| add.array.values | Add an array to values |
| add.colours.contours | Add color definitions to contours |
| add.field | Add field ID column to beams |
| add.vois | Combine 2 existing VOIS object into one |
| a.from.ion | A from Ion |
| alpha.beta.ion.range | Evaluation of ion alpha and beta LQ parameters |
| alpha.beta.ion.sequence | Evaluation of ion alpha and beta LQ parameters |
| alpha.beta.lqp | Evaluation of Linear-Quadratic (LQ) Poisson Model parameters |
| alpha.beta.mkm | Evaluation of alpha and beta LQ parameter (fast MKM) |
| alpha.fun.mkm | Evaluate alpha function (MKM) |
| available.beamlines | Available beamlines (PlanKIT) |
| available.constraint.types | Available constraints (Pure-dek) |
| available.variables | Available variables (Pure-dek) |
| available.variables.gate | Available variables (Gate) |
| beta.c | Evaluate beta (velocity/c) |
| check.gate | Check the configuration of Gate |
| check.plankit | Check the configuration of PlanKIT |
| check.prescription | Check the prescription |
| colormap.ct | Generate gray colormap for Hounsfield numbers |
| combine.beamLUTs | Combine beamLUTs |
| combine.values | Combine values |
| convert.fluence2mu | converte fluenze in beams da numero di particelle a MU |
| convert.mu2fluence | converte fluenze in beams da MU a numero di particelle |
| create.beam | Create an empty beam(s) object |
| create.constraint | Crea oggetto prescrizione (dataframe) |
| create.field | Create a field object (dataframe) |
| create.gate.structure | Create Gate structure |
| create.intervals | Generate bin intervals from points |
| create.noise.ct | noise sulla CT |
| create.plan | Generate Plan template (Pure-dek) |
| create.plan.gate | Generate Plan template (Gate) |
| create.values | Create values object |
| create.vois | Create a VOIS object from a contours object |
| create.vois.from.logical.array | Create a VOIS object from a logical array |
| create.waterbox.gate | Create a water box object (Gate) |
| dataframe.from.values | Generate data.frame from values object |
| demo.puredek | Evaluate a test planning |
| display.all.plan | procedura per creare un display complessivo da un "plan" |
| display.beamports | Beam-port splot |
| display.beams | Beam statistics plot |
| display.contours.legend | Add a legend with contours names/colours. |
| display.dvh | Display DVHs |
| display.dvh2d | plot di "dvh2D per un voi e due variabili specifiche |
| display.dvh2d.multiple | plot multiplo di dvh2D |
| display.dvh.bands | Visualizza una banda sul DVH |
| display.dvh.bands.multiple | Visualizza una banda sui DVH |
| display.dvh.combined | Display DVHs |
| display.lut | 2D display of the beam-lut |
| display.profile | Display profile |
| display.profiles | Display profiles |
| display.rays | Display rays (3D) |
| display.slice | Display a 2D slice |
| display.slice.all | Display a 2D slice superimposed to the CT |
| display.slice.ct | Display CT slices |
| display.slices.interactive | mostra slice in maniera interattiva |
| display.spots | Display spots (3D) |
| dumpslices.3d.2.png | fa un dump del file .3d in una serie di immagini png... |
| dvh.evaluate | Evaluate DVH |
| dvh.evaluate.all | calcola DVH per tutti i VOI |
| dvh.evaluate.bands | Evaluate DVH confidence band |
| embed.data | Embed data into plan |
| evaluate.bands | Evaluate percentile band |
| evaluate.epl | Evaluate the equivalent path length |
| file.variable.gate | Map the variable name to file name (Gate) |
| generate.contours | Generate the contours |
