# A Collection of Statistical Tools for Biologists

## Documentation for package ‘asbio’ version 1.12-2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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 between binary digits and 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
dec2bin | Conversion between binary digits and decimal numbers
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 | 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.comb.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