General Index

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abbott

Abies balsamea. See fir data

accuracy

AD Model Builder

AIC, corrected (AICc) quasi-(qAIC) weights

allometric growth

analysis of covariance (ANCOVA)

analysis of variance (ANOVA)

arguments, function

asymptote

asymptotically valid tests

autoregressive model

balloon plot

bar plot

base graphics

base rate fallacy

Bayes factor

Bayes' Rule

Beers' Law

Bernoulli distribution

beta-binomial distribution

Beta distribution

Beverton-Holt function. See also Michaelis-Menten function

BFGS (Broyden-Fletcher-Goldfarb-Shanno) optimization

bias, tradeoff with variance

Bible Code

BIC (Bayesian Information Criterion)

bimodal distribution

binomial distribution

biological significance

block random effects

Brent's method

bubble plot

BUGS. See also in the R Index: R2WinBUGS package

burn-in, for MCMC chains

candidate distribution

catalytic curve

Cauchy distribution

censored data, interval

central limit theorem

chain rule

characteristic scale

chi-bar-squared () distribution

chi-squared (X²) distribution,. See also Pearson chi-square test

circular data

C language

coefficient of variation (CV)

coercing variables

color

comments

competitive exclusion

compositional data

compounded distribution

conditional probability

confidence interval, bivariate region, profile, quadratic, univariate, See also credible interval

conjugate prior. See prior probability

constraints

continuous-time models

contrasts

convergence: of MCMC runs, of optimization

convolution

correlation, matrix

coverage

credible interval

critical point

crowding

CSV (comma-separated values) cubic

cumulative distribution function

curse of dimensionality

damselfish data

Dascyllus trimaculatus. See damselfish data

database

data dredging

data frame

data manipulation

degrees of freedom

delta method

demographic stochasticity

density (kernel estimation), plot for MCMC

density-dependent processes mortality

derivative, finite difference, estimates of, optimization based on, partial

design matrix

determinant

deterministic model

deviance, residual

DIC (deviance information criterion)

differential evolution

digamma function

direct search

dispersal

distribution function

dot chart

dot plot

doubling time

Ecological Detective, The

e-folding time

environmental stochasticity

Elacatinus evelynae. See goby data

Elacatinus prochilos. See goby data

Erlang distribution. See Gamma distribution

error bars, Erythronium glandiflorum. See glacier lilies

Euler's method

Excel (Microsoft)

expectation

experimental design

exploratory data analysis

exponential distribution

exponential function

extreme value distribution

factor

factorial

finite mixture distribution

fir data

fisheries models

Fisher's exact test

fishing expedition. See data dredging

food web

FORTRAN

frailty models

frequentist statistics

functional response Holling type I, Holling type II, Holling type III Holling type IV functions, defining in R

Gamma distribution

gamma () function

Gelman-Rubin (GR) convergence diagnostic

generalized distribution

generalized least squares, nonlinear

generalized linear models (GLM)

genetic algorithm

geometric distribution

Gibbs sampling

Gillespie algorithm

GIS

glacier lilies

goby data

Gompertz function

goodness of fit

gradient

gradient matching

graphics parameters

graphical user interface (GUI)

half-life

half-maximum

harmonic mean

Hassell function

Hessian

hierarchical model

histogram

hockey-stick function

Holling functional response. See functional response

homoscedasticity

horned beetles

humped function. See Unimodal

hyperbolic function

hyperbolic tangent function

Hyperolius spinigularis. See tadpole data

hypothesis testing

identifiability, weak

iid (independent and identically distributed)

independence

indexing data

individual-based model

inflection point

information criteria information matrix

integral

interaction

inverse (matrix)

JAGS

Jensen's inequality

JGR

joint probability

Kalman Filter, extended

Kenward-Roger correction

Kullback-Leibler distance

kurtosis

Lambert W function

Laplace approximation

large data sets, handling

L-BFGS-B (constrained BFGS) optimization

L'Hôpital's rule

likelihood, profile, quasi-, scaled slice surface

Likelihood Ratio test, boundary issues with

limit

linear

linearity

linearizing transformation. See transformation

linear predictor

link function

Linux

list (R data type)

location parameter

logarithmic scale,. See also transformation

log-binomial model

logistic function, growth, modified

logistic regression

logit scale

log-likelihood

lognormal distribution

lognormal-Poisson distribution

log-odds

lollipop plot. See 3D graphics long format. See shape

MacOS

marginal distribution

marginal likelihood

marginal model

marginal probability density

Markov chain Monte Carlo (MCMC)