| generate.ct | Generate a CT phantom |
| generate.ct.contours | Generate a complete phantom (CT + contours) |
| generate.materials.gate | Generate Materials (Gate) |
| generate.report | Generate report |
| generate.values.from.events | Create values form events |
| get.alpha.beta.beamLUT | Evaluate net alpha and beta from beamLUTs (pure-dek) |
| get.array.values | estrai array della variabile specificata dai values |
| get.bdose.beamLUT | Evaluate equivalent dose from beamLUTs (pure-dek) |
| get.beamLUTs | Get beamLUTs |
| get.beams | Get beams from plan |
| get.contours | Get contours from plan |
| get.coordinates | Get coordinates from voxel index |
| get.ct | Get ct object from plan object |
| get.ct.entrance.point | Get entrance point in CT |
| get.dektools.env | Get Environment Variables |
| get.dose.beamLUT | Evaluate net Dose from beamLUTs (pure-dek) |
| get.filepath | Filepath of objects |
| get.install.path | Get installing folder |
| get.isocenter | recupera isocentro |
| get.letd.beamLUT | Evaluate net dose averaged LET from beamLUTs (pure-dek) |
| get.origin | Get origin coordinates |
| get.prescription | recupera prescrizione |
| get.profile | Get profile |
| get.profiles | Get profiles |
| get.rays | Get rays from beams |
| get.rbe.beamLUT | Evaluate net RBE from beamLUTs (pure-dek) |
| get.sparse.array.gate | Get sparse array values (Gate) |
| get.subset.values | Get a subset of a 'values' object. |
| get.subset.vois | Get a subset of a 'vois' object. |
| get.values | Get values object |
| get.values_at.points | get values at coordinates |
| get.values.dataframe | recupera matrice di valori in formato dataframe |
| get.values.for.beam | Evaluate BeamLUT (obsolete) |
| get.values.gate | Get values object (Gate) |
| get.values.gate.plan | Get values object (Gate) |
| get.values.list | Get values objects |
| get.values.plankit.plan | Get values object (PlanKIT) |
| get.voiindex | Get the VOI index from the contours file |
| get.voi.logical | Evaluate VOI logical matrix |
| get.vois | Get VOIs from plan |
| get.voxel.index | Get voxel index from coordinates |
| get.zBP.fun | Return a function z.BP(E) |
| header2list | Convert DICOM header file/data.frame to nested list |
| identify.slice | identifica slice corrispondente alla coordinata |
| install.gate | Install Gate |
| install.plankit | Install Plankit (obsolete) |
| install.puredek | Install Pure-dek |
| install.survival | Install Survival |
| interpolate.values | Tri-linear interpolation |
| ion.from.z | Ion from Z |
| is.in.voi | Check if point(s) is(are) inside a VOI |
| load.test.data | carica dati per i test |
| lut.add.alpha | Add alpha values to lUT |
| lut.add.beta | aggiungi beta alla lut |
| lut.add.rbe.alpha | Aggiunge RBE.alpha alla LUT |
| lut.radial.integral | integra la lut radiale |
| merge.values | Merge a list of values |
| meshgrid | Create a meshgrid |
| mkm.lower | MKM lower limits |
| mkm.upper | MKM upper limits |
| my.ggplot.theme | imposta stile generale per ggplot2 |
| NTCP.cMKM | calcola NTCP con modello cMKM |
| ntcp.kallman | NTCP (Biological Dose, Relative Seriality Model... |
| ntcp.kallman.train | NTCP (Biological Dose, Relative Seriality Model... |
| NTCP.LL.cMKM | calcola la log likelihood di complicazioni (NTCP), per un... |
| NTCP.LL.LM | calcola la log likelihood di complicazioni (NTCP), per un... |
| NTCP.LM | calcola NTCP con modello LM |
| ntcp.S | NTCP (Relative Seriality Model [Kallman1992a]) |
| P | funzione spettro di potenza |
