Download this table as CTFSRFunctions.txt


CTFS R Function Index

FunctionFileDescriptionLink
abund.manycensusabundance/abundance.rCollect abundances of all species a...Help
abundanceabundance/abundance.rCalculates total abundance or basal...Help
abundance.sppabundance/abundance.rA wrapper to calculate total abunda...Help
abundanceperquadabundance/abundance.rFinds abundance, basal area, or agb...Help
abundmodel.fitdemogchange/abund.fit.CTFS.rSimply return the modeled histogram...Help
addBinParamutilities/distributions.rGiven parameters for a model with N...Help
agb.dbhmodelbiomass/biomass.CTFSdb.rCalculates biomass from density and...Help
AGB.dbtablebiomass/biomass.CTFSdb.rThis function looks up the database...Help
AGB.indbiomass/biomass.CTFSdb.rCompute biomass (agb) based on one ...Help
agb.modelbiomass/biomass.CTFSdb.rCalculates biomass from density, he...Help
AGB.treebiomass/biomass.CTFSdb.rComputes AGB of each tree in a tabl...Help
allquadratslopestopography/slope.rCalculating slope of all quadrats i...Help
angleBisectorutilities/geometry.rGiven 3 sets of coordinates definin...Help
Annulispatial/RipUvK.rCalculates the total area in a seri...Help
are.ptsinsideutilities/geometry.rChecks many points (dataframe pt wi...Help
arrangeParam.Gibbs.2Dutilities/lmerBayes.rUsed in the loop of a Gibbs sampler...Help
arrangeParam.llikeutilities/statistics.rUsed in likelihood function of a Gi...Help
arrangeParam.llike.2Dutilities/lmerBayes.rUsed in likelihood function of a Gi...Help
assemble.demographyutilities/utilitiesCTFS.rTakes output of a demographic analy...Help
assembleBinOutputgrowth/growthfit.bin.rUse the list output from piecewise ...Help
asymp.htutilities/distributions.rThe function from Sean Thomas which...Help
asymp.ht.fixmaxutilities/distributions.rSame formulation, but the asymptote...Help
asymptote.exputilities/distributions.rA 3-parameter function which asympt...Help
attach_if_neededutilities/utilities.rAttach one or more datafiles,checki...Help
autoregressionutilities/statistics.rAutocorrelation with a given lag of...Help
baabundance/abundance.rCalculates the individual basal are...Help
bad.asymexp.paramdemogchange/abund.fit.CTFS.rFor either the Gaussian, or asymexp...Help
bad.asympower.paramdemogchange/abund.fit.CTFS.rThe 3 parameters submitted to hyper...Help
bad.binparamgrowth/growthfit.bin.rThis prevents the bin parameters fr...Help
bad.binsdpargrowth/growthfit.bin.r...Help
bad.paretoparutilities/distributions.rTest whether parameters for the Par...Help
BadParamutilities/statistics.rThis is a default for model.xy, nev...Help
badSDutilities/lmerBayes.r...Help
basumabundance/abundance.rReturns the basal area summed over ...Help
beta.normalizedutilities/distributions.rNormalzing beta.total. No longer us...Help
beta.totalutilities/distributions.rA beta distribution on the interval...Help
betaproductutilities/distributions.rThis is equivalent to the normal pr...Help
binGraphManySpeciesgrowth/growthfit.graph.rMake a graph of AGB growth and mode...Help
binGraphManySpecies.Panelgrowth/growthfit.graph.rMake a graph, 4 panels, of AGB grow...Help
binGraphSampleSpeciesgrowth/growthfit.graph.rMake a single graph, 4 panels, of A...Help
biomass.changebiomass/biomass.CTFSdb.rFinds biomass in two censuses and c...Help
biomass.CTFSdbbiomass/biomass.CTFSdb.rCalculate biomass from existing R-f...Help
biomass.growthgrowth/growth.rLike growth(), but calculates chang...Help
bootconfutilities/statistics.rA simple calculation of confidence ...Help
bootstrap.corrutilities/statistics.rRunning bootstrap on a correlation....Help
border.distanceutilities/statistics.rReturns distance from a point to th...Help
calc.directionslopetopography/slope.rThis runs equations 1-3 of Seibert ...Help
calc.gradienttopography/slope.rCalculate flow using Seibert & McGl...Help
calcalphautilities/calcalpha.rCalculates alpha from a stem and sp...Help
calcMortIndivTabledemogchange/demogChange.rCalculate mortality rate per specie...Help
CalcRingAreaspatial/RipUvK.rGiven a dataframe that includes gx,...Help
calcS.alphautilities/calcalpha.rEstimated number of species in a sa...Help
