Package: LEEF.analysis 1.0.2

Rainer M. Krug

LEEF.analysis: Access Functions, Tests and Basic Analysis of the RRD Data from the LEEF Project

Provides simple access functions to read data out of the sqlite RRD database. SQL queries can be configured in a yaml config file and used.

Authors:Rainer M. Krug [aut, cre], SNF Project 310030_188431 [fnd]

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LEEF.analysis.pdf |LEEF.analysis.html✨
LEEF.analysis/json (API)

# Install 'LEEF.analysis' in R:
install.packages('LEEF.analysis', repos = c('https://leef-uzh.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/leef-uzh/leef.analysis/issues

On CRAN:

2.84 score 23 scripts 108 exports 89 dependencies

Last updated 2 months agofrom:ddef64e85f (on master). Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 10 2024
R-4.5-winWARNINGOct 10 2024
R-4.5-linuxWARNINGOct 10 2024
R-4.4-winWARNINGOct 10 2024
R-4.4-macWARNINGOct 10 2024
R-4.3-winWARNINGOct 10 2024
R-4.3-macWARNINGOct 10 2024

Exports:add_experiment_tablesadd_extracted_csv_to_dbadd_reclassified_to_dbadd_to_dbarrow_read_conductivityarrow_read_densityarrow_read_o2arrow_read_tablearrow_read_tocCalculateDensitiesclassify_bemovi_archiveclassify_bemovi_filesclassify_flowcam_archiveclassify_flowcam_filesconfigscreate_rrd_trimmeddb_disconnectdb_read_conductivitydb_read_densitydb_read_immigrationdb_read_light_declinedb_read_o2db_read_stressor_levelsdb_read_tabledb_read_tocdensity_flowcytometer_archiveextract_timestampsextract_traits_flowcytometer_archivegenerate_overlaysLEEF_1_biomass_bemovi_16LEEF_1_biomass_bemovi_25LEEF_1_biomass_bemovi_25_croppedLEEF_1_biomass_bemovi_25_non_croppedLEEF_1_biomass_flowcamLEEF_1_biomass_flowcytometerLEEF_2_add_experiment_tablesLEEF_2_biomass_bemoviLEEF_2_biomass_flowcamLEEF_2_classify_bemovi_archiveLEEF_2_classify_bemovi_filesLEEF_2_classify_flowcam_archiveLEEF_2_classify_flowcam_filesLEEF_2_density_flowcytometer_archiveLEEF_2_extract_traits_flowcytometer_archiveLEEF_2_make_view_densityLEEF_2_make_view_o2LEEF_2_make_view_tocLEEF_2_plot_bottles_per_timestampLEEF_2_plot_conductivity_per_bottle_per_timestampLEEF_2_plot_density_species_per_bottle_per_timestampLEEF_2_plot_flowcytometer_individual_per_bottle_per_timestampLEEF_2_plot_o2s_per_bottle_per_timestampLEEF_2_plot_response_incubatorLEEF_2_plot_tocs_per_bottle_per_timestampLEEF_2_rename_compositionLEEF_2_rename_speciesLEEF_2_rename_species_prob_columnsLEEF_2_rename_tocLEEF_2_report_diagnosticmake_view_conductivitymake_view_densitymake_view_immigration_eventmake_view_light_declinemake_view_o2make_view_tocmake_viewsobject_to_parquetoverlaysoverlays_from_foldersoverlays_from_reclassificationparquet_add_bemovi_16parquet_add_bemovi_25parquet_add_bemovi_25_croppedparquet_add_conductivityparquet_add_flowcamparquet_add_flowcytometerparquet_add_manualcountparquet_add_o2parquet_add_tocplot_bottles_per_timestampplot_density_species_per_bottle_per_timestampplot_no_species_per_bottle_per_timestampplot_o2s_per_bottle_per_timestampplot_response_incubatorplot_species_per_timestamp_per_measureplot_tocs_per_bottle_per_timestampprepare_rrdread_sqlreport_diagnosticreport_flowcytometerreport_interactivereport_reclassificationreport_sanity_checkRRD_create_indicesRRD_LEEF_1_renameRRD_newsanity_checksanity_check_bemovi.mag.16sanity_check_bemovi.mag.25sanity_check_flowcamsanity_check_flowcytometersanity_check_general.datasanity_check_manualcountsanity_check_o2metersanity_get_timestampSetNotFoundSpeciesTo0species_settraits_flowcytometer_archive

