CTFS R Function Index
| Function | File | Description | Link |
|---|---|---|---|
| abund.manycensus | abundance/abundance.r | Collect abundances of all species a... | Help |
| abundance | abundance/abundance.r | Calculates total abundance or basal... | Help |
| abundance.spp | abundance/abundance.r | A wrapper to calculate total abunda... | Help |
| abundanceperquad | abundance/abundance.r | Finds abundance, basal area, or agb... | Help |
| abundmodel.fit | demogchange/abund.fit.CTFS.r | Simply return the modeled histogram... | Help |
| addBinParam | utilities/distributions.r | Given parameters for a model with N... | Help |
| agb.dbhmodel | biomass/biomass.CTFSdb.r | Calculates biomass from density and... | Help |
| AGB.ind | biomass/biomass.CTFSdb.r | Compute biomass (agb) based on one ... | Help |
| agb.model | biomass/biomass.CTFSdb.r | Calculates biomass from density, he... | Help |
| AGB.tree | biomass/biomass.CTFSdb.r | Computes AGB of each tree in a tabl... | Help |
| allquadratslopes | spatial/slope.r | functions for calculating slope of ... | Help |
| allquadratslopes | topography/slope.r | functions for calculating slope of ... | Help |
| Annuli | spatial/RipUvK.r | Calculates the total area in a seri... | Help |
| are.ptsinside | utilities/geometry.r | Checks many points (dataframe pt wi... | Help |
| arrangeParam.Gibbs.2D | utilities/lmerBayes.r | Used in the loop of a Gibbs sampler... | Help |
| arrangeParam.llike | utilities/statistics.r | Used in likelihood function of a Gi... | Help |
| arrangeParam.llike.2D | utilities/lmerBayes.r | Used in likelihood function of a Gi... | Help |
| assemble.demography | utilities/utilitiesCTFS.r | Takes output of a demographic analy... | Help |
| assembleBinOutput | growth/growthfit.bin.r | Use the list output from piecewise ... | Help |
| asymp.ht | utilities/distributions.r | The function from Sean Thomas which... | Help |
| asymp.ht.fixmax | utilities/distributions.r | Same formulation, but the asymptote... | Help |
| asymptote.exp | utilities/distributions.r | A 3-parameter function which asympt... | Help |
| attach_if_needed | utilities/utilities.r | Attach one or more datafiles,checki... | Help |
| autoregression | utilities/statistics.r | Autocorrelation with a given lag of... | Help |
| ba | abundance/abundance.r | Calculates the individual basal are... | Help |
| bad.asymexp.param | demogchange/abund.fit.CTFS.r | For either the Gaussian, or asymexp... | Help |
| bad.asympower.param | demogchange/abund.fit.CTFS.r | The 3 parameters submitted to hyper... | Help |
| bad.binparam | growth/growthfit.bin.r | This prevents the bin parameters fr... | Help |
| bad.binsdpar | growth/growthfit.bin.r | ... | Help |
| bad.paretopar | utilities/distributions.r | Test whether parameters for the Par... | Help |
| BadParam | utilities/statistics.r | This is a default for model.xy, nev... | Help |
| badSD | utilities/lmerBayes.r | ... | Help |
| basum | abundance/abundance.r | Returns the basal area summed over ... | Help |
| beta.normalized | utilities/distributions.r | Normalzing beta.total. No longer us... | Help |
| beta.total | utilities/distributions.r | A beta distribution on the interval... | Help |
| betaproduct | utilities/distributions.r | This is equivalent to the normal pr... | Help |
| binGraphManySpecies | growth/growthfit.graph.r | Make a graph of AGB growth and mode... | Help |
| binGraphManySpecies.Panel | growth/growthfit.graph.r | Make a graph, 4 panels, of AGB grow... | Help |
| binGraphSampleSpecies | growth/growthfit.graph.r | Make a single graph, 4 panels, of A... | Help |
| biomass.change | biomass/biomass.CTFSdb.r | Finds biomass in two censuses and c... | Help |
| biomass.CTFSdb | biomass/biomass.CTFSdb.r | Calculate biomass from existing R-f... | Help |
| biomass.growth | growth/growth.r | Like growth(), but calculates chang... | Help |
| bootconf | utilities/statistics.r | A simple calculation of confidence ... | Help |