calcslopetopography/slope.rGiven the z-coordinate of 3 points ...Help
calculateBinModel.AICgrowth/growthfit.bin.rCalculate AIC of the model, using v...Help
calculateBinModel.bestpredgrowth/growthfit.bin.rCalculate mean predicted value at e...Help
calculateBinModel.BICgrowth/growthfit.bin.rCalculate Bayes Information Criteri...Help
cartesian.to.polarutilities/geometry.rConvert Cartesian coordinates to po...Help
center.predictorsutilities/distributions.rTransform all data by subtracting a...Help
charlocateutilities/utilities.rFinds position of a substring needl...Help
Chave.AGBbiomass/biomass.CTFSdb.rThe Chave 2005 Oecologia model for ...Help
CIutilities/statistics.rConfidence limits (quantiles) from ...Help
circleutilities/geometry.rCalculates points on a...Help
circleareaspatial/RipUvK.rSimply returns area of a circle of ...Help
clean.demographyutilities/utilitiesCTFS.rThis takes a CTFS demography table,...Help
coldata.to.imagematmap/mapresponse.rThese functions create maps of resp...Help
colMediansutilities/statistics.rFor convenient medians, like colMea...Help
compare.growthbinmodelgrowth/growthfit.graph.rCalculates various metrics of fit: ...Help
complete.plotmapmap/map.rThis creates a map with every indiv...Help
constantutilities/distributions.rA function to return a constant at ...Help
constant.binutilities/distributions.rA model like piecewise regression (...Help
constant.linearutilities/distributions.rA model which is constant for xHelp
convert.factorutilities/utilities.rConverts any character fields in a ...Help
convert.rowcolspatial/quadfunc.rConvert an integer to a character, ...Help
CountByGrouputilities/utilities.rGroups a dataframe by one or more c...Help
countEmptyutilities/utilities.rCounts vector elements that are NA ...Help
countNAutilities/utilities.rCounts vector elements that are NA....Help
countoneutilities/utilities.rCounts vector elements exactly one....Help
countpresentutilities/utilities.rCounts vector elements > 0. See cou...Help
countspputilities/utilitiesCTFS.rReturns the number of elements in a...Help
countUniqueutilities/utilities.rCount the number of unique elements...Help
countzeroutilities/utilities.rCounts vector elements exactly zero...Help
coverage.diagspeciesarea/spparea.rDraws a diagonal across a plot, fro...Help
covTocorrutilities/lmerBayes.rConvert covariance matrix to correl...Help
create.fulldateutilities/utilities.rConverts a vector of date character...Help
create.fulldate.splitutilities/utilities.rConverts the MySQL date format by s...Help
create.neighbordataspatial/quadfunc.rCalculates the mean density in neig...Help
CTFSplotutilities/utilitiesCTFS.rA convenience for attaching the R A...Help
cumul.aboveutilities/statistics.rGiven y values as a function of x, ...Help
d.calcS.alphautilities/calcalpha.rThe derivative for use in Newton's ...Help
dasymexputilities/distributions.rProbability distributions for a fol...Help
dasymexputilities/distributions.rProbability distributions for an as...Help
dasympowerutilities/distributions.rA bilateral power distribution, cen...Help
dbeta.reparamutilities/distributions.rThis reparameterizes the beta distr...Help
DBHtransitiongrowth/growth.rCalculates a transition matrix of i...Help
dbinomrevutilities/distributions.rA version of dbinom in which parame...Help
default.badparutilities/distributions.rNone given....Help
define.graphwindowmap/map.rThis defines an export device for a...Help
defineBinBreaksgrowth/growthfit.bin.rThis finds divisions of over the ve...Help
defineSDpargrowth/growthfit.bin.rFor default SD parameters, if nothi...Help
density.indbiomass/biomass.CTFSdb.rCreate a vector of wood density for...Help
detachfilesutilities/utilities.rdetachs from the searchpath files m...Help
dexp.sinutilities/distributions.rFour-parameter exponential sin, as ...Help
dgamma.meanutilities/distributions.rA version of dgamma where the param...Help
dgamma.meansdutilities/distributions.rProbability distribution of gamma, ...Help
dgamma.scaleutilities/distributions.rLike above, but with scale as the f...Help
dgammadexputilities/distributions.rPDF of a function formed by adding ...Help
