Man pages for uwescience/popcycle
Popcycle: An R package providing reproducible analytical methods to uniformly process and curate SeaFlow data
| add_abundance | Add volume-normalized abundance to gridded SeaFlow data |
| add_auto_classification | Define polygons for manual population gating. |
| add_coord_labels | Add string coordinate labels to a dataframe of gridded... |
| add_manual_classification | Define polygons for manual population gating. |
| auto_classify | Classify particles based on semisupervized clustering method... |
| classify_opp | Classify particles from an OPP data frame. |
| classify_opp_files | Classify particles for a list of OPP files. |
| clean_file_path | Clean a file path. |
| cmap_convert | Convert Seaflow data from all cruises into Simons CMAP... |
| concatenate.evt | Concatenate EVT files |
| concatenate.opp | Concatenate OPP files |
| copy_outlier_table | Copy outlier entries from src_db to dest_db. |
| copy_tables | Copy tables from one popcycle database to another. |
| create_breaks | Create breaks vector that can be used with cut(). |
| create_breaks2 | Create breaks vector that can be used with cut(), with log2... |
| create_filter_params | Construct filter parameters from 1µm bead coordinates |
| create_grid_bins | Create the breaks to use to grid VCT data. |
| create_gridded | Create gridded distribution data as particle counts and Qc... |
| create_meta | Create a metadata tibble for one quantile from the SFL table. |
| create_realtime_bio | Create a population data tibble for one quantile from the VCT |
| create_realtime_meta | Create a metadata tibble for one quantile appopriate for... |
| create_volume_table | Create a tibble of volumes that can be used to calculate... |
| csv_convert | Convert data from sqlite3 database into a csv file of curated... |
| delete_filter_params_by_id | Delete DB filter parameters by ID. |
| delete_gating_params_by_id | Delete DB gating parameters by gating ID. |
| delete_poly_by_id | Delete DB poly parameters by gating ID. |
| delete_poly_by_id_pop | Delete DB poly parameters by gating ID and population |
| empty_evt | Create an empty EVT data frame |
| empty_opp | Create an empty OPP data frame |
| filter_evt | Filter EVT particles. |
| filter_evt_files | Filter a list of EVT files. |
| find_common_dbs | Find common database files between two directories. |
| flowrate | Calculation of flow rate based on stream pressure measured by... |
| from_filename_date_str | Convert timestamp component of SeaFlow filenames to POSIXct. |
| get_clean_stat_table | Clean the stat table by selecting the best refractive index... |
| get_cruise | Get cruise name |
| get_evt_by_file | Get EVT data frame by file. |
| get_evt_files | Find EVT files with a recursive search down a directory tree. |
| get_filter_params_by_id | Get filter parameters by id. |
| get_filter_plan_table | Return a tibble for the filter_plan table. |
| get_filter_table | Return a tibble for the filter table. |
| get_gating_params_by_id | Get gating parameters by ID. |
| get_gating_plan_table | Return a tibble for the gating_plan table. |
| get_gating_table | Return a tibble for the gating table. |
| get_inst | Get instrument serial number |
| get_metadata_table | Return a tibble of the metadata table of cruise and... |
| get_opp2_table | Return a tibble for the opp2 table. |
| get_opp_by_date | Get tibble of filtered particles selecting by date. |
| get_opp_by_file | Get tibble of filtered particles selecting by file IDs. |
| get_opp_table | Return a tibble for the opp table. |
| get_outlier_table | Get tibble of outliers. |
| get_poly_log_by_gating_id_pop | Construct a gating polygon list for gating_id pop combo |
| get_poly_table | Return a data frame for the poly table. |
| get_processed_particles | Get a tibble of OPP or VCT particles |
| get_raw_stat_table | Get aggregate statistics data frame joining sfl, opp, and vct... |
| get_sfl_table | Return a tibble for the sfl table. |
| get_stat_table | Get aggregate statistics data frame along with estimates of... |
| get_vct_by_date | Get tibble of classified particles selecting by date. |
| get_vct_by_file | Get tibble of classified particles selecting by file IDs. |
| get_vct_quantile_range | Find quantiles for VCT data |
| get_vct_range | Find min/max for a data column / quantile pair in VCT files |
| get_vct_range_one_file | Find min/max for a data column / quantile pair in one VCT... |
| get_vct_table | Return a tibble for the vct table. |
| grid_bins_labels | Construct string labels for break points created by... |
| grid_one_file | Create gridded distribution data as particle counts and Qc... |
| group_gridded_by_time | Group gridded particle data at a lower time resolution |