| bootstrap.corr | utilities/statistics.r | Running bootstrap on a correlation.... | Help |
| border.distance | utilities/statistics.r | Returns distance from a point to th... | Help |
| calc.directionslope | spatial/slope.r | This runs equations 1-3 of Seibert ... | Help |
| calc.directionslope | topography/slope.r | This runs equations 1-3 of Seibert ... | Help |
| calc.gradient | spatial/slope.r | Calculate flow using Seibert & McGl... | Help |
| calc.gradient | topography/slope.r | Calculate flow using Seibert & McGl... | Help |
| calcalpha | utilities/calcalpha.r | Calculates alpha from a stem and sp... | Help |
| calcMortlmerTable | demogchange/demogChange.r | Calculate mortality rate per specie... | Help |
| CalcRingArea | spatial/RipUvK.r | Given a dataframe that includes gx,... | Help |
| calcS.alpha | utilities/calcalpha.r | Estimated number of species in a sa... | Help |
| calcslope | spatial/slope.r | None provided.... | Help |
| calcslope | topography/slope.r | None provided.... | Help |
| calculateBinModel.AIC | growth/growthfit.bin.r | Calculate AIC of the model, using v... | Help |
| calculateBinModel.bestpred | growth/growthfit.bin.r | Calculate mean predicted value at e... | Help |
| calculateBinModel.BIC | growth/growthfit.bin.r | Calculate Bayes Information Criteri... | Help |
| center.predictors | utilities/distributions.r | Transform all data by subtracting a... | Help |
| charlocate | utilities/utilities.r | Finds position of a substring needl... | Help |
| Chave.AGB | biomass/biomass.CTFSdb.r | The Chave 2005 Oecologia model for ... | Help |
| CI | utilities/statistics.r | Confidence limits (quantiles) from ... | Help |
| circle | utilities/geometry.r | Calculates points on a... | Help |
| circlearea | spatial/RipUvK.r | Simply returns area of a circle of ... | Help |
| clean.demography | utilities/utilitiesCTFS.r | This takes a CTFS demography table,... | Help |
| coldata.to.imagemat | map/mapresponse.r | These functions create maps of resp... | Help |
| colMedians | utilities/statistics.r | For convenient medians, like colMea... | Help |
| compare.growthbinmodel | growth/growthfit.graph.r | Calculates various metrics of fit: ... | Help |
| complete.plotmap | map/map.r | This creates a map with every indiv... | Help |
| constant | utilities/distributions.r | A function to return a constant at ... | Help |
| constant.bin | utilities/distributions.r | A model like piecewise regression (... | Help |
| constant.linear | utilities/distributions.r | A model which is constant for x| Help | |
| convert.factor | utilities/utilities.r | Converts any character fields in a ... | Help |
| convert.rowcol | spatial/quadfunc.r | Convert an integer to a character, ... | Help |
| CountByGroup | utilities/utilities.r | Groups a dataframe by one or more c... | Help |
| countEmpty | utilities/utilities.r | Counts vector elements that are NA ... | Help |
| countNA | utilities/utilities.r | Counts vector elements that are NA.... | Help |
| countone | utilities/utilities.r | Counts vector elements exactly one.... | Help |
| countpresent | utilities/utilities.r | Counts vector elements > 0. See cou... | Help |
| countspp | utilities/utilitiesCTFS.r | Returns the number of elements in a... | Help |
| countUnique | utilities/utilities.r | Count the number of unique elements... | Help |
| countzero | utilities/utilities.r | Counts vector elements exactly zero... | Help |
| coverage.diag | speciesarea/spparea.r | Draws a diagonal across a plot, fro... | Help |
| covTocorr | utilities/lmerBayes.r | Convert covariance matrix to correl... | Help |
| create.fulldate | utilities/utilities.r | Converts a vector of date character... | Help |
| create.fulldate.split | utilities/utilities.r | Converts the MySQL date format by s... | Help |
| create.neighbordata | spatial/quadfunc.r | Calculates the mean density in neig... | Help |
| CTFSplot | utilities/utilitiesCTFS.r | A convenience for attaching the R A... | Help |
