Man pages for lindesaysh/MRSea
Spatially adaptive regression splines using SALSA
| acffunc | calculate correlation for residuals by block |
| AICh | Function to calculate AICh (Hardin and Hilbe 2013) |
| anova.gamMRSea | Anova Tables for 'gamMRSea' Models |
| bootstrap.orig.data | Obtaining a data frame of bootstrapped data using resamples |
| checkfactorlevelcounts | Factor level response check This function checks that there... |
| choose.radii | Function to choose the radii for the CReSS local radial basis... |
| create.bootcount.data | Aggregate bootstrapped distance data into count data |
| create.bootstrap.data | Create bootstrap data for non-parametric bootstrapping |
| create.count.data | Aggregate distance data into count data |
| create.NHAT | Estimated number of individuals for each detection |
| cv.gamMRSea | Cross-validation for gamMRSea Models |
| dis.data.de | Line transect data with decrease post-impact |
| dis.data.no | Line transect data with no post-impact consequence |
| dis.data.re | Line transect data with redistribution post-impact |
| do.bootstrap.cress | Bootstrapping function without model selection using... |
| do.bootstrap.cress.robust | Bootstrapping function without model selection for a model of... |
| do.bootstrap.cress.robust.beta | Bootstrapping function without model selection for a model of... |
| drop.step_2d | Function that tries dropping knots to find an improvement in... |
| exchange.step_2d | Function for exchanging knot locations and re-fitting model... |
| fit.thinPlate_2d | Function to fit a local radial basis function (CReSS) as a... |
| gamMRSea | gamMRSea model function |
| generateNoise | Function to generate noisy data |
| getCVids | IDs for running cross validation |
| getDifferences | Identify any significant differences between predicted data... |
| getDispersion | dispersion parameter |
| getEmpDistribution | Function to generate the empirical distribution of the runs... |
| getGeoDist | Function to calculate geodesic distances |
| getKnotgrid | Generate a grid of knot locations to run SALSA2D. |
| getPlotdimensions | find the plotting dimensions for quilt.plot when using a... |
| getRadiiChoices | Function for obtaining a sequence of range parameters for the... |
| getRadiiChoices.vario | Function for obtaining a sequence of range parameters for the... |
| getRadiiSequence | Function for obtaining a sequence of range parameters for the... |
| improve.step_2d | Function to move knots to neighbours to see if there is any... |
| knotgrid.ns | Knot grid data for nearshore example |
| knotgrid.off | Knot grid data for offshore example |
| LocalRadialFunction | Function for creating an Gaussian basis function for a... |
| LRF.e | Function for creating an Exponential basis function for a... |
| LRF.g | Function for creating an Gaussian basis function for a... |
| makeBootCIs | Calculate percentile confidence intervals from a matrix of... |
| makeDists | Make Euclidean distance matrices for use in CReSS and SALSA... |
| make.gamMRSea | Function to make model of class 'gamMRSea' |
| makesplineParams | Constructing an object of spline parameters |
| MRSea | MRSea |
| ns.data.de | Nearshore data with decrease post-impact |
| ns.data.no | Nearshore data with no effect of impact |
| ns.data.re | Nearshore data with redistribution post-impact |
| ns.predict.data.de | Prediction grid data for nearshore post-impact decrease |
| ns.predict.data.no | Prediction grid data for nearshore with no effect of impact |
| ns.predict.data.re | Prediction grid data for nearshore post-impact redistribution |
| nysted.analysisdata | Nysted Data |
| nysted.coast | Polygon of the Nysted coastline |
| nysted.predictdata | Prediction grid data for Nysted Data |
| nysted.studybnd | Polygon of the outline of the Nysted study area |
| plotacf | run functions to create acf matrix and plot the results |
| plotCumRes | Calculate cumulative residuals and plot. |
| plotMeanVar | Functions to create a Mean-Variance plot for checking the... |
| plotRunsProfile | Calculate runs test and plot profile plot. The output is a... |
| predict.data.de | Prediction grid data for post-impact decrease |
| predict.data.no | Prediction grid data for no post-impact consequence |
| predict.data.re | Prediction grid data for post-impact redistribution |
| predict.gamMRSea | Function for making predictions for a model containing a... |
| QICb | Function to calculate QICb |
| qposbinom | qposbinom function |
| qzibinom | qzibinom function from the VGAM package |
| return.reg.spline.fit | Code for adaptively spacing knots for a given covariate. |
| return.reg.spline.fit.2d | Wrapper function for running SALSA2D |
| rpois.od | Generating overdispersed poisson data |
| runACF | run functions to create acf matrix and plot the results |
| runDiagnostics | functions to create observed vs fitted and fitted vs scaled... |
| runInfluence | Assessing the influece of each correlated block on both the... |
| runPartialPlots | Plot partial plots for each of the variables listed in... |
| runSALSA1D | Running SALSA for continuous one-dimensional covariates. |
| runSALSA2D | Running SALSA for a spatial smooth with a CReSS basis |
| runsTest | Runs Test for Randomness |
| rzibinom | rzibinom function from the VGAM package |
| selectFctrKnots | Select candidate knots for multi-level factor interaction |
| selectFctrStartk | Select starting knots for multi-level factor interaction |
| summary.gamMRSea | Summarising model fits from models fitted using the MRSea... |
| summaryshortnames | Shortening names in summary object |
| thinModels | function to thin the number of models |
| timeInfluenceCheck | Timing check to see how long it will take to run... |
| which.bin | Determining the distance bin |
