Lotka-Volterra competition and exploitation models |
| anm.LVe.tck | Animated depictions of Lotka-Volterra competition and exploitation models |
| anm.LVexp | Animated depictions of Lotka-Volterra competition and exploitation models |
| anm.mc.bvn | Animation of Markov Chain Monte Carlo walks in bivariate normal space |
| anm.mc.bvn.tck | Animation of Markov Chain Monte Carlo walks in bivariate normal space |
| anm.mc.norm | Animation of Markov Chain Monte Carlo walks in bivariate normal space |
| anm.samp.design | Animated demonstration of randomized sampling designs |
| anm.samp.design.tck | Animated demonstration of randomized sampling designs |
| anm.TM.tck | Transition matrix analysis |
| anm.transM | Transition matrix analysis |
| anolis | Anolis lizard contingency table data |
| anscombe | Anscombe's quartet |
| ant.dew | Ant honeydew data |
| AP.test | Agresti-Pendergrast test |
| asthma | Asthma repeated measures dataset from Littell et al. (2002) |
| auc | Area under a receiver operating characteristic (ROC) curve |
-- B --
| baby.walk | Baby walking times experimental data |
| bats | Bat forearm length as a function of bat age |
| Bayes.disc | Bayesian graphical summaries for discrete or categorical data. |
| Bayes.disc.tck | Bayesian graphical summaries for discrete or categorical data. |
| bayes.lm | Bayesian linear models with uniform priors |
| BCI.count | Barro Colorado Island Tree Counts |
| BCI.plant | Tree presence/absence data from Barro Colorado island |
| BDM.2way | Brunner-Dette-Munk test |
| BDM.test | Brunner-Dette-Munk test |
| bear | Grizzly bear litter sizes |
| beetle | Wood boring beetle data |
| best.agreement | Determine agreement of two classifications |
| bighorn.sel | Datasets for resource use and availability |
| bighornAZ.sel | Datasets for resource use and availability |
| bin2dec | Conversion of binary digits to decimal numbers |
| bombus | Bombus pollen data. |
| bone | Bone development data |
| bonf.cont | Conducts pairwise post hoc and planned comparisons associated with an ANOVA |
| bonfCI | Conducts pairwise post hoc and planned comparisons associated with an ANOVA |
| book.menu | Pulldown menus for 'asbio' interactive graphical functions |
| boot.ci.M | Bootstrap CI of M-estimators differences of two samples |
| bootstrap | A simple function for bootstrapping |
| bound.angle | Angle of azimuth to a boundary. |
| bplot | Barplots with error bars (including interval plots) |
| bromus | Bromus tectorum dataset |
| bv.boxplot | Bivariate boxplots |
| bvn.plot | Make plots of bivariate normal distributions |
-- C --
| C.isotope | Atmospheric carbon and D14C measurements |
| caribou | Caribou count data |
| case0902 | Dataset of mammal traits from Ramsey and Schaefer (1997) |
| case1202 | Dataset of salary attributes for male and female workers from Ramsey and Schafer (1997) |
| chi.plot | Chi plots for diagnosing multivariate independence. |
| chronic | Chronic ailment counts for urban and rural women in Australia |
| ci.boot | Bootstrap confidence intervals |
| ci.impt | Confidence interval for the product of two proportions |
| ci.median | Confidence interval for the median |
| ci.mu.oneside | One sided confidence interval for mu. |
| ci.mu.t | Z and t confidence intervals for mu. |
| ci.mu.z | Z and t confidence intervals for mu. |
| ci.p | Confidence interval estimation for the binomial parameter pi using five popular methods. |
| ci.prat | Confidence intervals for the ratio of binomial and multinomial proportions |
| ci.prat.ak | Confidence intervals for ratios of proportions when the denominator is known |
| ci.sigma | Confidence interval for sigma squared. |
| ci.strat | Confidence intervals for stratified random samples. |
| cliff.env | Environmental data for the community dataset cliff.sp |
| cliff.sp | Yellowstone NP cliff community data |
| concrete | Concrete strength dataset for data mining |
| ConDis.matrix | Calculation and display of concordant and discordant pairs |
| corn | Corn yield data |
| crab.weight | crab gill and body weight data |