| cumul.above | utilities/statistics.r | Given y values as a function of x, ... | Help |
| d.calcS.alpha | utilities/calcalpha.r | The derivative for use in Newton's ... | Help |
| dasymexp | utilities/distributions.r | Probability distributions for a fol... | Help |
| dasymexp | utilities/distributions.r | Probability distributions for an as... | Help |
| dasympower | utilities/distributions.r | A bilateral power distribution, cen... | Help |
| dbeta.reparam | utilities/distributions.r | This reparameterizes the beta distr... | Help |
| DBHtransition | growth/growth.r | Calculates a transition matrix of i... | Help |
| dbinomrev | utilities/distributions.r | A version of dbinom in which parame... | Help |
| default.badpar | utilities/distributions.r | None given.... | Help |
| define.graphwindow | map/map.r | This defines an export device for a... | Help |
| defineBinBreaks | growth/growthfit.bin.r | This finds divisions of over the ve... | Help |
| defineSDpar | growth/growthfit.bin.r | For default SD parameters, if nothi... | Help |
| density.ind | biomass/biomass.CTFSdb.r | Create a vector of wood density for... | Help |
| detachfiles | utilities/utilities.r | detachs from the searchpath files m... | Help |
| dexp.sin | utilities/distributions.r | Four-parameter exponential sin, as ... | Help |
| dgamma.mean | utilities/distributions.r | A version of dgamma where the param... | Help |
| dgamma.meansd | utilities/distributions.r | Probability distribution of gamma, ... | Help |
| dgamma.scale | utilities/distributions.r | Like above, but with scale as the f... | Help |
| dgammadexp | utilities/distributions.r | PDF of a function formed by adding ... | Help |
| dgammaMinusdexp | utilities/distributions.r | The PDF of the difference between a... | Help |
| dgammaPlusdexp | utilities/distributions.r | The PDF of the sum of gamma and neg... | Help |
| distance | spatial/quadfunc.r | Calculates the distance from one qu... | Help |
| distance.to.side | topography/imageJ.r | Called from imageJ.to.lxly where fo... | Help |
| ditch | utilities/utilities.r | Detaches all files at one or more s... | Help |
| dmixnorm | utilities/distributions.r | Mixed normal distribution. The para... | Help |
| dnormprod0 | utilities/distributions.r | Probability density of product of t... | Help |
| dnormrev | utilities/distributions.r | This reverses the order of paramete... | Help |
| doublenormal | utilities/distributions.r | Simulate draws from a double normal... | Help |
| dpois.max | utilities/distributions.r | A probability distribution which is... | Help |
| dpois.maxtrunc | utilities/distributions.r | A zero-truncated Poisson distributi... | Help |
| dpois.rearrange | utilities/distributions.r | This rearranges dpois so that it wo... | Help |
| dpower | utilities/distributions.r | A probability distribution defined ... | Help |
| draw.axes | map/mapresponse.r | Add axes to a graph, with ticks spa... | Help |
| drawrectangle | utilities/geometry.r | Draws a rectangle given a matrix or... | Help |
| drp | utilities/utilities.r | A version of drop which includes as... | Help |
| dsymexp | utilities/distributions.r | Probability distribution for a fold... | Help |
| dweibull.3param | utilities/distributions.r | PDF of three-parameter Weibull... | Help |
| elev.to.list | spatial/slope.r | A function which reads a dataframe ... | Help |
| elev.to.list | topography/slope.r | A function which reads a dataframe ... | Help |
| ellipse | utilities/geometry.r | Equation for (half) a canonical... | Help |
| exclude.unidentified | utilities/utilitiesCTFS.r | A more specialized version of unide... | Help |
| exp.2par | utilities/distributions.r | An exponential distribution with an... | Help |
| expon.model | utilities/distributions.r | Exponential model, y = a exp(b1*x1 ... | Help |
| exponential.sin | utilities/distributions.r | Five-parameter exponential sin... | Help |
| extract.growthdata | growth/growthfit.bin.r | Extract data for growth rates from ... | Help |