dgammaMinusdexputilities/distributions.rThe PDF of the difference between a...Help
dgammaPlusdexputilities/distributions.rThe PDF of the sum of gamma and neg...Help
discrete.modelutilities/distributions.rA model for a numeric response to a...Help
discrete.mortmodelutilities/distributions.rA model for mortality as a function...Help
distancespatial/quadfunc.rCalculates the distance from one qu...Help
distance.to.sidetopography/imageJ.rCalled from imageJ.to.lxly where fo...Help
ditchutilities/utilities.rDetaches all files at one or more s...Help
dmixnormutilities/distributions.rMixed normal distribution. The para...Help
dnormprod0utilities/distributions.rProbability density of product of t...Help
dnormrevutilities/distributions.rThis reverses the order of paramete...Help
doublenormalutilities/distributions.rSimulate draws from a double normal...Help
dpois.maxutilities/distributions.rA probability distribution which is...Help
dpois.maxtruncutilities/distributions.rA zero-truncated Poisson distributi...Help
dpois.rearrangeutilities/distributions.rThis rearranges dpois so that it wo...Help
dpowerutilities/distributions.rA probability distribution defined ...Help
draw.axesmap/mapresponse.rAdd axes to a graph, with ticks spa...Help
drawrectangleutilities/geometry.rDraw a rectangle given a matrix or ...Help
drputilities/utilities.rA version of drop which includes as...Help
dsymexputilities/distributions.rProbability distribution for a fold...Help
dweibull.3paramutilities/distributions.rPDF of three-parameter Weibull...Help
elev.to.listtopography/slope.rA function which reads a dataframe ...Help
ellipseutilities/geometry.rEquation for (half) a canonical...Help
enoughSamplePerBingrowth/growthfit.bin.rTest whether the number of elements...Help
exclude.unidentifiedutilities/utilitiesCTFS.rA more specialized version of unide...Help
exp.2parutilities/distributions.rAn exponential distribution with an...Help
explodeutilities/utilities.rSplit a single (atomic) character v...Help
expon.modelutilities/distributions.rExponential model, y = a exp(b1*x1 ...Help
exponential.sinutilities/distributions.rFive-parameter exponential sin...Help
extract.growthdatagrowth/growthfit.bin.rExtract data for growth rates from ...Help
fill.1dimensionutilities/utilities.rFilling a 1D array resulting from t...Help
fill.dimensionutilities/utilities.rThis function fills out an array of...Help
find.climitsmortality/mortality.rCalculates confidence limits around...Help
find.nonNAutilities/utilities.rReturns the first value of a vector...Help
find.xaxis.histdemogchange/abund.fit.CTFS.rGiven an abundance fit and x axis r...Help
findborderquadsspatial/quadfunc.rCalculate indices of neighboring qu...Help
findneighborabundspatial/quadfunc.rFor every quadrat, finds neighborin...Help
fit.beta.normalutilities/distributions.rFinding a normal distribution which...Help
fit.logisticutilities/distributions.rA function to fit a set of data y, ...Help
fit.pdfutilities/distributions.rFit a random variable x to any subm...Help
fitnormutilities/distributions.rFitting a normal distribution to da...Help
fitSeveralAbundModeldemogchange/abund.fit.CTFS.rRun model.littleR.Gibbs for a serie...Help
fromjulianutilities/utilities.rAccepts a julian date and returns a...Help
full.abundmodel.llikedemogchange/abund.fit.CTFS.rWith the table of abundances, hyper...Help
full.likelihood.lmerBayesutilities/lmerBayes.rCalculate full likelihood for any c...Help
full.xygridspatial/quadfunc.rCreate a complete of points x-y, gi...Help
fullcircleutilities/geometry.rCreate a dataframe for a full circl...Help
fullellipseutilities/geometry.rCreates a dataframe for a full elli...Help
fullplot.imageJtopography/imageJ.rReads quadrat maps created by image...Help
get.filenamemap/map.rThis sets a name for outputting a m...Help
getquadratnamespatial/quadfunc.rConvert x, y coordinates and plot d...Help
getsmallerquadsspatial/quadfunc.rTakes a vector of indices for a lar...Help
getTopoLinkstopography/solvetopo.rThis is solely for use by solve.top...Help