| points2intervals | Evaluate intervals |
| ray.tracing | Ray-tracing (intersections) |
| rbe.evaluate | Evaluation of dose-depending RBE |
| read.1d | Read 1D array |
| read.3d | Read 3d array (PlanKIT) |
| read.3d.dicom | Read 3d DICOM |
| read.3d.hdr | Read 3d array (Analyze/Gate) |
| read.beamLUT | Read a beamLUT (pure-dek) |
| read.beamLUTs | Read the beamLUTs (pure-dek) |
| read.beams | Read beams from file (PlanKIT) |
| read.contours | Read contours from file |
| read.contours.dicom | Read contours from DICOM file |
| read.lut | Read LUT (4d) |
| read.materials.gate | Read materials database (Gate) |
| read.plan | Read Plan |
| read.vois | Read VOIs from file |
| remove.atomic.mass | Remove atomic mass number |
| remove.values.outside.voi | Removes values outside VOI |
| render.isosurfaces | rendering di isosuperfici da matrice values (openGL) |
| render.isosurfaces.static | rendering di isosuperfici da matrice values |
| render.voi.isosurfaces | rendering 3D dei voi con isosuperfici |
| rest.energy | Rest energy |
| Rplanit-package | RT Ion planning simulations and analysis |
| run.dek.forward | Forward planning (Pure-dek) |
| run.dek.inverse | Inverse planning (Pure-dek) |
| run.gate.forward | Evaluate forward planning (Gate) |
| sanitize.contours | Correct consistency of contours |
| sanitize.ct | rimuove valori fuori range della ct |
| sanitize.filename | Sanitize file name |
| sanitize.values | Set not defined or not "physical" values to NA |
| save.plan | Save Plan |
| set.ct.gate | Set the CT/phantom (Gate) |
| set.dektools.env | Set Environment Variables |
| setenv.rplanit | Set the system environment variables |
| set.lut.folder | Set LUT folder |
| set.origin | Set origin coordinates |
| set.wepl.folder | Set WEPL folder |
| sparse.array.from.values | get sparse format data from a values object |
| srim.es.max | srim.limits |
| srim.es.min | srim.limits |
| srim.let.max | srim.limits |
| srim.let.min | srim.limits |
| TCP.cMKM | calcola TCP con modello cMKM |
| TCP.LL.cMKM | calcola la log likelihood di cura (TCP), per un singolo caso,... |
| TCP.LL.LM | calcola la log likelihood di cura (TCP), per un singolo caso,... |
| TCP.LM | calcola TCP con modello LM |
| tcp.lqp | TCP (Poissonian Model, Biological Dose) |
| tcp.lqp.train | TCP (Biological Dose, Poissonian Model, Variable fractions) |
| tcp.S | TCP (Poissonian Model) |
| threshold.values | Set values under threshold to NA |
| values.add.RBE | calcola l'RBE e l'agiunge in values a partire da alpha e beta... |
| values.add.RBE.alpha | Calcola l'RBE.alpha e l'aggiunge in values |
| values.add.survival.cMKM | Calcola la sopravvivenza secondo il modello cMKM e la... |
| values.add.survival.LM | Calcola la sopravvivenza secondo il modello LM e la aggiunge... |
| values.app | Values eploration (Web App) |
| values.from.sparse.array | Create values from sparse array |
| volume.contours | Evaluate volume from contours |
| write.3d | Write 3D array (Pure-dek) |
| write.analyze | Write 3D array (analyze) |
| write.beamLUT | scrive le matrici V_b,v (beamLUT) (obsolete) |
| write.beams | Write beams (RTIonPlan) |
| write.contours | Save contours |
| write.lut | salva la lut a partire dai dati in memoria |
| write.lut.4d | Write LUT 4d data array |
| write.lut.meta | Write LUT meta file |
| write.lut.optics | Write LUT optics (meta) file |
| write.lut.phasespace | Write LUT phase-space file |
| write.lut.zBP | Write LUT Bragg peaks depths file |
| Zeff | Evaluate the effective charge |
| z.from.ion | Z from ion |
