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asbio (version 1.0-5)
A collection of statistical tools for biologists
Description
Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL.
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Install
install.packages('asbio')
Monthly Downloads
4,313
Version
1.0-5
License
GPL (>= 2)
Maintainer
Ken Aho
Last Published
May 15th, 2014
Functions in asbio (1.0-5)
Search functions
G.mean
Geometric mean
MC.test
Monte Carlo hypothesis testing for two samples.
moose.sel
Datasets for resource use and availability
Preston.dist
Preston diversity analysis
baby.walk
Baby walking times experimental data
huber.NR
Huber M-estimator iterative least squares algorithm
chi.plot
Chi plots for diagnosing multivariate independence.
ci.prat.ak
Confidence intervals for ratios of proportions when the denominator is known
caribou
Caribou count data
trim.me
Trim data
cliff.env
Environmental data for the community dataset cliff.sp
bv.boxplot
Bivariate boxplots
ci.mu.z
Z and t confidence intervals for mu.
asthma
Asthma repeated measures dataset from Littell et al. (2002)
panel.cor.res
Functions for customizing correlation matrices
bear
Grizzly bear litter sizes
one.sample.z
One sample z-test
modlevene.test
Modified Levene's test
HL.mean
Hodges-Lehman estimator of location
potash
Potash/cotton strength data
corn
Corn yield data
K
Soil potassium analyses from 8 laboratories
see.ttest.tck
Visualize t-tests
pseudo.v
Jacknife pseudo-values
win
Winsorize data
world.co2
World CO2 levels, by country, from 1980 to 2006
snore
Snoring and heart disease contingency data
shade.norm
Shading functions for interpretation of pdf probabilities.
anm.coin
Animated demonstration of frequentist binomial convergence of probability using a coin flip.
stan.error
Variance and standard error estimators for the sampling distribution of the sample mean
alfalfa.split.plot
An agricultural split plot design
shade.norm.tck
GUI display of probability
alpha.div
Functions for calculating alpha diversity.
e.cancer
Esophageal cancer data modified slightly to create a balanced three-way factorial design
portneuf
Portneuf River longitudinal N and P data.
PM2.5
PM 2.5 pollutant data from Pocatello Idaho.
anm.samp.design
Animated demonstration of randomized sampling designs
power.z.test
Power analysis for a one sample z-test
pairw.anova
Conducts pairwise post hoc and planned comparisons associated with an ANOVA
world.pop
Population levels in various countries since 1980
D.sq
Mahalanobis distance for two sites using a pooled covariance matrix
H.mean
Harmonic mean
SM.temp.moist
Alpine soil temperature and moisture time series
MS.test
Mack-Skillings test
rat
Rat glycogen data from Sokal and Rohlf (2012).
cuckoo
Tippett cuckoo egg data
exercise.repeated
Repeated measures data for an exercise experiment.
sedum.ts
CO2 exchange time series data
km
Kaplan-Meier survivorship.
life.exp
Mouse life expectancy data.
starkey
DEM data from the Starkey experimental forest in NE Oregon.
auc
Area under a reciever operating characterisitic (ROC) curve
MC
Simple functions for MCMC demonstrations
deer
Maternal deer data
see.mixedII
Depiction of the effect of random level selection on inferences concerning fixed effects
anm.LV
Animated depictions of Lotka-Volterra competition and exploitation models
Kullback
Kullback test for equal covariance matrices.
Mode
Sample mode
BDM.test
Brunner-Dette-Munk test
anm.cont.pdf
Animated demonstration of density for a continuous pdf
R.hat
R hat MCMC convergence statistic
Fbird
Frigatebird drumming frequency data
ci.strat
Confidence intervals for stratified random samples.
ConDis.matrix
Calculation and display of concordant and discordant pairs
fire
Fire data from Yellowstone National Park
anolis
Anolis lizard contingency table data
Semiconductor
Split plot computer chip data from Littell et al. (2006).
AP.test
Agresti-Pendergrast test
Bayes.disc
Bayesian graphical summaries for discrete data.
BCI.plant
Tree presence/absence data from Barro Colorado island
bplot
Barplots with error bars for pairwise comparisons.
C.isotope
Atmospheric carbon and D14C measurements
bombus
Bombus pollen data.
see.M
Visualization of the M-estimation function
one.sample.t
One sample t-test
montane.island
Mountain island biogeographic data
PCB
PCBs and herring egg thickness
see.lma.tck
ANOVA linear models
bromus
Bromus tectorum dataset
crabs
Agresti crabs dataset
bootstrap
A simple function for bootstrapping
anm.ci
Animation demonstrations of confidence intervals.
anm.die
Animated depiction of six-sided die throws.
ES.May
May's effective specialization index
r.dist
Visualize the sampling distribution of Pearson's product moment correlation
BCI.count
Barro Colorado Island Tree Counts
see.HW
Visualize the Hardy Weinberg equlibrium
anm.ls
Animated plot of least squares function.
anm.ExpDesign
Animated depiction of experimental designs
huber.one.step
Huber one step M-estimator
death.penalty
Florida state death penalty data
Venn
Venn probability diagrams for an event with two outcomes
ci.mu.oneside
One sided confidence interval for mu.
ipomopsis
Ipomopsis fruit yield data
Kappa
Calculates kappa statistic and other classification error statistics
goats
Mountain goat data from Yellowstone National Park
aids
Aids and veterans dataset
bvn.plot
Make plots of bivariate normal distributions
cliff.sp
Yellowstone NP cliff community data
partial.resid.plot
Partial residual plots for interpretation of multiple regression.