| fill.1dimension | utilities/utilities.r | Filling a 1D array resulting from t... | Help |
| fill.dimension | utilities/utilities.r | This function fills out an array of... | Help |
| find.climits | mortality/mortality.r | Calculates confidence limits around... | Help |
| find.nonNA | utilities/utilities.r | Returns the first value of a vector... | Help |
| find.xaxis.hist | demogchange/abund.fit.CTFS.r | Given an abundance fit and x axis r... | Help |
| findborderquads | spatial/quadfunc.r | Calculate indices of neighboring qu... | Help |
| findneighborabund | spatial/quadfunc.r | For every quadrat, finds neighborin... | Help |
| fit.beta.normal | utilities/distributions.r | Finding a normal distribution which... | Help |
| fit.logistic | utilities/distributions.r | A function to fit a set of data y, ... | Help |
| fit.pdf | utilities/distributions.r | Fit a random variable x to any subm... | Help |
| fitnorm | utilities/distributions.r | Fitting a normal distribution to da... | Help |
| fitSeveralAbundModel | demogchange/abund.fit.CTFS.r | Run model.littleR.Gibbs for a serie... | Help |
| fromjulian | utilities/utilities.r | Accepts a julian date and returns a... | Help |
| full.abundmodel.llike | demogchange/abund.fit.CTFS.r | With the table of abundances, hyper... | Help |
| full.likelihood.lmerBayes | utilities/lmerBayes.r | Calculate full likelihood for any c... | Help |
| full.xygrid | spatial/quadfunc.r | Create a complete of points x-y, gi... | Help |
| fullcircle | utilities/geometry.r | Create a dataframe for a full circl... | Help |
| fullellipse | utilities/geometry.r | Creates a dataframe for a full elli... | Help |
| fullplot.imageJ | topography/imageJ.r | Reads quadrat maps created by image... | Help |
| gen.logistic | utilities/distributions.r | A general logistic function, simila... | Help |
| get.filename | map/map.r | This sets a name for outputting a m... | Help |
| getquadratname | spatial/quadfunc.r | Convert x, y coordinates and plot d... | Help |
| getsmallerquads | spatial/quadfunc.r | Takes a vector of indices for a lar... | Help |
| getTopoLinks | topography/solvetopo.r | This is solely for use by solve.top... | Help |
| Gibbs.normalmean | utilities/statistics.r | The standard Gibbs sampler for a no... | Help |
| Gibbs.normalvar | utilities/statistics.r | Gibbs draw for the variance of a no... | Help |
| Gibbs.regsigma | utilities/statistics.r | Updates the regression standard dev... | Help |
| Gibbs.regslope | utilities/statistics.r | Updates the regression slope (used ... | Help |
| graph.abundmodel | demogchange/abund.fit.CTFS.r | Output histograms of little.r acros... | Help |
| graph.growthmodel | growth/growthfit.graph.r | Graph growth rates and model fit.... | Help |
| graph.growthmodel.spp | growth/growthfit.graph.r | Use output of growth.flexbin to gra... | Help |
| graph.modeldiag | utilities/statistics.r | Graph diagnostics of model.xy... | Help |
| graph.mvnorm | utilities/distributions.r | Graphs contours for an mvnorm, with... | Help |
| graph.outliers | growth/growthfit.graph.r | Graph the outliers overlaid on the ... | Help |
| graph.outliers.spp | growth/growthfit.graph.r | Pass the output of extract.growth w... | Help |
| graph.quadrats | speciesarea/spparea.r | Make a graph of a series of quadrat... | Help |
| growth | growth/growth.r | The principle growth function, cons... | Help |
| growth.biomass.indiv | growth/growth.r | Like growth.indiv but based on agb ... | Help |
| growth.dbh | growth/growth.r | This calculates forest-wide growth ... | Help |
| growth.eachspp | growth/growth.r | This calculates growth for each spe... | Help |
| growth.flexbin | growth/growthfit.bin.r | Fitting a regression line through l... | Help |
| growth.indiv | growth/growth.r | This returns a complete table with ... | Help |
| gsp | utilities/utilities.r | Returns one of the objects at a giv... | Help |
| gxgy.to.hectindex | spatial/quadfunc.r | ... | Help |