| crabs | Agresti crabs dataset |
| cuckoo | Tippett cuckoo egg data |
-- D --
| D.sq | Mahalanobis distance for two sites using a pooled covariance matrix |
| 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 |
| DH.test | Doornik-Hansen test for multivariate normality. |
| dirty.dist | Animated and/or snapshot representations of a statistic's sampling distribution |
| dO2 | Dissolved levels in locations above and below a town |
| drugs | Contingency data for high school marijuana, alcohol, and cigarette use |
| dunnettCI | Conducts pairwise post hoc and planned comparisons associated with an ANOVA |
-- E --
| e.cancer | Esophageal cancer data modified slightly to create a balanced three-way factorial design |
| eff.rbd | Efficiency of a randomized block design compared to a CRD |
| elk.sel | Datasets for resource use and availability |
| enzyme | Enzymatic rate data for the phospholipase protein ExoU |
| ES.May | May's effective specialization index |
| exercise.repeated | Repeated measures data for an exercise experiment. |
| ExpDesign | Animated depiction of experimental designs |
-- F --
| 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 |
| FR.multi.comp | Multiple pairwise comparison procedure to accompany a Friedman test. |
| frog | Australian frog calls following fire |
| fruit | Fruit weight data from Littell et al. (2002) |
-- G --
| G.mean | Geometric mean |
| g.test | Likelihood ratio test for tabular data |
| garments | Garment Latin square data from Littell et al. (2002) |
| 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 |
-- H --
| H.mean | Harmonic mean |
| heart | Heart rate data from Milliken and Johnson (2009) |
| HL.mean | Hodges-Lehman estimator of location |
| huber.mu | Huber M-estimator of location |
| huber.NR | Huber M-estimator iterative least squares algorithm |
| huber.one.step | Huber one step M-estimator |
-- I --
| illusions | Visual illusions illustrating human perception errors. |
| ipomopsis | Ipomopsis fruit yield data |
-- J --
| joint.ci.bonf | Calculates joint confidence intervals for parameters in linear models using a Bonferroni procedure. |
| juniper.sel | Datasets for resource use and availability |
-- K --
| K | Soil potassium analyses from 8 laboratories |
| Kappa | Calculates kappa statistic and other classification error statistics |
| km | Kaplan-Meier survivorship. |
| Kullback | Kullback test for equal covariance matrices. |
| kurt | Sample skewness and kurtosis |
| KW.multi.comp | Multiple pairwise comparison procedure to accompany a Kruskal-Wallis test |
-- L --
| larrea | Creosote bush counts |
| life.exp | Mouse life expectancy data |
| lm.select | AIC, AICc, BIC, Mallow's Cp, and PRESS evaluation of linear models |
| loglik.binom.plot | Animated plots of log-likelihood functions |
| loglik.custom.plot | Animated plots of log-likelihood functions |
| loglik.exp.plot | Animated plots of log-likelihood functions |
| loglik.norm.plot | Animated plots of log-likelihood functions |
| loglik.plot | Animated plots of log-likelihood functions |
| loglik.pois.plot | Animated plots of log-likelihood functions |
| lsdCI | Conducts pairwise post hoc and planned comparisons associated with an ANOVA |
-- M --
| magnets | Magnet pain relief data |
| mat.pow | Simple functions for MCMC demonstrations |
| MC | Simple functions for MCMC demonstrations |
| MC.test | Monte Carlo hypothesis testing for two samples. |
| mcmc.norm.hier | Gibbs sampling of normal hierarchical models |
| ML.k | Maximum likelihood algorithm for determining the binomial dispersal coefficient |
| Mode | Sample mode |
| modlevene.test | Modified Levene's test |
| montane.island | Mountain island biogeographic data |
| moose.sel | Datasets for resource use and availability |
| mosquito | Mosquito wing length data |
| MS.test | Mack-Skillings test |
| mule.sel | Datasets for resource use and availability |
| myeloma | Patient responses to myeloma drug treatments |
-- N --
| near.bound | Nearest neighbor boundary coordinates |
| norm.hier.summary | Gibbs sampling of normal hierarchical models |
