A Collection of Statistical Tools for Biologists


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Documentation for package ‘asbio’ version 1.6-7

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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 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
loess.surf Loess 2D and 3D smooth plots
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.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.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.sampd.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.pop Population levels in various countries from 1980-2006