Man pages for mcneilco/racas
R Package for ACAS
| acasEntityHierarchy | The hierarcy of ACAS entities |
| addError | Non-fatal error tracking |
| addFileLink | Saves a file that will show up as a link in Seurat |
| analysis_group_save_from_tsv | Save file paths using tsv loader |
| api_createProtocol | Create acas protocol |
| api_doseResponse_experiment | Fits experiment dose response data |
| api_doseResponse_fitData_to_curveDetail | fitData object to json response |
| appendCodeNames | Appends code names to supplied valueKinds |
| appendToContainerName | Change container names |
| applicationSettings | Configuration settings for the applicaiton |
| changeEntityMode | Change mode ACAS entity |
| checkExistence | Check for protocol or experiment existence |
| checkValueKinds | Check valueKinds |
| convertSELExperimentMetaDataToSEL | Converts an Experiment Meta Data data.frame to a pivoted... |
| createCodeTablesFromJsonArray | createCodeTablesFromJsonArray |
| createHtmlSummary | Create an HTML summary |
| createLogger | Creates a new logger |
| createNamedExperiment | Create experiment with name |
| createSELCalculatedResults | Creates a data.frame that contains the elements of the... |
| createSELExperimentMetaData | Creates a data.frame that contains the elements of the... |
| createSELFile | Creates an SEL formatted file |
| createSELRawResults | Creates a data.frame that contains the elements of the Raw... |
| createStateValue | Creates a state value |
| createSubjectContainerInteraction | create subject container interaction |
| createTag | Creates a tag |
| dbWriteTableMatchCol | Write table with matching columns names |
| deleteAnalysisGroupsByExperiment | Delete analysis groups by experiment |
| deleteLinkFile | Deletes a file that shows up as a link |
| dose_response | Fit dose response data |
| dose_response_session | Fit dose response data |
| fit_data_to_acas_experiment_response | fitData object to json response |
| flattenDeepEntity | Flattens Nested ACAS Entities |
| flattenEntity | Flattens ACAS Entities |
| flattenLabel | Flattens an lsLabel |
| flattenLabels | Flattens a list of lsLabels |
| flattenState | Flattens an lsState |
| flattenValue | Flattens an lsValue |
| formatEntityAsTsvAndUpload | Save data using tsv |
| getAcasFileLink | Get url for ACAS file |
| getAllValueKinds | valueKinds |
| getAllValueTypes | valueTypes |
| getCompoundName | Gets parts of batch code |
| getConfiguredEntityTypes | Gets configured entity type |
| getContainerByLabelText | Get Containers by label text |
| getCurveData | Extract the parameters of a given set of curveids (of the... |
| getDDictKinds | getDdictKinds |
| getDDictValuesByTypeKindFormat | Get ddict values by type and kind |
| getEntity | Retrieves a list of entities (experiments or prototocols) by... |
| getEntityById | Gets an entity by id |
| getErrorText | Get error text for users |
| getExperimentById | Gets an experiment |
| getExperimentsByName | Experiment search by name |
| getExperimentStatesByTypeAndKind | Get Experiment States |
| getExperimentValuesByTypeAndKind | Get Experiment Values |
| getFileEncoding | Check file encoding |
| getOrCreateDDictKinds | getOrCreateDDictKinds |
| getOrCreateDDictTypes | getOrCreateDDictTypes |
| getOrCreateEntityState | Gets a state |
| getOrCreateExperimentState | Gets an experiment state |
| get_or_create_value_kinds | Get Or Create Value Kind |
| getPreferredId | Gets preferred ids |
| getPreferredId2 | Gets preferred ids |
| getPreferredIdInternal | Gets preferred ids |
| getPreferredLabelText | Get preferred label text |
| getPreferredName | Gets Entity Name |
| getProtocolById | Gets a protocol |
| getProtocolsByName | Protocol search by name |
| getSection | Get dataframe sections |
| getSSLString | Returns "http://" for blank, null, or FALSE inputs;... |
| getStatesByTypeAndKind | Gets states from an entity |
| get_text_file_contents | Get text file contents as character |
| getUploadedFilePath | Returns file path for uploaded files |
| getURLcheckStatus | Get URL and check status |
| getValuesByTypeAndKind | Gets values from a state |
| getWarningText | Get warning text for users |
| hello | Function to say hello from racas |
| interpretJSONBoolean | Turns 'true' and 'false' into TRUE and FALSE |
| linkOldContainers | Links new subjects to old containers |
| load_value_type_and_kinds | Loads a set of default lsKinds per module |
| logger | Creates a new logger object or returns the "racasLogger" |
| meltBatchCodes | Turns a batchCode column into rows in a long format |
| meltBatchCodes2 | Turns a batchCode column into rows in a long format |
| meltConcentrations | Turns concentration columns into rows in a long format |
| meltConcentrations2 | Turns concentration columns into rows in a long format |
| meltTimes | Turns time columns into rows in a long format |
| meltTimes2 | Turns time columns into rows in a long format |
| meltWideData | Melt our data sets |
| Messenger | Messenger |
| ModelFit-class | ModelFit |
| modules | Known acas modules which require lsKinds to exist |
| moveFileToExperimentFolder | File Saving (deprecated) |
| moveFileToFileServer | Move file to file server |
| naIfNull | Turn NULL into NA |
| parentAcasEntity | Get parent of ACAS entity |
| pickBestLabel | Get preferred labels |
| pickBestName | Pick Best Name |
| pingPong | Ping-pong table generator |
| plotCurve | Curve plotting function |
| prepareTableForDD | Direct Database preparation |
| query | Query the application data server. |
| query_replace_string_with_values | Replace character in query string with values over n times... |
| readConfigFile | Read a configuration file to racas::applicationSettings |
| readExcelOrCsv | Reading of Excel or CSV |
| readTsvDataFileDD | Read tsv file for direct database load |
| saveAcasEntities | Save ACAS entities to the server |
| saveAcasFile | save file in ACAS |
| saveAcasFileToExperiment | save file in ACAS |
| saveAllViaDirectDatabase | Save data frames using direct database load |
| saveAllViaTsv | Save data frames using tsv loader |
| saveAnalysisResults | Save the HTML summary into the experiment |
| saveContainer | save container objects Currently, this cannot accept labels... |
| saveDataDirectDatabase | Save data tables direct to database |
| saveEntitiesDD | Helper functions for saving direct to database |
| saveInputParameters | Save experiment parameters |
| saveLabelsFromLongFormat | Save labels from a long format |
| saveStatesFromLongFormat | Save states from a long format |
| saveTsvData | Save from tsv |
| saveValueKinds | Saves value kinds |
| saveValuesDD | Save values direct database |
| saveValuesFromLongFormat | saves "raw only" values |
| setExperimentHtml | Experiment html |
| setExperimentStatus | Experiment status |
| simple_to_advanced_fit_settings | Convert a simple dose response request to an advanced dose... |
| stopUser | Fatal error tracking |
| tryCatchLog | Error and warning trapping and logging |
| tryCatch.W.E | Error and warning trapping |
| tsv_url_to_data_table | tsv service url to data.table |
| updateOrCreateStateValue | Update a value |
| updateValueByTypeAndKind | Update Values |
| validate | Check that strings can be coerced to others |
| validateSharedMetaData | Meta data validation |
| validateValueKindsFromDataFrame | validateValueKindsFromDataFrame |
| warnUser | Warning tracking |