| gxgy.to.index | spatial/quadfunc.r | Assign any location(s) a single ind... | Help |
| gxgy.to.lxly | spatial/quadfunc.r | Given global coordinates and quadra... | Help |
| gxgy.to.quad | spatial/quadfunc.r | Calculate a quadrat name (column nu... | Help |
| gxgy.to.rowcol | spatial/quadfunc.r | ... | Help |
| harmonic.mean | utilities/statistics.r | Harmonic mean of a vector x. NAs an... | Help |
| hist.compare | utilities/statistics.r | Compares two histograms with a Kolm... | Help |
| hyper.abundGibbs | demogchange/abund.fit.CTFS.r | Likelihood function for hyperparame... | Help |
| hyper.mortGibbs | demogchange/abund.fit.CTFS.r | Likelihood function for logMu and l... | Help |
| IfElse | utilities/utilities.r | A more convenient version of the R ... | Help |
| image.dataframe | map/mapresponse.r | Creates a color response map based ... | Help |
| imageGraph | map/mapresponse.r | Maps a response variable with R's c... | Help |
| imageJ.to.lxly | topography/imageJ.r | Convert map pixels from digitzing p... | Help |
| index.to.gxgy | spatial/quadfunc.r | Calculate the x and y coordinates g... | Help |
| index.to.rowcol | spatial/quadfunc.r | Calculate the row and column given ... | Help |
| individual_grow.table | demogchange/demogChange.r | Create a table of individual trees ... | Help |
| individual_mort.table | demogchange/demogChange.r | Create a table of individual trees ... | Help |
| inside.rect | utilities/geometry.r | Determines whether any of the 4 cor... | Help |
| insideRectangle | utilities/geometry.r | Checks a vector of coordinates x, y... | Help |
| intersection.of.lines | utilities/geometry.r | Finds the point where 2 lines inter... | Help |
| invlogit | utilities/distributions.r | Inverse logit transformation, turns... | Help |
| is.leap | utilities/utilities.r | Return a logical indicating which e... | Help |
| is.odd | utilities/statistics.r | A trivial function to test whether ... | Help |
| ispt.inside | utilities/geometry.r | Check a single pt (x and y) against... | Help |
| left | utilities/utilities.r | A standard left function. Returns t... | Help |
| leftbut | utilities/utilities.r | Returns the leftmost characters of ... | Help |
| line.intersection | utilities/geometry.r | Old version of function to return p... | Help |
| line.intersection.pts | utilities/geometry.r | Finds the point where 2 lines inter... | Help |
| linear.model | utilities/distributions.r | A simple linear model, where the fi... | Help |
| linear.model.ctr | utilities/distributions.r | A simple linear model, where the fi... | Help |
| linearmodel.bin | utilities/distributions.r | Multiple bin model predicting y as ... | Help |
| linearmodel.bin.set | utilities/distributions.r | This does the work of calculating p... | Help |
| llike.GaussModel | utilities/statistics.r | This is for model.xy. It takes the ... | Help |
| llike.GaussModelSD | utilities/statistics.r | This is for model.xy. Take the func... | Help |
| llike.linearbin.optim | growth/growthfit.bin.r | This is for optim, a single functio... | Help |
| llike.model.lmer | utilities/lmerBayes.r | A llikelihood function for one set ... | Help |
| lmerBayes | utilities/lmerBayes.r | A Metropolis MCMC version of lmer. ... | Help |
| lmerBayes.hyperllike.mean | utilities/lmerBayes.r | This is the hyper-likelihood for up... | Help |
| lmerBayes.hyperllike.sigma | utilities/lmerBayes.r | This is the hyper-likelihood for up... | Help |
| lmerMortFixedTime | demogchange/demogChange.r | A model for mortality as a function... | Help |
| lmerMortLinear | demogchange/demogChange.r | A model for mortality as a function... | Help |
| load.species | utilities/utilitiesCTFS.r | A function for extracting a single ... | Help |
| log.model | utilities/distributions.r | Logarithmic model, y = a + b1 log(x... | Help |
| logical.grep | utilities/utilities.r | A form of grep returning logical in... | Help |