-- O --
| one.sample.t | One sample t-test |
| one.sample.z | One sample z-test |
-- P --
| paik | Paik diagrams |
| pairw.anova | Conducts pairwise post hoc and planned comparisons associated with an ANOVA |
| pairw.fried | Multiple pairwise comparison procedure to accompany a Friedman test. |
| pairw.kw | Multiple pairwise comparison procedure to accompany a Kruskal-Wallis test |
| pairw.oneway | Welch tests controlled for simultaneous inference |
| panel.cor.res | Functions for customizing correlation matrices |
| panel.lm | Functions for customizing correlation matrices |
| partial.R2 | Partial correlations of determination in multiple regression |
| partial.resid.plot | Partial residual plots for interpretation of multiple regression. |
| PCB | PCBs and herring egg thickness |
| perm.fact.test | Permutation test for two and three way factorial designs |
| pika | Nitrogen content of soils under pika haypiles |
| plantTraits | Plant traits for 136 species |
| plot.pairw | Plots confidence intervals and/or bars with letters indicating significant differences for objects from class pairw |
| plotAncova | Creates plots for one way ANCOVAs |
| plotCI.reg | Plots a simple linear regression along with confidence and prediction intervals. |
| pm | Unbalanced and balanced linear models |
| pm1 | Regression linear model derivation from linear algebra |
| PM2.5 | PM 2.5 pollutant data from Pocatello Idaho |
| polyamine | Polyamine data from Hollander and Wolfe (1999) |
| portneuf | Portneuf River longitudinal N and P data |
| potash | Potash/cotton strength data |
| potato | Fisher's Rothamsted potato data |
| power.z.test | Power analysis for a one sample z-test |
| press | prediction sum of squares |
| Preston.dist | Preston diversity analysis |
| print.addtest | Tukey's test of additivity. |
| print.bci | Bootstrap CI of M-estimators differences of two samples |
| print.BDM | Brunner-Dette-Munk test |
| print.blm | Bayesian linear models with uniform priors |
| print.bootstrap | A simple function for bootstrapping |
| print.ci | Z and t confidence intervals for mu. |
| print.ciboot | Bootstrap confidence intervals |
| print.kback | Kullback test for equal covariance matrices. |
| print.max_agree | Determine agreement of two classifications |
| print.mltest | Modified Levene's test |
| print.oneSamp | One sample z-test |
| print.pairw | Conducts pairwise post hoc and planned comparisons associated with an ANOVA |
| print.prp.index | Perpendicularity |
| prostate | Prostate cancer data |
| prp | Perpendicularity |
| pseudo.v | Jacknife pseudo-values |
-- Q --
| qq.Plot | Normal quantile plots for single or multiple factor levels |
| quail.sel | Datasets for resource use and availability |
-- R --
| r.bw | Biweight midvariance, and biweight midcorrelation. |
| r.dist | Visualize the sampling distribution of Pearson's product moment correlation |
| r.eff | Visualize random effects model |
| R.hat | R hat MCMC convergence statistic |
| r.pb | Percentage bend correlation |
| 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 (2012) |
| refinery | Refinery CO dataset |
| Rf | Simple functions for MCMC demonstrations |
| rinvchisq | Random draws from a scaled inverse chi-square distribution |
| rmvm | A multivariate normal dataset for data mining |
-- S --
| samp.design | Animated demonstration of randomized sampling designs |
| samp.dist | Animated and/or snapshot representations of a statistic's sampling distribution |
| samp.dist.mech | Animated representation of sampling distribution basics |
| samp.dist.mech.tck | Animated representation of sampling distribution basics |
| samp.dist.method.tck | Animated and/or snapshot representations of a statistic's sampling distribution |
| samp.dist.n | Animated and/or snapshot representations of a statistic's sampling distribution |
| samp.dist.snap | Animated and/or snapshot representations of a statistic's sampling distribution |
| samp.dist.snap.tck1 | Animated and/or snapshot representations of a statistic's sampling distribution |