Gibbs.normalmeanutilities/statistics.rThe standard Gibbs sampler for a no...Help
Gibbs.normalvarutilities/statistics.rGibbs draw for the variance of a no...Help
Gibbs.regsigmautilities/statistics.rUpdates the regression standard dev...Help
Gibbs.regslopeutilities/statistics.rUpdates the regression slope (used ...Help
graph.abundmodeldemogchange/abund.fit.CTFS.rOutput histograms of little.r acros...Help
graph.growthmodelgrowth/growthfit.graph.rGraph growth rates and model fit....Help
graph.growthmodel.sppgrowth/growthfit.graph.rUse output of growth.flexbin to gra...Help
graph.modeldiagutilities/statistics.rGraph diagnostics of model.xy...Help
graph.mvnormutilities/distributions.rGraphs contours for an mvnorm, with...Help
graph.outliersgrowth/growthfit.graph.rGraph the outliers overlaid on the ...Help
graph.outliers.sppgrowth/growthfit.graph.rPass the output of extract.growth w...Help
graph.quadratsspeciesarea/spparea.rMake a graph of a series of quadrat...Help
graphFilledBandutilities/utilities.rFill the area between two curves on...Help
growthgrowth/growth.rThe principle growth function, cons...Help
growth.biomass.indivgrowth/growth.rLike growth.indiv but based on agb ...Help
growth.dbhgrowth/growth.rThis calculates forest-wide growth ...Help
growth.eachsppgrowth/growth.rThis calculates growth for each spe...Help
growth.flexbingrowth/growthfit.bin.rFitting a regression line through l...Help
growth.indivgrowth/growth.rThis returns a complete table with ...Help
gsputilities/utilities.rReturns one of the objects at a giv...Help
gxgy.to.hectindexspatial/quadfunc.r...Help
gxgy.to.indexspatial/quadfunc.rAssign any location(s) a single ind...Help
gxgy.to.lxlyspatial/quadfunc.rGiven global coordinates and quadra...Help
gxgy.to.quadspatial/quadfunc.rCalculate a quadrat name (column nu...Help
gxgy.to.rowcolspatial/quadfunc.rReturns row and column for any set ...Help
harmonic.meanutilities/statistics.rHarmonic mean of a vector x. NAs an...Help
hist.compareutilities/statistics.rCompares two histograms with a Kolm...Help
hyper.abundGibbsdemogchange/abund.fit.CTFS.rLikelihood function for hyperparame...Help
hyper.mortGibbsdemogchange/abund.fit.CTFS.rLikelihood function for logMu and l...Help
IfElseutilities/utilities.rA more convenient version of the R ...Help
image.dataframemap/mapresponse.rCreates a color response map based ...Help
imageGraphmap/mapresponse.rMaps a response variable with R's c...Help
imageJ.to.lxlytopography/imageJ.rConvert map pixels from digitzing p...Help
index.to.gxgyspatial/quadfunc.rCalculate the x and y coordinates g...Help
index.to.rowcolspatial/quadfunc.rCalculate the row and column given ...Help
individual_grow.tabledemogchange/demogChange.rCreate a table of individual trees ...Help
individual_mort.tabledemogchange/demogChange.rCreate a table of individual trees ...Help
inside.rectutilities/geometry.rDetermines whether any of the 4 cor...Help
insideRectangleutilities/geometry.rChecks a vector of coordinates x, y...Help
intersection.line.curveutilities/geometry.rFinds the points where a straight l...Help
intersection.of.linesutilities/geometry.rFinds the point where 2 lines inter...Help
invlogitutilities/distributions.rInverse logit transformation, turns...Help
is.betweenutilities/geometry.rCheck whether a point x,y falls bet...Help
is.leaputilities/utilities.rReturn a logical indicating which e...Help
is.oddutilities/statistics.rA trivial function to test whether ...Help
ispt.insideutilities/geometry.rCheck a single pt (x and y) against...Help
leftutilities/utilities.rA standard left function. Returns t...Help
leftbututilities/utilities.rReturns the leftmost characters of ...Help
line.intersection.ptsutilities/geometry.rFinds the point where 2 lines inter...Help
linear.modelutilities/distributions.rA simple linear model, where the fi...Help
linear.model.ctrutilities/distributions.rA simple linear model, where the fi...Help
linear.mortmodelutilities/distributions.rA model for mortality as a function...Help
linearmodel.binutilities/distributions.rMultiple bin model predicting y as ...Help
linearmodel.bin.setutilities/distributions.rThis does the work of calculating p...Help
