File-System Toolbox for RAVE Project
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Documentation for package ‘raveio’ version 0.1.0
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A B C D E F G H I J L M N P R S T U V W
-- A --
| add_module_registry | 'RAVE' module registry |
| ants_coreg | Register 'CT' or 'MR' images via "ANTs" |
| ants_morph_electrode | Register 'CT' or 'MR' images via "ANTs" |
| ants_mri_to_template | Register 'CT' or 'MR' images via "ANTs" |
| as_rave_project | Convert character to 'RAVEProject' instance |
| as_rave_subject | Get 'RAVESubject' instance from character |
| as_rave_unit | Convert numeric number into print-friendly format |
| auto_process_blackrock | Monitors 'BlackRock' output folder and automatically import data into 'RAVE' |
-- B --
| backup_file | Back up and rename the file or directory |
| BlackrockFile | Class definition to load data from 'BlackRock' 'Micro-systems' files |
-- C --
| cache_path | Manipulate cached data on the file systems |
| cache_root | Manipulate cached data on the file systems |
| catgl | Print colored messages |
| clear_cached_files | Manipulate cached data on the file systems |
| cmd-external | External shell commands for 'RAVE' |
| cmd_afni_home | Find and execute external command-line tools |
| cmd_dcm2niix | Find and execute external command-line tools |
| cmd_execute | External shell commands for 'RAVE' |
| cmd_freesurfer_home | Find and execute external command-line tools |
| cmd_fsl_home | Find and execute external command-line tools |
| cmd_homebrew | Find and execute external command-line tools |
| cmd_run_3dAllineate | External shell commands for 'RAVE' |
| cmd_run_ants_coreg | Register 'CT' or 'MR' images via "ANTs" |
| cmd_run_ants_mri_to_template | Register 'CT' or 'MR' images via "ANTs" |
| cmd_run_dcm2niix | External shell commands for 'RAVE' |
| cmd_run_flirt | External shell commands for 'RAVE' |
| cmd_run_niftyreg_coreg | Register 'CT' to 'MR' images via "NiftyReg" |
| cmd_run_nipy_coreg | Register 'CT' to 'MR' images via "nipy" script |
| cmd_run_recon_all | External shell commands for 'RAVE' |
| collapse2 | Collapse high-dimensional tensor array |
| collapse2.array | Collapse high-dimensional tensor array |
| collapse2.FileArray | Collapse high-dimensional tensor array |
| collapse2.Tensor | Collapse high-dimensional tensor array |
| collapse_power | Collapse power array with given analysis cubes |
| collapse_power.array | Collapse power array with given analysis cubes |
| collapse_power.FileArray | Collapse power array with given analysis cubes |
| configure_knitr | Configure "rmarkdown" files to build 'RAVE' pipelines |
| convert-fst | Convert 'fst' files to other formats |
| convert_blackrock | Convert 'BlackRock' 'NEV/NSx' files |
| convert_fst_to_csv | Convert 'fst' files to other formats |
| convert_fst_to_hdf5 | Convert 'fst' files to other formats |
-- D --
| dir_create2 | Force creating directory with checks |
-- E --
| ECoGTensor | 'iEEG/ECoG' Tensor class inherit from 'Tensor' |
-- F --
| find_path | Try to find path along the root directory |
-- G --
| generate_reference | Generate common average reference signal for 'RAVE' subjects |
| get_modules_registries | 'RAVE' module registry |
| get_projects | Get all possible projects in 'RAVE' directory |
| get_val2 | Get value or return default if invalid |
-- H --
| h5_names | Returns all names contained in 'HDF5' file |
| h5_valid | Check whether a 'HDF5' file can be opened for read/write |
-- I --
| import_electrode_table | Import electrode table into subject meta folder |
| IMPORT_FORMATS | Validate raw files in 'rave' directory |
| install_modules | Install 'RAVE' modules |
| is.blank | Check If Input Has Blank String |
| is.zerolenth | Check If Input Has Zero Length |
| is_dry_run | Find and execute external command-line tools |
| is_valid_ish | Check if data is close to "valid" |