Mathematica

MATLAB

matrix (R data type)

matrix inversion

maximum likelihood estimate

mean

mean squared error

measurement error

mechanistic model

median

metadata

method of moments

Metropolis algorithm, Metropolis-Hastings variant, Metropolis-Szymura-Barton variant

Michaelis-Menten function (M-M)

Microsoft. See Excel; Windows

mixed model

mixture models

mode

model averaging

model criticism

model selection

Monod function. See Michaelis-Menten function

monomolecular function

monotonic function

Morpho

mosaic plot

multilevel model

multiple comparisons

multiple minima

multiple regression

multivariate data

multivariate normal distribution (MVN)

mutually exclusive events

myxomatosis data

negative binomial distribution

Nelder-Mead simplex

nested designs

nested functions

nested model

Newton's method

Neyman-Pearson statistics

Neyman type A distribution

“no free lunch,”

nonparametric statistics

non-rectangular hyperbola

normal distribution

normalization constant

numerical integration

objective function

object-oriented programming

observation error

Occam's razor. See parsimony

odds

odds ratio

one-step-ahead fitting

OpenBUGS

ordinary differential equations (ODEs)

overcompensation

overdispersion, parameter,. See also beta-binomial distribution; likelihood; negative binomial

overfitting

packages

pair plot

parameterization

parsimony

particle filtering

path (to files)

Pearson chi-square test

penalized optimization

Phantom Tollbooth, The

phenomenological model

piecewise function

plaintext files

plotting characters

plug-in estimate

point estimate

point null hypothesis

Poisson cluster process

Poisson distribution

Poisson regression

polynomial function regression

population prediction interval

portmanteau function

positive definite matrix

posterior probability distribution, mean of, mode of

power, statistical

power function

power rule

precision: of estimates, inverse of variance

predation, model

prediction

prior probability conjugate, flat, improper, uniform, uninformative, weak

probability density

process error

product rule

profile confidence limits. See confidence interval

proposal distribution. See candidate distribution

pseudoreplication

p-value

quadratic function

quantile

quasi-likelihood. See likelihood

quasi-Newton optimization

quotient rule

Raftery-Lewis (RL) convergence diagnostic

random effects

rate parameter

rational function

reading data into R

recruitment

reef fish

regression: linear, model II, quadratic, reduced major axis

repeated measures models

reshaping data

Richards model

Ricker function generalized, power truncated

robust statistics

Rogers random-predator equation. See also functional response

sample space

SAS PROC GENMOD, PROC GLIMMIX PROC GLM PROC NLMIXED

SANN,. See also simulated annealing

saturating

scale parameter

scatterplot matrix (pairs plot)

Schwarz criterion. See BIC

SciViews

seed removal data

sequential importance sampling

shape (data),. See also in the R Index: reshape package

Shepherd function

shooting. See trajectory matching

SIMEX algorithm

simulated annealing

simulation

sinusoidal function

size refuge

Skellam model

skewness

small multiples

smoothing

spatial aggregation

spatial models

spline

SPSS

standard deviation

starting parameters, estimating

state-space models

stepwise modeling

stochastic global optimization

Student t distribution

survival

survival analysis

survival curves

tadpole data

tail probability

Taylor expansion

t-distribution. See Student t distribution

telemetry data

temperature, of simulated annealing

text files. See plaintext files

theta-logistic

3D graphics bar plots

threshold function

time-series models

Tinn-R

trace (matrix)

trace plot, for MCMC diagnostics

trajectory matching

transformation, additive log ratio, arcsine-square root, linearizing, log, log(1+x), logit, of parameters, square root, of likelihood profile

transpose (matrix)

2Dt distribution. See Student t distribution

type III sum of squares

unconditional probability

uniform distribution

unimodal

Unix

U-shaped

variable names

variance

variance (of estimators)

variance-covariance matrix

variance-to-mean ratio

vector (R data type)

von Bertalanffy function

Weibull distribution

wide format. See shape

WinBUGS, See also BUGS; in the R Index: R2WinBUGS package

Windows (Microsoft)

WINE

zero-inflated distribution beta-binomial, binomial, negative binomial, Poisson