Package index
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ArchiveAndDeleteControls()
- Archive and Delete Wetlab EPPIcenter Samples
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ArchiveAndDeleteSamples()
- Archive and Delete Samples
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Backup_SampleDB()
- Backup Sample Database
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ColumnData()
- Create a ColumnData S3 object
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DeleteEmptyContainer()
- Delete Empty Wetlab Containers in the EPPIcenter SampleDB database
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DeleteWholeBloodSamples()
- Delete Whole Blood Controls
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ErrorData
- ErrorData class
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MoveContainers()
- Move Wetlab Containers in the EPPIcenter SampleDB database
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MoveSamples()
- Move Wetlab Samples
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RenameContainers()
- Rename Wetlab Containers in the EPPIcenter SampleDB database
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Run_SampleDB()
- Run sampleDB as a R Shiny App
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SampleDB_Setup()
- Set up and deploy the SampleDB environment, database, and Shiny server.
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SearchByType()
- Search for Wetlab Samples in the EPPIcenter SampleDB database
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SearchControls()
- Get all malaria blood controls
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UpdateReferences()
- Update References in the EPPIcenter SampleDB database
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UploadSpecimens()
- Upload Wetlab Samples
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ValidationErrorCollection
- ValidationErrorCollection class
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add_bags_if_not_exist()
- Add new bags to the database if they don't exist
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add_malaria_blood_controls_if_not_exist()
- Add malaria blood controls to the database if they don't exist
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add_new_blood_spot_collections()
- Add New Blood Spot Collections
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add_new_dbs_control_sheets()
- Add new DBS control sheets to the database
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add_position_column()
- Add a position column based on column attributes
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add_row_numbers()
- Add row numbers to a dataframe
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add_to_errors()
- Add an Error to the Error List
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append_strains_to_db()
- Append Strains to the Database Table
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append_study_to_db()
- Append Studies to the Database Table
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append_whole_blood_tubes()
- Add whole blood tubes to the database if they don't exist
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bind_new_data()
- Add Data to User Data
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check_control_exists()
- Check for Control Existence
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check_cryovial_barcodes_exist()
- Check Cryovial Barcodes in Database
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check_cryovial_box_exists()
- Check If Cryovial Box Exists in the Database
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check_duplicated_rows()
- Check for duplicated rows in a data frame
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check_longitudinal_study_dates()
- Check if collection dates are missing for samples in a longitudinal study
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check_micronix_barcodes_exist()
- Check Micronix Barcodes in Database
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check_micronix_plate_exists()
- Check If Micronix Plate Exists in the Database
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check_missing_data()
- Check for missing data in required fields
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check_strain_percentage_match()
- Validate that the strain and percentage columns have matching semicolon counts
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check_unique_positions()
- Check Unique Positions
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collapse_and_nest_columns()
- Collapse and Nest Strain and Percentage Columns
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concat_position()
- Concatenate Position from Column and Row Information
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convert_density_representations()
- Convert Density Representations to Real Numbers
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convert_density_to_numeric()
- Convert string values with 'k' or 'K' to numeric values
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copy_database()
- Copy SQLite Database
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copy_if_not_exists()
- Copy a file to a destination if it does not exist there.
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create_control_label()
- Create Control Label with Density and Composition Values
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create_controls_for_batch()
- Create Controls for the batch
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create_flat_view_by_sample_type()
- Flatten all database tables by sample type
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create_flat_view_of_extractions()
- View all extractions in the database
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create_unique_id()
- Create a unique identifier for compositions
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create_unique_id_from_sorted()
- Create a unique identifier from sorted strains and percentages
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cryovial_na
- Cryovial NA
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denormalize_composition_ids()
- Denormalize Composition IDs from User Data
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display_app_url()
- Display the URL of the deployed Shiny application.
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.Backup()
- Internal function to backup a SQLite database
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.Compress()
- Internal function to compress a file
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.Uncompress()
- Internal function to uncompress a file
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execute_sql()
- Execute SQL Queries on a Database
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extract_search_criteria()
- Extract Search Criteria from User CSV File
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find_column_name()
- Find First Matching Column Name
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find_header()
- Identify the row in a CSV file that matches the header based on required column names.