| logistic.ctr | utilities/distributions.r | This is logistic function with inte... | Help |
| logistic.inter | utilities/distributions.r | Logistic function with intercept pa... | Help |
| logistic.multiplicative | utilities/distributions.r | Logistic with a pair of parameters ... | Help |
| logistic.power | utilities/distributions.r | This is the Gaussian logistic funct... | Help |
| logistic.power.mode | utilities/distributions.r | This is the Gaussian logistic funct... | Help |
| logistic.power_simple | utilities/distributions.r | This is a mixture of logistic and l... | Help |
| logistic.standard | utilities/distributions.r | This is standard logistic function,... | Help |
| logistic.sum.squares | utilities/distributions.r | Sets a prediction based on a genera... | Help |
| logit | utilities/distributions.r | Logit transformation for a probabil... | Help |
| majoraxisreg | utilities/statistics.r | A major axis regression with parame... | Help |
| majoraxisreg.no.int | utilities/statistics.r | Major axis regression with no inter... | Help |
| map | map/map.r | Function to draw map of one or more... | Help |
| map1species | map/map.r | This does the mapping for a single ... | Help |
| map2species | map/map.r | Map 2 species to a 2-panel pdf. Two... | Help |
| maptopo | map/map.r | Draws contours on a plot map. Elevm... | Help |
| match.dataframe | utilities/utilities.r | Matches two dataframes using two or... | Help |
| merge.data | utilities/utilities.r | Combine many dataframes as elements... | Help |
| mergeParam | utilities/utilities.r | Merges a list of parameter matrices... | Help |
| metrop1step | utilities/statistics.r | Takes a single metropolis step on a... | Help |
| metrop1step.discrete | utilities/statistics.r | A version for metrop1step where the... | Help |
| midPoint | utilities/statistics.r | Midpoint of any vector.... | Help |
| minum.beta.normal | utilities/distributions.r | Function to be minimized for fittin... | Help |
| minum.mixnorm | utilities/distributions.r | Fit a mixture of 2 normals.... | Help |
| minum.normal | utilities/distributions.r | The likelihood function for use by ... | Help |
| minum.perpdist | utilities/statistics.r | The sum of squares used by majoraxi... | Help |
| model.littleR.Gibbs | demogchange/abund.fit.CTFS.r | The main function for fitting the p... | Help |
| model.xy | utilities/statistics.r | Generic Bayesian routine for fittin... | Help |
| mortality | mortality/mortality.r | Mortality is the main function, and... | Help |
| mortality.calculation | mortality/mortality.r | This is the calculation of mortalit... | Help |
| mortality.dbh | mortality/mortality.r | Calculate forest-wide mortality in ... | Help |
| mortality.eachspp | mortality/mortality.r | Calculate mortality for each specie... | Help |
| mvrnormRC | utilities/distributions.r | Function that takes a variance-cova... | Help |
| NDcount | spatial/NeighborDensityFun.r | Calculates the count of neighbors w... | Help |
| NeighborDensities | spatial/NeighborDensityFun.r | Calculates the density of conspecif... | Help |
| neighbors | spatial/quadfunc.r | Finds proportion of neighboring qua... | Help |
| nhd | utilities/utilities.r | A version of head with only 6 colum... | Help |
| normalproduct | utilities/distributions.r | A function which returns the produc... | Help |
| order.by.rowcol | utilities/utilities.r | Reorder rows and columns of a matri... | Help |
| order.bynumber | utilities/utilities.r | Returns ordering of a character vec... | Help |
| overlay.growthbinmodel | growth/growthfit.graph.r | Show model fits for 1, 2, 3, and 4 ... | Help |
| parallel.line | utilities/geometry.r | Finds the slope and intercept of th... | Help |
| partialcirclearea | spatial/RipUvK.r | Calculates the area of a circle of ... | Help |
| pdf.allplot | map/map.r | Export a pdf with one or more speci... | Help |
| perpendicular.distance | utilities/geometry.r | Distance from a point to a line (so... | Help |