llike.GaussModelutilities/statistics.rThis is for model.xy. It takes the ...Help
llike.GaussModelSDutilities/statistics.rThis is for model.xy. Take the func...Help
llike.linearbin.optimgrowth/growthfit.bin.rThis is for optim, a single functio...Help
llike.model.lmerutilities/lmerBayes.rA llikelihood function for one set ...Help
llike.model.lmerutilities/lmerBayes.rA llikelihood function for one set ...Help
lmerBayesutilities/lmerBayes.rA Metropolis MCMC version of lmer. ...Help
lmerBayes.hyperllike.meanutilities/lmerBayes.rThis is the hyper-likelihood for up...Help
lmerBayes.hyperllike.sigmautilities/lmerBayes.rThis is the hyper-likelihood for up...Help
lmerMortFixedTimedemogchange/demogChange.rA model for mortality as a function...Help
lmerMortLineardemogchange/demogChange.rA linear model of an annual mortali...Help
load.speciesutilities/utilitiesCTFS.rA function for extracting a single ...Help
log.modelutilities/distributions.rLogarithmic model, y = a + b1 log(x...Help
logical.greputilities/utilities.rA form of grep returning logical in...Help
logistic.ctrutilities/distributions.rThis is logistic function with inte...Help
logistic.interutilities/distributions.rLogistic function with intercept pa...Help
logistic.multiplicativeutilities/distributions.rLogistic with a pair of parameters ...Help
logistic.powerutilities/distributions.rThis is the Gaussian logistic funct...Help
logistic.power.modeutilities/distributions.rThis is the Gaussian logistic funct...Help
logistic.power_simpleutilities/distributions.rThis is a mixture of logistic and l...Help
logistic.standardutilities/distributions.rThis is standard logistic function,...Help
logistic.sum.squaresutilities/distributions.rSets a prediction based on a genera...Help
logisticmodel.binutilities/distributions.rMultiple bin model predicting y as ...Help
logitutilities/distributions.rLogit transformation for a probabil...Help
lxly.to.p5spatial/quadfunc.rGiven local, or within-quadrat, co...Help
majoraxisregutilities/statistics.rA major axis regression with parame...Help
majoraxisreg.no.intutilities/statistics.rMajor axis regression with no inter...Help
make.CredIntervalVectutilities/utilities.rTake a vector y having mean then lo...Help
mapmap/map.rFunction to draw map of one or more...Help
map1speciesmap/map.rThis does the mapping for a single ...Help
map2speciesmap/map.rMap 2 species to a 2-panel pdf. Two...Help
maptopomap/map.rDraws contours on a plot map. Elevm...Help
match.dataframeutilities/utilities.rMatches two dataframes using two or...Help
merge.datautilities/utilities.rCombine many dataframes as elements...Help
mergeParamutilities/utilities.rMerges a list of parameter matrices...Help
metrop1steputilities/statistics.rTakes a single metropolis step on a...Help
metrop1step.discreteutilities/statistics.rA version for metrop1step where the...Help
midPointutilities/statistics.rMidpoint of any vector....Help
minum.beta.normalutilities/distributions.rFunction to be minimized for fittin...Help
minum.mixnormutilities/distributions.rFit a mixture of 2 normals....Help
minum.normalutilities/distributions.rThe likelihood function for use by ...Help
minum.perpdistutilities/statistics.rThe sum of squares used by majoraxi...Help
model.littleR.Gibbsdemogchange/abund.fit.CTFS.rThe main function for fitting the p...Help
model.xyutilities/statistics.rGeneric Bayesian routine for fittin...Help
modelBayesutilities/modelBayes.rA Metropolis MCMC version for any m...Help
mortalitymortality/mortality.rMortality is the main function, and...Help
mortality.calculationmortality/mortality.rThis is the calculation of mortalit...Help
mortality.dbhmortality/mortality.rCalculate forest-wide mortality in ...Help
mortality.eachsppmortality/mortality.rCalculate mortality for each specie...Help
mvrnormRCutilities/distributions.rFunction that takes a variance-cova...Help
NDcountspatial/NeighborDensityFun.rCalculates the count of neighbors w...Help
NeighborDensitiesspatial/NeighborDensityFun.rCalculates the total number or basa...Help
neighborsspatial/quadfunc.rFinds proportion of neighboring qua...Help
