Man pages for LEEF-UZH/LEEF.analysis
Access Functions, Tests and Basic Analysis of the RRD Data from the LEEF Project
| add_experiment_tables | Add 'composition' and 'experimetal_design' table to db. |
| add_extracted_csv_to_db | Title |
| add_reclassified_to_db | Title |
| add_to_db | Add data to RRD database into existing table |
| arrow_read_conductivity | Read 'conductivity' table from an arrow database and return... |
| arrow_read_density | Read 'density' table from an arrow database and return as a... |
| arrow_read_o2 | Read 'o2' table from an arrow database and return as a... |
| arrow_read_table | Read a table from an arrow database and return as an Dataset... |
| arrow_read_toc | Read 'toc' table from an arrow database and return as a... |
| CalculateDensities | Re-calculate densities |
| classify_bemovi_archive | Classify bemovi data by using the archived data |
| classify_bemovi_files | Classify algae_traits data.frame |
| classify_flowcam_archive | Classify algae_traits data.frame |
| classify_flowcam_files | Classify algae_traits data.frame |
| configs | Return names of all configs in config file |
| create_rrd_trimmed | Create trimmed down density-only version of the database |
| db_disconnect | Disconnect the 'tbl_SQLiteConnection' |
| db_read_conductivity | Read 'condi=uctivity' from RRD database and return as an... |
| db_read_density | Read 'density' from RRD database and return as an... |
| db_read_immigration | Read 'immigration_sevent' from RRD database and return as an... |
| db_read_light_decline | Read 'light_decline' from RRD database and return as an... |
| db_read_o2 | Read 'o2' from RRD database and return as an... |
| db_read_stressor_levels | Read 'stressor_levels' from RRD database and return as an... |
| db_read_table | Read a table from RRD database and return as an... |
| db_read_toc | Read 'toc' measurements from RRD database and return as an... |
| density_flowcytometer_archive | Gate and extract densities from flowcytometer data by using... |
| extract_timestamps | Extract data from table |
| extract_traits_flowcytometer_archive | Extract traits from flowcytometer data by using the archived... |
| generate_overlays | Just a function to update the overlays. |
| LEEF_1_biomass_bemovi_16 | LEEF-1 - Add biomass to traits |
| LEEF_1_biomass_bemovi_25 | LEEF-1 - Add biomass to traits |
| LEEF_1_biomass_bemovi_25_cropped | LEEF-1 - Add biomass to traits |
| LEEF_1_biomass_bemovi_25_non_cropped | LEEF-1 - Add biomass to traits |
| LEEF_1_biomass_flowcam | LEEF-1 - Add biomass to traits |
| LEEF_1_biomass_flowcytometer | LEEF-1 - Add biomass to traits |
| LEEF_2_add_experiment_tables | Add 'composition' and 'experimetal_design' table to db. |
| LEEF_2_biomass_bemovi | LEEF-1 - Add biomass to traits |
| LEEF_2_biomass_flowcam | LEEF-2 - Add biomass to traits |
| LEEF_2_classify_bemovi_archive | Classify bemovi data by using the archived data |
| LEEF_2_classify_bemovi_files | Classify algae_traits data.frame |
| LEEF_2_classify_flowcam_archive | Classify algae_traits data.frame |
| LEEF_2_classify_flowcam_files | Classify algae_traits data.frame |
| LEEF_2_density_flowcytometer_archive | Gate and extract densities from flowcytometer data by using... |
| LEEF_2_extract_traits_flowcytometer_archive | Extract traits from flowcytometer data by using the archived... |
| LEEF_2_make_view_density | Create 'density' view wgich contains all density data from... |
| LEEF_2_make_view_o2 | Create 'o2' view which contains selected fields from the os... |
| LEEF_2_make_view_toc | Create 'toc' view wich contains selected fields from the... |
| LEEF_2_plot_bottles_per_timestamp | Plot diagnostic plot to check bottles per timestamp |
| LEEF_2_plot_conductivity_per_bottle_per_timestamp | Plot diagnostic plot to check number of species per timestamp |
