| Acoustics_datasets_directory | Set the directory of the acoustic data used by the sonR... |
| blockshift | Returns a matrix with blocks of dimension 'd' stacked... |
| circle | Returns a matrix of two columns representing x- and y-values... |
| cm.school | Calculates the center of mass of a (simulated) school in 1D,... |
| combine.events | (Internal) Merge segmentation events, used in... |
| compr.event | This funciton compresses the data stored in 'x' by averaging... |
| contains | Returning a categorical array (0 and 1) for the condition... |
| correctVessel | Shifts the vessel information 'rtzv', 'lonv', 'latv', and... |
| CTD2TSD | Converts a CTD file to the TSD format for the variables... |
| CTDtimeandpos | Reads the time and position of a CTD file in the cnv format. |
| echoIBM.getSchoolfileType | Function for extracting the type (dynamic or static) of the... |
| echoIBM.pdns | Calculates the periodic noise for all voxels based on... |
| echoIBM.segment.event | NA |
| echoIBM.vbsc2p.event | Estimates the probability of not school in voxels of sonar... |
| edgedir1D | Calculates the edge points of an ecousounder based on the... |
| edgedir2D | Calculates the edge points of an acoustic device based on the... |
| edgedir3D | Calculates the edge points of an acoustic device based on the... |
| EKRaw2TSD | Convert from Simrad or LSSS Profos files to TSD files. |
| ellipse | Returns a matrix of two columns representing x- and y-values... |
| event.path | Returns a list of the following strings: (1) the path to the... |
| extractBeams | Extracts a beams from TSD-data, so that if a one dimensional... |
| extract_event | Extracts events from a directory of raw files. |
| extract.range.TSD | Extracts a subset of TSD data according to the ranges given... |
| extractTimeStep | Extracts a time step from TSD-data, so that if a one... |
| extrapolate.matrix | Extrapolates or shrinks a matrix to according to the... |
| filter2 | Expands the fucntion filter() to the edges, instead of... |
| find_voxels.TSD | Finds the voxels in which the positions in 'pos' are located.... |
| generate.event | Generate a simulation event. |
| get.bgns.event | Estimates the mean of exponentially distributed background... |
| getFanWidth | Calculates the width of a 2-D sonar fan given the... |
| get.hins.event | Estimates high intensity noise in acoustic data by... |
| get.hins.event_small | Estimates high intensity noise in an underwater acoustic... |
| get.nrns.event | Estimates the mean over time steps of close range noise for... |
| get.pdns_phase.event | Estimates the phase of the periodic noise of the MS70 sonar.... |
| get.pdns_phase.TSD | Estimates the phase of the periodic noise of the MS70 sonar.... |
| getRuns | Generates runs of length 'n' of the vector 't' of time steps. |
| get.specs.esnm | Returns specifications of the acoustic instrument 'esnm'... |
| getVoxelWidth2D | Calculates edge values for voxels in a 2-D sonar fan. If a... |
| getzfromctd | Computes the z-position based on CTD data (if missing). |
| harx.SH80_oneping | Calculates the horizontal area of the voxels of the SH80... |
| is.sonar | Identifies whether the acoustic system is a sonar, fishery... |
| kernSmooth1 | (Usually Gaussian) smoothing an array along the first... |
| ksmooth.SG | Applies a Gaussian 1-D, 2-D, or 3-D kernel on the data 'x'... |
| ksmooth.SG.TSD | Applies a Gaussian 1-D, 2-D, or 3-D kernel on the 'data'... |
| list.files_caseInsensitive | Sorts in a case insensitive matter. Created to solve the... |
| locate.noise_file | (Internal) Locate noise file. |
| meanexp.quantile | Estimates the parameter of an exponentially distributed 'X'... |
| meanexp.quantile_a | Estimates the parameter 'beta' of an exponentially... |
| meanSv.TSD | Locates the point at which the kernel desity estimate of the... |
| median3d | Median along the dimension given by 'along'. The same as... |
| medSmooth1 | Median smoothing an array along the first dimension. |