nhdutilities/utilities.rA version of head with only 6 colum...Help
normalproductutilities/distributions.rA function which returns the produc...Help
order.by.rowcolutilities/utilities.rReorder rows and columns of a matri...Help
order.bynumberutilities/utilities.rReturns ordering of a character vec...Help
overlay.growthbinmodelgrowth/growthfit.graph.rShow model fits for 1, 2, 3, and 4 ...Help
parallel.lineutilities/geometry.rFinds the slope and intercept of th...Help
partialcircleareaspatial/RipUvK.rCalculates the area of a circle of ...Help
pdf.allplotmap/map.rExport a pdf with one or more speci...Help
perpendicular.distanceutilities/geometry.rDistance from a point to a line (so...Help
perpendicular.lineutilities/geometry.rFinds the slope and intercept of th...Help
pexp.sinutilities/distributions.rCDF of four-parameter exponential s...Help
plot.waveletspatial/block.analysis.rFunction to plot the wavelet varian...Help
png.allplotmap/map.rExport species maps as png. There w...Help
polar.to.cartesianutilities/geometry.rConvert polar coordinates to Cartes...Help
pop.changeabundance/abundance.rFinds abundance, basal area, or agb...Help
pop.change.dbhabundance/abundance.rFinds abundance or basal area in tw...Help
pospowerutilities/distributions.rRaise to any power, but with negati...Help
predht.asymbiomass/biomass.CTFSdb.rAn allometric model predicting an a...Help
prob.N1demogchange/abund.fit.CTFS.rCalculates the probability of obser...Help
pstutilities/utilities.rA version of paste with sep=''....Help
psymexputilities/distributions.rThe CDF for the symmetric exponenti...Help
pts.to.interceptslopeutilities/geometry.rReturns intercept and slope of a li...Help
pweibull.3paramutilities/distributions.rCDF of three-parameter Weibull (htt...Help
qasymexputilities/distributions.rQuantiles of dasymexp...Help
qasympowerutilities/distributions.rQuantiles from the bilateral power ...Help
quad.to.gxgyspatial/quadfunc.rConvert quadrat names into x-y coor...Help
quadslopetopography/slope.rGiven the elevation at four corners...Help
randomRowutilities/utilities.rReturn a random row from a datafram...Help
randomRowutilities/utilities.rReturn a random element from a vect...Help
rarefy.diversityutilities/calcalpha.rtakes a full plot dataframe and cal...Help
rasterizespatial/block.analysis.rFunction to calculate the count (ty...Help
rasympowerutilities/distributions.rRandom draws from the bilateral pow...Help
readelevdatatopography/slope.rA function to read a table of eleva...Help
rearrangeSurveyDatatopography/solvetopo.rTakes a table of survey sightings w...Help
recalculate.lmerBayesllikeutilities/lmerBayes.rWalk through entire chain of parame...Help
recruitmentrecruitment/recruitment.rFunctions for calculating recruitme...Help
recruitment.eachspprecruitment/recruitment.rA wrapper to calculate recruitment ...Help
regress.loglogutilities/statistics.rPerforms regression and graphs in a...Help
regress.plotutilities/statistics.rPerforms regression in convenient w...Help
regression.Bayesutilities/statistics.rRegression using the Gibbs sampler,...Help
regslopeutilities/statistics.rReturns slope of regression as sing...Help
regslope.nointutilities/statistics.rReturns slope of regression with no...Help
regsumutilities/statistics.rThis carries out either first or se...Help
resetParamutilities/lmerBayes.rThis starts a new 3D parameter arra...Help
residual.llike.lmerBayesutilities/lmerBayes.rCalculate likelihood of residual st...Help
residual.llike.modelBayesutilities/modelBayes.rCalculate likelihood of residual st...Help
restoreParamFileutilities/lmerBayes.rReverses the steps of saveParamFile...Help
rgamma.meansdutilities/distributions.rRandom draws of gamma, parameterize...Help
rightutilities/utilities.rReturns the rightmost n characters ...Help
rightbututilities/utilities.rReturns the rightmost characters of...Help
RipUvKspatial/RipUvK.rRipley's K using splancs. Computes ...Help
rmixnormutilities/distributions.rRandom draw on the mixed normal dis...Help
rndown5utilities/utilitiesCTFS.rRounds a numeric value to the next ...Help
