Man pages for aproudian2/rapt
Atom Probe Tomography Analysis
| absmax | absmax and absmin |
| absmin | absmax and absmin |
| anomF3est-deprecated | Perfrom anomaly F3est on a 'pp3' object. |
| anomG3est-deprecated | Perform anomaly G3est on a 'pp3' object. |
| anomK3est-deprecated | Perfrom anomaly K3est on a 'pp3' object. |
| anomlocalK3est | Perform localK3est with 50th percentile of a RRL subtracted... |
| argmax | Find the peaks of a finite data set using smoothing. |
| average_relabelings | Functionto take all relabelings and return averages and... |
| bcc.gen-deprecated | Generate body centerd cubic (BCC) lattice of points in 3D. |
| bdist.points | Distance to Boundary of Domain |
| bdist.points3.multi | Cardinal Direction Distances to Boundary of Domain |
| bdist.points.pp3 | Distance to Boundary of Domain |
| bdist.points.ppp | Distance to Boundary of Window |
| bK3est | 3D Border correction for K3est |
| calc_summary_funcs | function to calculate all summary functions on point pattern |
| calc_T_vals | Calculate T value |
| clustersim | Simulate clusters of marks on an RCP background point... |
| crAdjust | Helper for 'makecluster' for 'type' = "cr" and 'fast' = FALSE |
| crAdjust.new | Helper for 'makecluster' for 'type' = "cr" and 'fast' = TRUE |
| createDet | Create a "ppp" from an ATO. |
| createSpat | Create a pp3 from a POS or ATO |
| createSpec | Create a 'MassSpectrum' from a POS or ATO |
| create_training_data | Feature Extraction |
| detectorGIF | Create a GIF that steps through detector hits. |
| dissocDensity | Project hits along a dissociation track |
| dissocTime | Estimate the dissociation time |
| dissocTrack | Parameterized dissociation track on a multiple hit |
| drawRange | Color ranges on a MassSpectrum |
| drawRNG | Color ranges from an RNG on a MassSpectrum |
| envPlot-deprecated | Plot envelopes of K3est test |
| f3features | F features |
| findClusters.pp3 | Find Clusters by NN Adjacency Marks |
| finite_deriv | Find the numerical derivative of a finite set of points. |
| fitIonInit | Initialize 'nls' Fitting Using Ions |
| G3cross | Multitype Nearest Neighbour Distance Function (i-to-j) |
| g3features | G features |
| G3multi | Marked Nearest Neighbour Distance Function |
| g3Xfeatures | GX features |
| gema | Identify Clusters in a Point Pattern Using GEMA |
| gema.gema | Reprocess Clusters Identified Using GEMA |
| gema.pp3 | Identify Clusters in a Point Pattern Using GEMA |
| hcpcluster | Generate spherical clusters with hexagonal close packed... |
| hcp.gen | Generate an HCP Lattice |
| indexMultiples | Index multiple hits |
| intensity.pp3-deprecated | Extends 'intensity' to 'pp3'. |
| ionFormula | Helper Function for 'fitIonInit' |
| isoLabel | Label a prettyPlot with isotope patterns |
| k3features | Extract features from 3D K function output This is the same... |
| k3metrics | Extract metrics from 3D K function output |
| K3scaled | Locally Scaled K-function in Three Dimensions |
| lattice | Generate a spatial lattice |
| local.den.engine | Find the local intensity density estimate based on nearest... |
| local.den.onevol | Helper for 'local.den.engine'. |
| localk3engine | Wrapper function for the C code under 'localK3est'. |
| localK3est | Extends 'localK' to 3D. |
| makecluster | Simulate point clustering in an RCP matrix |
| marktable | Tabulate Marks in Neighbourhood of Every Point in a Point... |
| marktable.pp3 | Tabulate Marks in Neighbourhood of Every Point in a Point... |
| marktable.ppp | Tabulate Marks in Neighbourhood of Every Point in a Point... |
| morph_gb | Simulate morphology of guest molecules on a grain boundary |
| morph_gyroid | Simulate morphology of guest molecules in gyroid pattern |