| medSmooth1_median3d | Median smoothing an array along the first dimension. |
| medSmooth1_runmed | Median smoothing an array along the first dimension. |
| merge_TSD_by_Time | Merges the last file of the current file number and the first... |
| merge_TSD_by_var | This function returns a list of indices of files of common... |
| noise.path | Locates the paths to files holding the noise estimates and... |
| pol.school | Cacluates the polarization of a school as one of the... |
| psx.TSD | (Internal) Get midpoints of voxels. |
| read.event | Extracts variables from acoustic events. |
| read.event_generate_noise | Estimates the noise in MS70 data. |
| read.event_get.clsz | Extracts clusters of segmentation data. |
| read.event_insertNA | Adds empty list elements of NAs (if vectors) to data read in... |
| read.event_read_other_ctd | Reads ctd-variables. Used in read.event(). |
| read.event_read_sgsc | Reads segmentation indices 'sgsc'. |
| read.event_read_vessel | Reads all files of a specific type. Used in read.event(). |
| read.event_sgsc2pos.TSD | Transforms from 'sgsc' to positions, in a similar way as used... |
| read.event_unzip_vbsc | Merges time steps of acoustic data located in the neighbor... |
| readProfosPP | Plot output from readProfosPP. |
| removeDuplicated_tlist | Removes duplicated time steps from the list of time step... |
| resampleHigh | Resamples large values from the remaining values (useful in... |
| rmUNIX_SgPM | Remove the files with basenames UNIX_time.tsd and sgPM.tsd.... |
| rotate3D | Rotates the set of 'n' three dimensional points 'x' by the... |
| rotfun | Returns a function representing the product of three... |
| rotfun_slow | Returns a function representing the product of three... |
| rotx | Returns three dimensional rotation matrices for rotation... |
| roty | Returns three dimensional rotation matrices for rotation... |
| rotz | Returns three dimensional rotation matrices for rotation... |
| runif.sph | Generates uniformly distributed variables in the spherical... |
| segfilename2segpar | Parses segmentaiton file names and extracts segmentation... |
| segmaskEchosounder | Create theoretical segmentation data for echosounder. |
| sgPM | Reads the ordered matrix of segmentation parameters from the... |
| Simrad_bwt | Converts from Simrad beam widths to x and y beam widths. |
| Simrad_dir | Converts from Simrad beam directions to azimuth and elevation... |
| sonR | Library for reading, processing and converting sonar data to... |
| sonR_implemented | Test for implemented acosutical systems in echoIBM(). |
| soundbeam | Computes the path of a ray of sound for the given... |
| soundbeam.TSD | Calculates the midpoints (or edges along the beams, depending... |
| speedofsound | Computes the speed of sound of the ocean for the given... |
| subset_TSD | Extracts a subset of TSD data according to the array subset... |
| summary_event | Calculates variaous measures of mean sv, and total... |
| summarySeg | (Internal) Returns a summary of segmentation data. |
| summary_TSD | Calculates variaous measures of mean sv, and total... |
| sv2MaskOnePing | Bayesian segmentation method for one ping |
| track.circle | Returns a list of x-values and y-values of points defined by... |
| UNIX_time | Writes and returns the UNIX_time file of an event. |
| vl2rt.TSD | Transforms from velocity data to rotation data, given as... |
| volx1D_oneping | Calculates the volumes of the voxels of the EK60... |
| volx2D_oneping | Calculates the volumes of the voxels of an omnidirectional... |
| volx3D_oneping | Calculates the volumes of the voxels of the MS70 multibeam... |
| volx.TSD | Calculates the voxel volumes of acoustic instruments... |
| voxel.edge.TSD | Calculates a matrix of edge points of voxels of an underwater... |
| writeNetCDF4 | Write data to a netCDF4 file |
| write.noise.cruise | Estimates and writes the noise in av underwater acoustic... |