rowcol.to.indexspatial/quadfunc.rNone given....Help
rpois.maxutilities/distributions.rRandom draws on dpois.max...Help
rpois.truncutilities/distributions.rRandom draws on dpois.trunc. This i...Help
rpowerutilities/distributions.rRandom draws based on the integral....Help
rsymexputilities/distributions.rDrawing a random variate on the sym...Help
run.growthbin.manysppgrowth/growthfit.bin.rRun the model to fit growth rate in...Help
run.growthfit.bingrowth/growthfit.bin.rFind best fits for linearmodel.bin,...Help
save.searchpathutilities/utilities.rSaves all functions in position n t...Help
saveParamFileutilities/lmerBayes.rThis saves a run of the full parame...Help
SectionCorrectiontopography/imageJ.rThis function is called by fullplot...Help
segmentPtutilities/geometry.rDraw a line segment between two poi...Help
selectrandomquadspeciesarea/spparea.rDraws rectangular quadrats in a plo...Help
selectrandomquad2speciesarea/spparea.rCreates randomly drawn quadrats, us...Help
selectrandomquad3speciesarea/spparea.rCreates randomly drawn quadrats, us...Help
setsizemap/map.rAn internal function, called by map...Help
simpleutilities/distributions.rAn even more trivial model to retur...Help
simple.modelutilities/distributions.rA trivial model to return a differe...Help
skewnessutilities/statistics.rSample skewness. The biased portion...Help
skewnessutilities/statistics.rStandard error of skewness. Depends...Help
skewnessutilities/statistics.rSample kurtosis. The biased portion...Help
skewnessutilities/statistics.rStandard error of kurtosis. Depends...Help
slope.intercept.fromptsutilities/geometry.rThis is an old version of pts.to.in...Help
solve.topotopography/solvetopo.rThis is based on the problem and so...Help
split.datautilities/utilities.rConverts a big dataframe into a lis...Help
spmean.mort.abundGibbsdemogchange/abund.fit.CTFS.rLikelihood function for a species m...Help
spparea.sqspeciesarea/spparea.rFunction for calculating the number...Help
standardreg.no.intutilities/statistics.rStandard regression with no interce...Help
startCTFSstartCTFS/startCTFS.rFunction to source all components o...Help
StringToVectutilities/utilities.rConverts a character string into a ...Help
summaryMCMCutilities/lmerBayes.rMake summary calculations based on ...Help
summaryModelMCMCutilities/modelBayes.rMake summary calculations based on ...Help
sumsqutilities/statistics.rA trivial function used in minimizi...Help
testmcmcfuncutilities/statistics.rFor testing mcmc1step. No longer us...Help
TextToRdatautilities/utilities.rReads a tab-delimited text file and...Help
tojulianutilities/utilities.rAccepts any character representatio...Help
torus.shiftspatial/quadfunc.rCreates a torus-shifted quadrat top...Help
trimutilities/utilities.rTrims leading and trailing blanks f...Help
trim.growthgrowth/growth.rThis is where growth rates are excl...Help
unidentified.speciesutilities/utilitiesCTFS.rTakes a string of species names or ...Help
vectToCommasutilities/utilities.rGiven a vector of character variabl...Help
wavelet.allspspatial/block.analysis.rFunction to calculate the wavelet v...Help
wavelet.bivariatespatial/block.analysis.rFunction to calculate the wavelet v...Help
wavelet.univariatespatial/block.analysis.rFunction to calculate the univariat...Help
weibull.mean.3paramutilities/distributions.rMean of three-parameter Weibull...Help
weibull.median.3paramutilities/distributions.rMedian of three-parameter Weibull...Help
weibull.sd.3paramutilities/distributions.rSD of three-parameter Weibull...Help
which.allnonNAutilities/utilities.rFinds all values of a vector which ...Help
which.maxNAsutilities/utilities.rAn unfortunate bug in which.max: if...Help
which.nonNAutilities/utilities.rReturns the first index at which a ...Help
which.vmatchutilities/utilities.rFinds which subsequent element of a...Help
wideEnoughBinsgrowth/growthfit.bin.rTest whether all the bin widths exc...Help
xydistutilities/geometry.rDistance between two pairs of x-y c...Help
xydistmatutilities/geometry.rDistance between two x-y coordinate...Help
xydistvectutilities/geometry.rDistance between two x-y coordinate...Help