-- J --
| join_tensors | Join Multiple Tensors into One Tensor |
-- L --
| LazyFST | R6 Class to Load 'fst' Files |
| LazyH5 | Lazy 'HDF5' file loader |
| LFP_electrode | Definitions of reference with 'LFP' signal type |
| LFP_reference | Definitions of reference with 'LFP' signal type |
| load_bids_ieeg_header | Read in description files from 'BIDS-iEEG' format |
| load_fst | Read a 'fst' file |
| load_fst_or_h5 | Function try to load 'fst' arrays, if not found, read 'HDF5' arrays |
| load_h5 | Lazy Load 'HDF5' File via 'hdf5r-package' |
| load_json | Save or load R object in 'JSON' format |
| load_meta2 | Load 'RAVE' subject meta data |
| load_snippet | 'RAVE' code snippets |
| load_targets | 'RAVE' pipeline functions |
| load_yaml | A port to 'read_yaml' |
| LOCATION_TYPES | The constant variables |
-- M --
| mgh_to_nii | Convert 'FreeSurfer' "mgh" to 'Nifti' |
| MNI305_to_MNI152 | The constant variables |
| module_add | Add new 'RAVE' (2.0) module to current project |
| module_registry | 'RAVE' module registry |
| module_registry2 | 'RAVE' module registry |
-- N --
| new_electrode | Create new electrode channel instance or a reference signal instance |
| new_reference | Create new electrode channel instance or a reference signal instance |
| niftyreg_coreg | Register 'CT' to 'MR' images via "NiftyReg" |
| normalize_commandline_path | Find and execute external command-line tools |
-- P --
| pipeline | Creates 'RAVE' pipeline instance |
| pipeline-knitr-markdown | Configure "rmarkdown" files to build 'RAVE' pipelines |
| PipelineResult | Pipeline result object |
| PipelineTools | Class definition for pipeline tools |
| pipeline_attach | 'RAVE' pipeline functions |
| pipeline_build | 'RAVE' pipeline functions |
| pipeline_clean | 'RAVE' pipeline functions |
| pipeline_create_subject_pipeline | 'RAVE' pipeline functions |
| pipeline_create_template | 'RAVE' pipeline functions |
| pipeline_debug | 'RAVE' pipeline functions |
| pipeline_description | 'RAVE' pipeline functions |
| pipeline_eval | 'RAVE' pipeline functions |
| pipeline_find | 'RAVE' pipeline functions |
| pipeline_fork | 'RAVE' pipeline functions |
| pipeline_hasname | 'RAVE' pipeline functions |
| pipeline_install | Install 'RAVE' pipelines |
| pipeline_install_github | Install 'RAVE' pipelines |
| pipeline_install_local | Install 'RAVE' pipelines |
| pipeline_list | 'RAVE' pipeline functions |
| pipeline_load_extdata | 'RAVE' pipeline functions |
| pipeline_progress | 'RAVE' pipeline functions |
| pipeline_read | 'RAVE' pipeline functions |
| pipeline_root | 'RAVE' pipeline functions |
| pipeline_run | 'RAVE' pipeline functions |
| pipeline_run_bare | 'RAVE' pipeline functions |
| pipeline_save_extdata | 'RAVE' pipeline functions |
| pipeline_settings_get | Get or change pipeline input parameter settings |
| pipeline_settings_get_set | Get or change pipeline input parameter settings |
| pipeline_settings_set | Get or change pipeline input parameter settings |
| pipeline_setup_rmd | Configure "rmarkdown" files to build 'RAVE' pipelines |
| pipeline_target_names | 'RAVE' pipeline functions |
| pipeline_vartable | 'RAVE' pipeline functions |
| pipeline_visualize | 'RAVE' pipeline functions |
| pipeline_watch | 'RAVE' pipeline functions |
| power_baseline | Calculate power baseline |
| power_baseline.array | Calculate power baseline |
| power_baseline.ECoGTensor | Calculate power baseline |
| power_baseline.FileArray | Calculate power baseline |
| power_baseline.rave_prepare_power | Calculate power baseline |
| prepare_subject_bare | Prepare 'RAVE' single-subject data |
| prepare_subject_bare0 | Prepare 'RAVE' single-subject data |
| prepare_subject_power | Prepare 'RAVE' single-subject data |
| prepare_subject_raw_voltage_with_epoch | Prepare 'RAVE' single-subject data |
| prepare_subject_voltage_with_epoch | Prepare 'RAVE' single-subject data |