huber.mu
Huber M-estimator of location
samp.dist
Animated and/or snapshot representations of a statistic's sampling distribution
frog
Australian frog calls following fire
ci.p
Confidence interval estimation for the binomial parameter pi using five popular methods.
enzyme
Enzymatic rate data for the phospholipase protein ExoU
prostate
Prostate cancer data
crab.weight
crab gill and body weight data
bats
Bat forearm length as a function of bat age
ML.k
Maximum likelihood algorithm for determining the binomial dispersal coefficient
eff.rbd
Efficiency of a randomized block design compared to a CRD
dO2
Dissolved levels in locations above and below a town
bound.angle
Angle of azimuth to a boundary.
polyamine
Polyamine data from Hollander and Wolfe (1999)
illusions
Visual illusions illustrating human preception errors.
ci.boot
Bootstrap confidence intervals
r.pb
Percentage bend correlation
Glucose2
Glucose Levels Following Alcohol Ingestion
bone
Bone development data
DH.test
Doornick-Hansen test for multivariate normality.
anm.ls.reg
Animated plot of least squares function.
deer.296
Mule deer telemetry data
see.lmr.tck
Regression linear model derivation from linear algebra
drugs
Contingency data for high school marijuana, alcohol, and cigarette use
chronic
Chronic ailment counts for urban and rural women in Australia
fly.sex
Fly sex and longevity
joint.ci.bonf
Calculates joint confidence intervals for parameters in linear models using a Bonferroni procedure.
ci.prat
Confidence intervals for the ratio of binomial and multinomial proportions
ci.median
Confidence interval for the median
agrostis
Agrostis variabiis cover measurements
book.menu
Pulldown menus for 'asbio' interactive graphical functions
anscombe
Anscobe's quartet
perm.fact.test
Permutation test for two and three way factorial designs
bayes.lm
Bayesian linear models with uniform priors
larrea
Creosote bush counts
grass
Agricultural factorial design
pairw.fried
Multiple pairwise comparison procedure to accompany a Friedman test.
selftest.se.tck1
Interactive self-testing statistical questions
pairw.kw
Multiple pairwise comparison procedure to accompany a Kruskal-Wallis test
see.logic
Interactive worksheet for logical and fallacious arguments
mosquito
Mosquito wing length data
sc.twin
Matched pairs schizophrenia data
fruit
Fruit weight data from Littell et al. (2002)
anm.mc.bvn
Animation of Markov Chain Monte Carlo walks in bivariate normal space
see.exppower.tck
Visualize exponential power functions
samp.dist.mech
Animated representation of sampling distribution basics
refinery
Refinery CO dataset
plotCI.reg
Plots a simple linear regression along with confidence and prediction intervals.
ant.dew
Ant honeydew data
skew
Sample skewness and kurtosis
loess.surf
Loess 2D and 3D smooth plots
lm.select
AIC, AICc, BIC, Mallow's Cp, and PRESS evaluation of linear models
anm.loglik
Animated plots of log-likelihood functions
myeloma
Patient responses to myeloma drug treatments
so2.us.cities
SO2 data for 32 US cities with respect to 6 explanatory variables
plantTraits
Plant traits for 136 species
see.nlm
Visualize important non-linear functions
magnets
Magnet pain relief data
see.typeI_II
Interactive depiction of type I and II error
see.regression.tck
Demonstration of regression mechanics
ci.sigma
Confidence interval for sigma squared.
garments
Garment Latin square data from Littell et al. (2002)
partial.R2
Partial correlations of determination in multiple regression
press
prediction sum of squares
see.move
Interactive visualization of least squares regression.
near.bound
Nearest neighbor boundary coordinates
see.ancova.tck
Visualize ANCOVA mechanics
paik
Paik diagrams
mcmc.norm.hier
Gibbs sampling of normal hierarchical models
see.rEffect.tck
Visualize random effects model
bin2dec
Conversion of binary digits to decimal numbers
r.bw
Biweight midvariance, and biweight midcorrelation.
potato
Fisher's Rothamsted potato data
prp
Perpendicularity
plot.pairw
Plots confidence intervals for objects from class pairw
transM
Transition matrix analysis
trim.test
Robust one way trimmed means test.
see.lmu.tck
Unbalanced and balanced linear models
depression
Hamilton depression scores before and after drug treatment
g.test
Likelihood ratio test for tabular data
see.power
Interactive depiction of type I and type II error and power
see.mnom.tck
Interactive depiction of the multinomial distribution
see.accPrec.tck
Interactive depiction of precision and accuracy
heart
Heart rate data from Milliken and Johnson (2009)
see.cor.range.tck
Depict the effect of range on correlation
pika
Nitrogen content of soils under pika haypiles.
tukey.add.test
Tukey's test of additivity.
see.anova.tck
Interactive depiction of the ANOVA mechanism
wheat
Agricultural randomized block design
se.jack
Jackknife standard error from a set of pseudovalues
webs
Spider web length data
see.norm.tck
Visualize pdfs
trim.ranef.test
Robust test for random factors using trimmed means.
vs
Scandinavian site by species community matrix
shad
American gizzard shad data
see.smooth.tck
Interactive smoother demonstrations
see.roc.tck
Interactive depiction of ROC curves
rinvchisq
Random draws from a scaled inverse chi-square distribution
beetle
Wood boring beetle data.
wildebeest
Wildebeest carcass categorical data
veneer
Veneer data from Littell et al. (2002)
trag
Salsify height dataset
wash.rich
Species richness and environmental variables from Mt Washburn
whickham
Whickham contingency table data for smokers and survivorship
anm.geo.growth
Animated depictions of population growth
boot.ci.M
Bootstrap CI of M-estimators differences of two samples