| identify_noise | Return logical index vector for noise particle rows |
| identify_saturated | Return logical index vector for saturated particle rows |
| inflection_point | Estimate coordinates of the inflection point (location of 1µm... |
| is_transformed | Check if an EVT data frame has been transformed. |
| make_popcycle_db | Create a new, empty sqlite3 popcycle database. |
| manual_classify | Classify particles based on manually defined population... |
| migrate_tables | Migrate filtering, gating, and outlier related tables to a... |
| mktempname | Create a temporary file name |
| plan_from_table | Create a tibble of start dates for gating / filter IDs based... |
| plot_cruisetrack | Plot cruise track on a map. |
| plot_cyt | Plot EVT or OPP cytogram with only builtin R graphics. |
| plot_cytogram | Plot EVT or OPP cytogram. |
| plot_filter_cytogram | Plot cytograms for exploring filtering parameters. |
| plot_histogram | Plot histogram. |
| plot_map | Plot population distribution on a map. |
| plot_time | plot population dynamics over time |
| plot_vct_cytogram | Plot cytogram with particles colored by population. |
| read_calib_csv | Read Abundance calibration file |
| read_mie_csv | Read Mie theory calibration file |
| read_par_csv | Read table of PAR calibration values |
| read_parquet_one_quantile | Read an OPP/VCT parquet file, only grabbing columns needed to... |
| read_reference_filter_params | Read table of reference filter parameters for a single... |
| read_refraction_csv | Read table of indexes of refraction for cruise and population... |
| readSeaflow | Read an EVT or OPP binary file. |
| read_sfl_tsv | Read SFL tab-delimited file |
| remove_boundary_points | Remove boundary points. |
| reset_filter_plan_table | Delete all rows in filter plan table. |
| reset_filter_table | Delete all rows in filter table. |
| reset_gating_plan_table | Delete all rows in gating plan table. |
| reset_gating_table | Delete all rows in gating table. |
| reset_metadata_table | Delete all rows in metadata table. |
| reset_opp2_table | Delete all rows in opp2 table. |
| reset_opp_table | Delete all rows in opp table. |
| reset_outlier_table | Delete all rows in outlier table. |
| reset_poly_table | Delete all rows in poly table. |
| reset_sfl_table | Delete all rows in sfl table. |
| reset_table | Delete all rows in an arbitrary SQLite3 DB table. |
| reset_vct_table | Delete all rows in vct table. |
| save_filter_params | Save filter parameters to the filter table, appending unless... |
| save_filter_params_from_file | Save filter parameters from a TSV file. |
| save_filter_plan | Save filter plan to db |
| save_filter_plan_from_file | Save filter parameters from a TSV file. |
| save_gating_params | Save gating parameters. |
| save_gating_params_from_file | Save gating parameters from a TSV file. |
| save_gating_plan | Save gating plan to db |
| save_gating_plan_from_file | Save gating parameters from a TSV file. |
| save_metadata | Save metadata to db |
| save_opp2_stats | Save opp2 |
| save_opp_stats | Save OPP aggregate statistics for one file/quantile combo to... |
| save_outliers | Save Outliers in the database |
| save_poly | Save gating polygon coordinates in the poly table. |
| save_poly_from_file | Save gating polygon coordinates from a TSV file. |
| save_sfl | Save SFL to db |
| save_sfl_from_file | Save SFL and metadata from a TSV file. |
| save_vct_stats | Save VCT aggregate population statistics for one file to vct... |
| set_gating_params | Define polygons for population gating. |
| size_carbon_conversion | Estimate cell diameter and carbon cell quotas and biomass of... |
| sql_dbExecute | Wrapper to run dbExecute and clean up connection on error. |
| sql_dbGetQuery | Wrapper to run dbGetQuery and clean up connection on error. |
| sql_dbListTables | Wrapper to get list of tables in a database and clean up... |
| sql_dbWriteTable | Wrapper to run dbWriteTable and clean up connection on error. |
| stat_calibration | Calibrate abundance based on Influx data |
| to_date_str | Convert POSIXct date to standard SeaFlow timestamp string. |
| to_filename_date_str | Convert POSIXct date to standard SeaFlow filename timestamp... |
| transformData | Exponentiate SeaFlow log data |
| untransformData | Log SeaFlow linear data |
| update_plan_table | Update the gating_plan or filter_plan table based on vct or... |
| validate_gridded | Show messages for rows in gridded particle data that fail... |
| write_realtime_bio_tsdata | Write population data as a TSDATA file |
| write_realtime_meta_tsdata | Write SFL metadata as a TSDATA file |
| writeSeaflow | Write an EVT or OPP binary file. |