| prepare_subject_with_blocks | Prepare 'RAVE' single-subject data |
| prepare_subject_with_epoch | Prepare 'RAVE' single-subject data |
| progress_with_logger | Enhanced progress with logger message |
| py_nipy_coreg | Register 'CT' to 'MR' images via "nipy" script |
-- R --
| rave-pipeline | 'RAVE' pipeline functions |
| rave-prepare | Prepare 'RAVE' single-subject data |
| rave-raw-validation | Validate raw files in 'rave' directory |
| rave-server | Install and configure 'RAVE' server as background service using shiny-server |
| rave-snippet | 'RAVE' code snippets |
| RAVEAbstarctElectrode | Abstract definition of electrode class in RAVE |
| RAVEEpoch | Definition for epoch class |
| raveio-constants | The constant variables |
| raveio-option | Set/Get 'raveio' option |
| raveio_confpath | Set/Get 'raveio' option |
| raveio_getopt | Set/Get 'raveio' option |
| raveio_resetopt | Set/Get 'raveio' option |
| raveio_setopt | Set/Get 'raveio' option |
| RAVEPreprocessSettings | Defines preprocess configurations |
| RAVEProject | Definition for 'RAVE' project class |
| RAVESubject | Defines 'RAVE' subject class |
| rave_brain | Load 'FreeSurfer' or 'AFNI/SUMA' brain from 'RAVE' |
| rave_command_line_path | Find and execute external command-line tools |
| rave_directories | Returns a list of 'RAVE' directories |
| rave_export | Export 'RAVE' data |
| rave_export.default | Export 'RAVE' data |
| rave_export.rave_prepare_power | Export 'RAVE' data |
| rave_export.rave_prepare_subject_raw_voltage_with_epoch | Export 'RAVE' data |
| rave_export.rave_prepare_subject_voltage_with_epoch | Export 'RAVE' data |
| rave_import | Import data into 'rave' projects |
| rave_server_configure | Install and configure 'RAVE' server as background service using shiny-server |
| rave_server_install | Install and configure 'RAVE' server as background service using shiny-server |
| rave_subject_format_conversion | Compatibility support for 'RAVE' 1.0 format |
| read-brainvision-eeg | Load from 'BrainVision' file |
| read-write-fst | Read a 'fst' file |
| read_csv_ieeg | Read comma separated value file and ignore headers |
| read_edf_header | Read 'EDF(+)' or 'BDF(+)' file headers |
| read_edf_signal | Read 'EDF(+)' or 'BDF(+)' file signals |
| read_eeg_data | Load from 'BrainVision' file |
| read_eeg_header | Load from 'BrainVision' file |
| read_mat | Read 'Matlab' files |
| read_mat2 | Read 'Matlab' files |
| read_nsx_nev | Read 'BlackRock' event and signal files |
-- S --
| safe_read_csv | Read comma separated value files with given column classes |
| safe_write_csv | Save data to comma separated value files with backups |
| save_fst | Read a 'fst' file |
| save_h5 | Save objects to 'HDF5' file without trivial checks |
| save_json | Save or load R object in 'JSON' format |
| save_meta2 | Function to save meta data to 'RAVE' subject |
| save_yaml | Write named list to file |
| SIGNAL_TYPES | The constant variables |
-- T --
| Tensor | R6 Class for large Tensor (Array) in Hybrid Mode |
| test_hdspeed | Simple hard disk speed test |
| time_diff2 | Calculate time difference in seconds |
-- U --
| update_local_snippet | 'RAVE' code snippets |
| url_neurosynth | Get 'Neurosynth' website address using 'MNI152' coordinates |
-- V --
| validate_raw_file | Validate raw files in 'rave' directory |
| validate_subject | Validate subject data integrity |
| validate_time_window | Validate time windows to be used |
| voltage_baseline | Calculate voltage baseline |
| voltage_baseline.array | Calculate voltage baseline |
| voltage_baseline.FileArray | Calculate voltage baseline |
| voltage_baseline.rave_prepare_subject_raw_voltage_with_epoch | Calculate voltage baseline |
| voltage_baseline.rave_prepare_subject_voltage_with_epoch | Calculate voltage baseline |
-- W --
| with_future_parallel | Enable parallel computing provided by 'future' package within the context |