| pexp.sin | utilities/distributions.r | CDF of four-parameter exponential s... | Help |
| plot.wavelet | spatial/block.analysis.r | Function to plot the wavelet varian... | Help |
| png.allplot | map/map.r | Export species maps as png. There w... | Help |
| pop.change | abundance/abundance.r | Finds abundance, basal area, or agb... | Help |
| pop.change.dbh | abundance/abundance.r | Finds abundance or basal area in tw... | Help |
| pospower | utilities/distributions.r | Raise to any power, but with negati... | Help |
| predht.asym | biomass/biomass.CTFSdb.r | An allometric model predicting an a... | Help |
| prob.N1 | demogchange/abund.fit.CTFS.r | Calculates the probability of obser... | Help |
| pst | utilities/utilities.r | A version of paste with sep=''.... | Help |
| psymexp | utilities/distributions.r | The CDF for the symmetric exponenti... | Help |
| pts.to.interceptslope | utilities/geometry.r | Gets slope and intercept of a line ... | Help |
| pweibull.3param | utilities/distributions.r | CDF of three-parameter Weibull (htt... | Help |
| qasympower | utilities/distributions.r | Quantiles from the bilateral power ... | Help |
| quad.to.gxgy | spatial/quadfunc.r | Convert quadrat names into x-y coor... | Help |
| quadslope | spatial/slope.r | None provided.... | Help |
| quadslope | topography/slope.r | None provided.... | Help |
| randomRow | utilities/utilities.r | Return a random row from a datafram... | Help |
| randomRow | utilities/utilities.r | Return a random element from a vect... | Help |
| rarefy.diversity | utilities/calcalpha.r | takes a full plot dataframe and cal... | Help |
| rasterize | spatial/block.analysis.r | Function to calculate the count (ty... | Help |
| rasympower | utilities/distributions.r | Random draws from the bilateral pow... | Help |
| readelevdata | spatial/slope.r | A function to read a table of eleva... | Help |
| readelevdata | topography/slope.r | A function to read a table of eleva... | Help |
| rearrangeSurveyData | topography/solvetopo.r | Takes a table of survey sightings w... | Help |
| recalculate.lmerBayesllike | utilities/lmerBayes.r | Walk through entire chain of parame... | Help |
| recruitment | recruitment/recruitment.r | Functions for calculating recruitme... | Help |
| recruitment.eachspp | recruitment/recruitment.r | A wrapper to calculate recruitment ... | Help |
| regress.loglog | utilities/statistics.r | Performs regression and graphs in a... | Help |
| regress.plot | utilities/statistics.r | Performs regression in convenient w... | Help |
| regression.Bayes | utilities/statistics.r | Regression using the Gibbs sampler,... | Help |
| regslope | utilities/statistics.r | Returns slope of regression as sing... | Help |
| regslope.noint | utilities/statistics.r | Returns slope of regression with no... | Help |
| regsum | utilities/statistics.r | This carries out either first or se... | Help |
| resetParam | utilities/lmerBayes.r | This starts a new 3D parameter arra... | Help |
| residual.llike.lmerBayes | utilities/lmerBayes.r | Calculate likelihood of residual st... | Help |
| restoreParamFile | utilities/lmerBayes.r | Reverses the steps of saveParamFile... | Help |
| rgamma.meansd | utilities/distributions.r | Random draws of gamma, parameterize... | Help |
| right | utilities/utilities.r | Returns the rightmost n characters ... | Help |
| rightbut | utilities/utilities.r | Returns the rightmost characters of... | Help |
| RipUvK | spatial/RipUvK.r | Ripley's K using splancs. Computes ... | Help |
| rmixnorm | utilities/distributions.r | Random draw on the mixed normal dis... | Help |
| rndown5 | utilities/utilitiesCTFS.r | Rounds a numeric value to the next ... | Help |
| rowcol.to.index | spatial/quadfunc.r | None given.... | Help |
| rpois.max | utilities/distributions.r | Random draws on dpois.max... | Help |
| rpois.trunc | utilities/distributions.r | Random draws on dpois.trunc. This i... | Help |
| rpower | utilities/distributions.r | Random draws based on the integral.... | Help |