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format_composition_types()
- Format composition types
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format_error()
- Create Formatting Error Data Frame
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format_labels()
- Format labels for compositions in a dplyr pipeline
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fuzzy_merge_unique_compositions()
- Fuzzy Merge Unique Compositions
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generate_upgrade_script_path()
- Generate Path to Database Upgrade Script
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get_all_control_types()
- Get all control types
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get_all_sample_types()
- Get all sample types
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get_batches()
- Get all batches from the database
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get_composition_types()
- Get all composition type from the database
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get_container_by_sample()
- Get containers by specified sample type
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get_container_table_name()
- Get the Relevant Table Name Based on Container Class
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get_control_action_types()
- Get action types for a specific control
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get_control_file_columns()
- Retrieve ColumnData for a given control type and action
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get_control_types()
- Get control types from a JSON file
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get_db_version()
- Retrieve Current Database Version
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get_densities()
- Get all densities from the database
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get_dereferenced_values()
- Get dereferenced values using sample_values and shared_values
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get_destination_container_by_control()
- Get destination container by specified control type
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get_destination_location_by_control()
- Get destination location by specified control type
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get_duplicated_rows()
- Find duplicate rows in a data frame
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get_environ_file_path()
- Get environ file path
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get_expected_versions()
- Retrieve Expected Versions from JSON File
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get_file_types_for_control()
- Get file types for a specific control
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get_file_types_for_sample()
- Get file types for a specific sample
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get_location_by_sample()
- Get locations by specified sample type
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get_normalized_path()
- Get normalized path
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get_percentages()
- Get all batches from the database
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get_position_column_by_sample()
- Get the expected position column for a sample type
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get_reference_file_columns()
- Retrieve ColumnData for a given reference type.
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get_sample_action_types()
- Get action types for a specific sample
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get_sample_file_columns()
- Retrieve ColumnData for a given sample type and action.
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get_sample_types()
- Get sample types from a JSON file
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get_sample_types_by_action()
- Get sample types from a JSON file by action
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get_storage_container_by_control()
- Get source container by specified control type
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get_storage_location_by_control()
- Get source location by specified control type
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get_strains()
- Get all strains from the database
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get_studies()
- Get all studies from the database
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get_unique_compositions_from_database()
- Extract unique compositions from the database
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get_unique_compositions_from_user_data()
- Normalize Percentages by Group
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get_values()
- Get values with priority to sample_values over shared_values.
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handle_unknown_date_tokens()
- Handle Unknown Date Tokens
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handle_upgrade_error()
- Handle any errors during the database upgrade
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init_and_copy_to_db()
- Initialize Database Connection and Copy User Data
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init_db_conn()
- Initialize a Database Connection
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initialize_database_with_base_version()
- Initialize Database with Base Version
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is_linux_platform()
- Check if the system platform is Linux.
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is_shiny_server_installed()
- Check if Shiny server is installed.
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join_blood_spot_collections()
- Join Blood Spot Collections
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join_composition_ids()
- Process user data to handle malaria blood control details
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join_dbs_control_sheets()
- Join DBS control sheets based on bag ID and label
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join_locations_and_bags()
- Join locations and bags from user data to the database
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join_locations_and_boxes()
- Process Whole Blood Box Data
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join_malaria_controls()
- Join malaria controls based on density and study subject ID
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merge_configs()
- Merge Configuration Lists
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message_not_site_install()
- Display a message indicating the need for a site install.
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message_not_supported_platform()
- Display a message indicating Shiny server isn't supported.
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message_shiny_not_installed()
- Display a message indicating Shiny server isn't installed.
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micronix_na
- Micronix NA
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normalize_composition_ids()
- Normalize Composition IDs from User Data
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perform_batch_db_validations()
- Perform Database-Related Validations for Batches
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perform_composition_db_validations()
- Perform Database-Related Validations for Compositions
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perform_cryovial_db_validations()
- Perform Database-Related Validations for Cryovials
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perform_dbs_sample_db_validations()
- Perform Database-Related Validations for DBS Samples
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perform_dbs_sheet_db_validations()
- Perform Database-Related Validations for DBS Sheets
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perform_micronix_db_validations()
- Perform Database-Related Validations for Micronix
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perform_strain_db_validations()
- Perform Database-Related Validations for Strains
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perform_whole_blood_db_validations()
- Perform Database-Related Validations for Whole Blood Controls
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prepare_control_data_for_validation()
- Prepare DataFrame for Control Validation
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prepare_control_for_upload()
- Prepare Control for Upload
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prepare_new_compositions()
- Prepare new compositions for database upload
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prepare_reference_data_for_validation()
- Prepare DataFrame for Reference Validation
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prepare_specimen_data_for_validation()
- Prepare DataFrame for Specimen Validation
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print(<ColumnData>)
- Print method for ColumnData objects
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process_and_append_compositions()
- Process and append new compositions to the database
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process_bag_data()
- Process user data to handle bag details
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process_blood_spot_collection_data()
- Process Blood Spot Collection Data
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process_control_csv()
- Process and Validate Control CSV File
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process_dbs_control_sheet_data()
- Process user data to handle DBS control sheet details
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process_malaria_blood_control_data()
- Process user data to handle malaria blood control details
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process_reference_csv()
- Process and Validate Reference CSV File
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process_specimen_csv()
- Process and Validate Specimen User CSV File
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process_whole_blood_location_container()
- Process Whole Blood Box Data
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read_and_preprocess_csv()
- Read and Preprocess User CSV File
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rejoin_dbs_control_sheet_ids()
- Rejoin to Get New DBS Control Sheet IDs
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rejoin_malaria_controls()
- Rejoin malaria controls based on density and study subject ID
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rejoin_to_get_bag_ids()
- Rejoin the payload with the database to retrieve bag IDs
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remove_na_columns_in_row()
- Remove columns that have NA in a row
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reshape_identifier_to_long_form()
- Reshape Identifier Data to Long Form
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retrieve_compositions_by_identifier()
- Retrieve compositions from the database by identifier
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retrieve_compositions_by_label()
- Retrieve compositions from the database by label
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search_by_study_subject_file_upload()
- Search by Study Subject (and other longitudinal study criteria)
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search_compositions()
- Search for Compositions in Database
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search_micronix_tube()
- Search Micronix Tube Samples
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select_relevant_columns()
- Select relevant columns from the user CSV file
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set_header_row()
- Set a Specific Row as the Header
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set_user_file_header()
- Set the header row for the user CSV file
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setup_database()
- Setup or upgrade the database
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setup_directory()
- Setup a directory if it does not exist.