| morph_lamellar | Simulate lamellar morphology for mixed guest-host system. |
| morph_rods | Simulate morphology of guest rods in a two-phase system |
| msa | Identify Clusters in a Marked Point Pattern Using MSA |
| multiples | Generate a vector of multiplicity orders |
| nmers | Select n-mer Clusters |
| nncrossden.pp3 | Similar to 'nndensity.pp3', but specifically for marked... |
| nndensity.pp3 | Extension of 'nndensity' to handle pp3 objects. |
| paraOrthoRec | paraOrthoRec |
| paraOrthoX | Internal function used by 'paraOrthoRec'. |
| paraOrthoY | Internal function used by 'paraOrthoRec'. |
| paraRec | Reconstruction using a parabolic tip shape assumption. |
| pb_gen-deprecated | Generate random position shifts |
| pEnvelope | Create an Envelope in Parallel |
| percentSelect | Randomly select a percent of the points in a 'pp3' object. |
| pF3est-deprecated | Perform F3est on random relabelings in parallel |
| pG3est-deprecated | Perform G3est on random relabelings in parallel |
| pK3est-deprecated | Perform K3est on random relabelings in parallel |
| plot3d.pp3 | Plot a 'pp3' in a manipulatable 3D plot. |
| plot_summary | Plot summary functions |
| plot_summary_raw | Plot summary functions |
| polyCurve | Shade regions under a curve |
| prettyPlot | Plot a pretty 'MassSpectrum'. |
| pRlabel | Relabel a Point Pattern in Parallel |
| quadratcount.pp3 | Count Points in Sub-Volumes of a 3D Point Pattern |
| quadrats.pp3 | Divide a 3D Point Pattern into Sub-Volumes |
| quantess.pp3 | Quantile Tessellation |
| randomInsert | Helper for 'makecluster' to insert random cluster points |
| randomTakeAway | Helper for 'makecluster' to take away random cluster points |
| rangeCount | Count Hits in Range |
| rangePOS | Extract Hits in Range |
| rapt-deprecated | Deprecated functions in package 'rapt'. |
| readATO | Read an ATO File |
| readPOS | Read a POS File |
| read.rcp | Read an RCP Simulation |
| readResult | Read TAPSim Results |
| readRRNG | Read an RRNG File |
| relabel_summarize | Relabel input point pattern and calcluate summary functions |
| rescale_pattern | rescale_pattern Function |
| resultToDet | Convert TAPSim Result to Detector "ppp" |
| resultToPOS | Convert TAPSim Results to POS |
| rgblur | Helper for 'makecluster' to 3D gaussian blur cluster... |
| rjitter | Random Perturbation of a Point Pattern |
| rjitter.pp3 | Random Perturbation of a Point Pattern |
| rjitter.ppp | Random Perturbation of a Point Pattern |
| rngCount | Count Hits in RRNG |
| rngPOS | Extract Hits in RRNG |
| rownames.pp3 | Extends 'rownames' to 'pp3'. |
| rownames.pp3-set | Extends 'rownames' to 'pp3'. |
| rpoint3 | Generate N Random Points |
| rPoissonCluster3 | Simulate 3D Poisson Cluster Process |
| sample.pp3 | Sample A 3D Point Pattern |
| sample.ppp | Sample a Planar Point Pattern |
| saxeyCor | Create a Corrected 2D correlation histogram |
| saxeyPlot | Create a 2D correlation histogram |
| scaleRCP | Scale RCP Data |
| shift.pp3 | Apply Vector Translation |
| sphereRec | Reconstruction using the sphere on cone method |
| splitpp3-deprecated | Helper for 'makecluster' that splits a 'pp3' into two. |
| stitch.size | Stitches together a RCP point pattern with periodic boundary... |
| studpermu.test | Studentised Permutation Test |
| studpermu.test.hyperframe | Studentised Permutation Test |
| studpermu.test.list | Studentised Permutation Test |
| studpermu.test.pp3 | Studentised Permutation Test |
| studpermu.test.ppp | Studentised Permutation Test |
| subSample | Cut pp3 object to size |
| subSquare | Select a subsection from the center of a 'pp3' data file. |
| superimpose.pp3 | Superimpose Several Geometric Patterns |
| Tstat.pp3 | Extends Tstat to pp3 |
| writeNode | Write a TAPSim Node File |
| writePOS | Write a POS File |