| rsymexp | utilities/distributions.r | Drawing a random variate on the sym... | Help |
| run.growthbin.manyspp | growth/growthfit.bin.r | Run the model to fit growth rate in... | Help |
| run.growthfit.bin | growth/growthfit.bin.r | Find best fits for linearmodel.bin,... | Help |
| save.searchpath | utilities/utilities.r | Saves all functions in position n t... | Help |
| saveParamFile | utilities/lmerBayes.r | This saves a run of the full parame... | Help |
| SectionCorrection | topography/imageJ.r | This function is called by fullplot... | Help |
| segmentPt | utilities/geometry.r | Draw a line segment between two poi... | Help |
| selectrandomquad | speciesarea/spparea.r | Draws rectangular quadrats in a plo... | Help |
| selectrandomquad2 | speciesarea/spparea.r | Creates randomly drawn quadrats, us... | Help |
| selectrandomquad3 | speciesarea/spparea.r | Creates randomly drawn quadrats, us... | Help |
| setsize | map/map.r | An internal function, called by map... | Help |
| simple.model | utilities/distributions.r | A trivial model to return a differe... | Help |
| skewness | utilities/statistics.r | Skewness. See formulae in wikipedia... | Help |
| slope.intercept.frompts | utilities/geometry.r | Old version of pts.to.interceptslop... | Help |
| solve.topo | topography/solvetopo.r | This is based on the problem and so... | Help |
| split.data | utilities/utilities.r | Converts a big dataframe into a lis... | Help |
| spmean.mort.abundGibbs | demogchange/abund.fit.CTFS.r | Likelihood function for a species m... | Help |
| spparea.sq | speciesarea/spparea.r | Function for calculating the number... | Help |
| standardreg.no.int | utilities/statistics.r | Standard regression with no interce... | Help |
| startCTFS | startCTFS/startCTFS.r | Function to source all components o... | Help |
| StringToVect | utilities/utilities.r | Converts a character string into a ... | Help |
| summaryMCMC | utilities/lmerBayes.r | Make summary calculations based on ... | Help |
| sumsq | utilities/statistics.r | A trivial function used in minimizi... | Help |
| testmcmcfunc | utilities/statistics.r | For testing mcmc1step. No longer us... | Help |
| TextToRdata | utilities/utilities.r | Reads a tab-delimited text file and... | Help |
| tojulian | utilities/utilities.r | Accepts any character representatio... | Help |
| torus.shift | spatial/quadfunc.r | Creates a torus-shifted quadrat top... | Help |
| trim | utilities/utilities.r | Trims leading and trailing blanks f... | Help |
| trim.growth | growth/growth.r | This is where growth rates are excl... | Help |
| unidentified.species | utilities/utilitiesCTFS.r | Takes a string of species names or ... | Help |
| vectToCommas | utilities/utilities.r | Given a vector of character variabl... | Help |
| wavelet.allsp | spatial/block.analysis.r | Function to calculate the wavelet v... | Help |
| wavelet.var | spatial/block.analysis.r | Function to calculate the wavelet v... | Help |
| weibull.mean.3param | utilities/distributions.r | Mean of three-parameter Weibull... | Help |
| weibull.median.3param | utilities/distributions.r | Median of three-parameter Weibull... | Help |
| weibull.sd.3param | utilities/distributions.r | SD of three-parameter Weibull... | Help |
| which.allnonNA | utilities/utilities.r | Finds all values of a vector which ... | Help |
| which.maxNAs | utilities/utilities.r | An unfortunate bug in which.max: if... | Help |
| which.nonNA | utilities/utilities.r | Returns the first index at which a ... | Help |
| which.vmatch | utilities/utilities.r | Finds which subsequent element of a... | Help |
| wideEnoughBins | growth/growthfit.bin.r | Test whether all the bin widths exc... | Help |
| xydist | utilities/geometry.r | Distance between two pairs of x-y c... | Help |
| xydistmat | utilities/geometry.r | Distance between two x-y coordinate... | Help |
| xydistvect | utilities/geometry.r | Distance between two x-y coordinate... | Help |