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split_and_sort()
- Split and sort strains and percentages
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split_and_unnest_columns()
- Split and Unnest Strain and Percentage Columns
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stop_app_error()
- Stop with an application error
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stop_formatting_error()
- Stop with a formatting error
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stop_validation_error()
- Stop with a validation error
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update_configuration_file()
- Update Configuration File
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update_env_variable()
- Update environment variable
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upgrade_database()
- Upgrade Database
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upload_compositions()
- Upload compositions to the database
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upload_controls()
- Upload Controls to the Database
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upload_extracted_dna()
- Upload Extracted DNA Data to SampleDB
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validate_and_format_control_file()
- Check if the user CSV file for control meets the requirements
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validate_and_format_reference_file()
- Check if the user CSV file for control meets the requirements
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validate_and_format_specimen_file()
- Check if the user CSV file meets the requirements
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validate_batch()
- Validate Batch Data
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validate_box_uniqueness()
- Check if boxes have enough unique cryovial barcodes to be easily identifiable.
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validate_composition()
- Validate Compositions Data
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validate_composition_sum()
- Validate if control compositions sum correctly
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validate_controls()
- Validate Control Specimens
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validate_cryovial()
- Validate Cryovial Specimen Data
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validate_cryovial_collection_dates()
- Confirm that Cryovials with no barcodes have collection dates if there's already a sample from that study subject.
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validate_cryovial_moves()
- Validate Cryovial Moves
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validate_cryovial_position()
- Validate Cryovial-specific position rules
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validate_cryovial_uploads()
- Validate Cryovial Uploads
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validate_date_format()
- Validate Date Format
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validate_dates_with_tokens()
- Validate Dates with Tokens
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validate_dbs_bag_label_is_unique()
- Validate DBS Bag Label is unique at a location
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validate_dbs_sample()
- Validate DBS Specimen Data
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validate_dbs_sample_label_uniqueness()
- DBS Specimen paper identifier uniqueness check
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validate_dbs_sample_moves()
- Validate DBS Specimen Moves
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validate_dbs_sample_uploads()
- Validate Micronix Uploads
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validate_dbs_sheet()
- Validate DBS Sheet Control Data
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validate_dbs_sheet_create()
- Validate DBS Sheet Create
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validate_dbs_sheet_extraction()
- Validate DBS Sheet Extraction
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validate_empty_cryovial_well_upload()
- Cryovial Empty Well Validation
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validate_empty_micronix_well_upload()
- Micronix Empty Well Validation
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validate_existing_barcodes_by_study()
- Validate if barcodes already exist for a given study
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validate_extraction_counts_with_totals()
- Validate Extraction Counts Against Blood Spot Collection Totals
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validate_location_reference_db()
- Validate location references (Database Version)
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validate_longitudinal_study()
- Ensure uniqueness of study subjects and collection dates within longitudinal studies.
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validate_matrix_container()
- Validate Matrix Container position
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validate_micronix()
- Validate Micronix Specimen Data
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validate_micronix_barcode_length()
- Validate Micronix-specific barcode length rules
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validate_micronix_moves()
- Validate Micronix Moves
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validate_micronix_position()
- Validate Micronix-specific position rules
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validate_micronix_uploads()
- Validate Micronix Uploads
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validate_non_longitudinal_study_subjects()
- Check uniqueness of StudySubject within non-longitudinal studies.
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validate_references()
- Validate References
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validate_specimen_type_db()
- Validate specimen type references (Database Version)
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validate_specimens()
- Validate Specimens Main Function
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validate_strain()
- Validate Strains Data
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validate_strains_in_database()
- Validate strains recorded in the database
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validate_study_reference_db()
- Validate study references (Database Version)
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validate_study_short_code()
- Validate that study does not have a date for it's short code
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validate_whole_blood()
- Validate Whole Blood Control Data
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validate_whole_blood_create()
- Validate Whole Blood Create
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validate_whole_blood_extraction()
- Validate Whole Blood Extraction
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validate_whole_blood_tube_exists()
- Validate Cryovial Tube Exists