| samp.dist.snap.tck2 | Animated and/or snapshot representations of a statistic's sampling distribution |
| samp.dist.tck | Animated and/or snapshot representations of a statistic's sampling distribution |
| savage | Mammalian BMR and biomass data from Savage et al. (2004) |
| sc.twin | Matched pairs schizophrenia data |
| scheffe.cont | Conducts pairwise post hoc and planned comparisons associated with an ANOVA |
| scheffeCI | Conducts pairwise post hoc and planned comparisons associated with an ANOVA |
| se.jack | Jackknife standard error from a set of pseudovalues |
| se.jack1 | Jackknife standard error from a set of pseudovalues |
| sedum.ts | CO2 exchange time series data |
| see.accPrec.tck | Interactive depiction of precision and accuracy |
| see.adddel | Interactive visualization of least squares regression. |
| see.ancova.tck | Visualize ANCOVA mechanics |
| see.anova.tck | Interactive depiction of the ANOVA mechanism |
| see.beta.tck | Visualize pdfs |
| see.betacdf.tck | Visualize pdfs |
| see.bin.tck | Visualize pdfs |
| see.bincdf.tck | Visualize pdfs |
| see.chi.tck | Visualize pdfs |
| see.chicdf.tck | Visualize pdfs |
| see.cor.range.tck | Depict the effect of range on correlation |
| see.disc.unif.tck | Visualize pdfs |
| see.disc.unifcdf.tck | Visualize pdfs |
| see.exp.tck | Visualize pdfs |
| see.expcdf.tck | Visualize pdfs |
| see.exppower.tck | Visualize exponential power functions |
| see.F.tck | Visualize pdfs |
| see.Fcdf.tck | Visualize pdfs |
| see.gam.tck | Visualize pdfs |
| see.gamcdf.tck | Visualize pdfs |
| see.geo.tck | Visualize pdfs |
| see.geocdf.tck | Visualize pdfs |
| see.HW | Visualize the Hardy Weinberg equilibrium |
| see.HW.tck | Visualize the Hardy Weinberg equilibrium |
| see.hyper.tck | Visualize pdfs |
| see.hypercdf.tck | Visualize pdfs |
| see.lma.tck | ANOVA linear models |
| see.lmr.tck | Regression linear model derivation from linear algebra |
| see.lmu.tck | Unbalanced and balanced linear models |
| see.lnorm.tck | Visualize pdfs |
| see.lnormcdf.tck | Visualize pdfs |
| see.logic | Interactive worksheet for logical and fallacious arguments |
| see.logis.tck | Visualize pdfs |
| see.logiscdf.tck | Visualize pdfs |
| see.M | Visualization of the M-estimation function |
| see.mixedII | Depiction of the effect of random level selection on inferences concerning fixed effects |
| see.mnom.tck | Interactive depiction of the multinomial distribution |
| see.move | Interactive visualization of least squares regression. |
| see.nbin.tck | Visualize pdfs |
| see.nbincdf.tck | Visualize pdfs |
| see.nlm | Visualize important non-linear functions |
| see.norm.tck | Visualize pdfs |
| see.normcdf.tck | Visualize pdfs |
| see.pdf.conc.tck | Animated demonstration of density for a continuous pdf |
| see.pdfdriver | Visualize pdfs |
| see.pdfdriver.tck | Visualize pdfs |
| see.pois.tck | Visualize pdfs |
| see.poiscdf.tck | Visualize pdfs |
| see.power | Interactive depiction of type I and type II error and power |
| see.power.tck | Interactive depiction of type I and type II error and power |
| see.r.dist.tck | Visualize the sampling distribution of Pearson's product moment correlation |
| see.rEffect.tck | Visualize random effects model |
| see.regression.tck | Demonstration of regression mechanics |
| see.roc.tck | Interactive depiction of ROC curves |
| see.smooth.tck | Interactive smoother demonstrations |
| see.t.tck | Visualize pdfs |
| see.tcdf.tck | Visualize pdfs |
| see.ttest.tck | Visualize t-tests |
| see.typeI_II | Interactive depiction of type I and II error |
| see.unif.tck | Visualize pdfs |
| see.unifcdf.tck | Visualize pdfs |
| see.weib.tck | Visualize pdfs |
| see.weibcdf.tck | Visualize pdfs |
| selftest.ANOVAmixed.tck1 | Interactive self-testing questions |
| selftest.ANOVAsiminf.tck1 | Interactive self-testing questions |
| selftest.ANVOVA_design.tck | Interactive self-testing questions |
| selftest.ANVOVA_design_review.tck | Interactive self-testing questions |
| selftest.bayes4.tck | Interactive self-testing questions |
| selftest.bayes5.tck | Interactive self-testing questions |