| LEEF_2_plot_density_species_per_bottle_per_timestamp | Plot diagnostic plot to check number of species per timestamp... |
| LEEF_2_plot_flowcytometer_individual_per_bottle_per_timestamp | Plot diagnostic plot to check is plte has an impact on... |
| LEEF_2_plot_o2s_per_bottle_per_timestamp | Plot diagnostic plot to check number of species per timestamp |
| LEEF_2_plot_response_incubator | Plot diagnostic plot to check number of species per timestamp |
| LEEF_2_plot_tocs_per_bottle_per_timestamp | Plot diagnostic plot to check number of species per timestamp |
| LEEF_2_rename_composition | FUNCTION_TITLE |
| LEEF_2_rename_species | FUNCTION_TITLE |
| LEEF_2_rename_species_prob_columns | FUNCTION_TITLE |
| LEEF_2_rename_toc | FUNCTION_TITLE |
| LEEF_2_report_diagnostic | Report for checking pipeline and sampling |
| LEEF.analysis-package | LEEF.analysis: Access Functions, Tests and Basic Analysis of... |
| make_view_conductivity | Create 'o2' view wgich contains selected fields from the... |
| make_view_density | Create 'density' view wgich contains all density data from... |
| make_view_immigration_event | Create 'immigration_event' view which adds the experimental... |
| make_view_light_decline | Create 'light_decline' view which adds the experimental day |
| make_view_o2 | Create 'o2' view wgich contains selected fields from the os... |
| make_views | Create all views |
| make_view_toc | Create 'toc' view wich contains selected fields from the... |
| overlays | Create overlays |
| overlays_from_folders | Create overlays |
| overlays_from_reclassification | Create overlays |
| parquet | FUNCTION_TITLE |
| plot_bottles_per_timestamp | Plot diagnostic plot to check bottles per timestamp |
| plot_density_species_per_bottle_per_timestamp | Plot diagnostic plot to check number of species per timestamp |
| plot_no_species_per_bottle_per_timestamp | Plot diagnostic plot to check number of species per timestamp |
| plot_o2s_per_bottle_per_timestamp | Plot diagnostic plot to check number of species per timestamp |
| plot_response_incubator | Plot diagnostic plot to check number of species per timestamp |
| plot_species_per_timestamp_per_measure | Plot diagnostic plot to check species per timestamp per... |
| plot_tocs_per_bottle_per_timestamp | Plot diagnostic plot to check number of species per timestamp |
| prepare_rrd | Prepare the RRD database for usage with the other functions... |
| read_sql | Read data from the RRD database |
| render_quarto_temp | Render a quarto file in a temporary directory and copy the... |
| report_diagnostic | Report for checking pipeline and sampling |
| report_flowcytometer | Report for checking pipeline and sampling |
| report_interactive | Run interactive report |
| report_reclassification | Do the reclassification and create a report |
| report_sanity_check | Report for the sanity check of the data for submission to the... |
| RRD_create_indices | Create indices in RRD database |
| RRD_LEEF_1_rename | Rename columns and species in the RRD |
| RRD_new | Create new RRD database |
| sanity_check | Sanity check data for pipeline |
| sanity_check_bemovi.mag.16 | Sanity check for bemovi.mag.16 |
| sanity_check_bemovi.mag.25 | Sanity check for bemovi.mag.25 |
| sanity_check_flowcam | Sanity check for flowcam |
| sanity_check_flowcytometer | Sanity check for flowcytometer |
| sanity_check_general.data | Sanity check for 0.general.data |
| sanity_check_manualcount | Sanity check for manualcount |
| sanity_check_o2meter | Sanity check for o2meter |
| sanity_get_timestamp | Extract timestamp from 'sample_metadata.yml' file |
| SetNotFoundSpeciesTo0 | Set number of Not Found species to 0 |
| species_set | Defines sets of species |
| traits_flowcytometer_archive | Gate and extract densities from flowcytometer data by using... |