| selftest.codettest.tck | Interactive self-testing questions |
| selftest.conf.tck1 | Interactive self-testing questions |
| selftest.corr.tck1 | Interactive self-testing questions |
| selftest.H0.tck | Interactive self-testing questions |
| selftest.jack.tck | Interactive self-testing questions |
| selftest.ML_OLS.tck | Interactive self-testing questions |
| selftest.nonparametric6.tck | Interactive self-testing questions |
| selftest.pdfs.tck | Interactive self-testing questions |
| selftest.prob.tck | Interactive self-testing questions |
| selftest.regapproaches.tck1 | Interactive self-testing questions |
| selftest.regapproaches.tck2 | Interactive self-testing questions |
| selftest.regapproaches.tck3 | Interactive self-testing questions |
| selftest.regapproaches.tck4 | Interactive self-testing questions |
| selftest.regchar.tck1 | Interactive self-testing questions |
| selftest.regdiag.tck1 | Interactive self-testing questions |
| selftest.regdiag.tck2 | Interactive self-testing questions |
| selftest.regdiag.tck3 | Interactive self-testing questions |
| selftest.regGLM.tck1 | Interactive self-testing questions |
| selftest.sampd.tck1 | Interactive self-testing questions |
| selftest.science.tck1 | Interactive self-testing questions |
| selftest.se.tck1 | Interactive self-testing questions |
| selftest.stats.tck | Interactive self-testing questions |
| selftest.stats.tck1 | Interactive self-testing questions |
| selftest.ttest.tck | Interactive self-testing questions |
| selftest.typeIISS.tck1 | Interactive self-testing questions |
| Semiconductor | Split plot computer chip data from Littell et al. (2006) |
| SexDeterm | Fern environmental sex determination data |
| shad | American gizzard shad data |
| shade | Shading functions for interpretation of pdf probabilities. |
| shade.bin | Shading functions for interpretation of pdf probabilities. |
| shade.bin.tck | GUI display of probability |
| shade.chi | Shading functions for interpretation of pdf probabilities. |
| shade.chi.tck | GUI display of probability |
| shade.F | Shading functions for interpretation of pdf probabilities. |
| shade.F.tck | GUI display of probability |
| shade.norm | Shading functions for interpretation of pdf probabilities. |
| shade.norm.tck | GUI display of probability |
| shade.poi | Shading functions for interpretation of pdf probabilities. |
| shade.poi.tck | GUI display of probability |
| shade.t | Shading functions for interpretation of pdf probabilities. |
| shade.t.tck | GUI display of probability |
| shade.wei | Shading functions for interpretation of pdf probabilities. |
| simberloff | Compilations of genus and species counts from Simberloff (1970) |
| Simp.index | Functions for calculating alpha diversity. |
| skew | Sample skewness and kurtosis |
| 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 |
| stan.error | Variance and standard error estimators for the sampling distribution of the sample mean |
| stan.error.sq | Variance and standard error estimators for the sampling distribution of the sample mean |
| starkey | DEM data from the Starkey experimental forest in NE Oregon |
| suess | del14C in the atmosphere from 1700-1950 |
| SW.index | Functions for calculating alpha diversity. |
-- T --
| trag | Salsify height dataset |
| transM | Transition matrix analysis |
| trim.me | Trim data |
| trim.ranef.test | Robust test for random factors using trimmed means. |
| trim.test | Robust one way trimmed means test. |
| tukey.add.test | Tukey's test of additivity. |
| tukeyCI | Conducts pairwise post hoc and planned comparisons associated with an ANOVA |
-- V --
| varespec | Scandinavian site by species community matrix |
| veneer | Veneer data from Littell et al. (2002) |
| Venn | Venn probability diagrams for an event with two outcomes |
| Venn.tck | Venn probability diagrams for an event with two outcomes |
| vs | Scandinavian site by species community matrix |
-- W --
| 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 |
| win | Winsorize 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 |