Dependencies:arrowassertthatbase64encbitbit64blobbslibcachemclicliprcolorspacecpp11crayoncurldata.tableDBIdbplyrdigestdplyrevaluatefansifarverfastmapfontawesomeforcatsfsfstfstcoregenericsggplot2gluegtablehavenhighrhmshtmltoolsisobandjquerylibjsonliteknitrlabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeparquetizepbapplypbmcapplypillarpkgconfigplogrprettyunitsprocessxprogresspspurrrquartoR6rappdirsRColorBrewerRcppreadrrlangrmarkdownRSQLiterstudioapisassscalesstringistringrtibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Add 'composition' and 'experimetal_design' table to db.add_experiment_tables
Titleadd_extracted_csv_to_db
Titleadd_reclassified_to_db
Add data to RRD database into existing tableadd_to_db
Read 'conductivity' table from an arrow database and return as a tibble.arrow_read_conductivity
Read 'density' table from an arrow database and return as a tibble.arrow_read_density
Read 'o2' table from an arrow database and return as a tibble.arrow_read_o2
Read a table from an arrow database and return as an Dataset object.arrow_read_table
Read 'toc' table from an arrow database and return as a tibble.arrow_read_toc
Re-calculate densitiesCalculateDensities
Classify bemovi data by using the archived dataclassify_bemovi_archive
Classify algae_traits data.frameclassify_bemovi_files
Classify algae_traits data.frameclassify_flowcam_archive
Classify algae_traits data.frameclassify_flowcam_files
Return names of all configs in config fileconfigs
Create trimmed down density-only version of the databasecreate_rrd_trimmed
Disconnect the 'tbl_SQLiteConnection'db_disconnect
Read 'condi=uctivity' from RRD database and return as an 'tbl_SQLiteConnection'.db_read_conductivity
Read 'density' from RRD database and return as an 'tbl_SQLiteConnection'.db_read_density
Read 'immigration_sevent' from RRD database and return as an 'tbl_SQLiteConnection'.db_read_immigration
Read 'light_decline' from RRD database and return as an 'tbl_SQLiteConnection'.db_read_light_decline
Read 'o2' from RRD database and return as an 'tbl_SQLiteConnection'.db_read_o2
Read 'stressor_levels' from RRD database and return as an 'tbl_SQLiteConnection'.db_read_stressor_levels
Read a table from RRD database and return as an 'tbl_SQLiteConnection'.db_read_table
Read 'toc' measurements from RRD database and return as an 'tbl_SQLiteConnection'.db_read_toc
Gate and extract densities from flowcytometer data by using the archived datadensity_flowcytometer_archive
Extract data from tableextract_timestamps
Extract traits from flowcytometer data by using the archived dataextract_traits_flowcytometer_archive
Just a function to update the overlays.generate_overlays
LEEF-1 - Add biomass to traitsLEEF_1_biomass_bemovi_16
LEEF-1 - Add biomass to traitsLEEF_1_biomass_bemovi_25
LEEF-1 - Add biomass to traitsLEEF_1_biomass_bemovi_25_cropped
LEEF-1 - Add biomass to traitsLEEF_1_biomass_bemovi_25_non_cropped
LEEF-1 - Add biomass to traitsLEEF_1_biomass_flowcam
LEEF-1 - Add biomass to traitsLEEF_1_biomass_flowcytometer
Add 'composition' and 'experimetal_design' table to db.LEEF_2_add_experiment_tables
LEEF-1 - Add biomass to traitsLEEF_2_biomass_bemovi
LEEF-2 - Add biomass to traitsLEEF_2_biomass_flowcam
Classify bemovi data by using the archived dataLEEF_2_classify_bemovi_archive
Classify algae_traits data.frameLEEF_2_classify_bemovi_files
Classify algae_traits data.frameLEEF_2_classify_flowcam_archive
Classify algae_traits data.frameLEEF_2_classify_flowcam_files
Gate and extract densities from flowcytometer data by using the archived dataLEEF_2_density_flowcytometer_archive
Extract traits from flowcytometer data by using the archived dataLEEF_2_extract_traits_flowcytometer_archive
Create 'density' view wgich contains all density data from all measurements for LEEF-2LEEF_2_make_view_density
Create 'o2' view which contains selected fields from the os measurement for LEEF-2LEEF_2_make_view_o2
Create 'toc' view wich contains selected fields from the toc__toc measurement for LEEF-2LEEF_2_make_view_toc
Plot diagnostic plot to check bottles per timestampLEEF_2_plot_bottles_per_timestamp
Plot diagnostic plot to check number of species per timestampLEEF_2_plot_conductivity_per_bottle_per_timestamp
Plot diagnostic plot to check number of species per timestamp for LEEF-2LEEF_2_plot_density_species_per_bottle_per_timestamp
Plot diagnostic plot to check is plte has an impact on flowcytometer for LEEF-2LEEF_2_plot_flowcytometer_individual_per_bottle_per_timestamp
Plot diagnostic plot to check number of species per timestampLEEF_2_plot_o2s_per_bottle_per_timestamp
Plot diagnostic plot to check number of species per timestampLEEF_2_plot_response_incubator
Plot diagnostic plot to check number of species per timestampLEEF_2_plot_tocs_per_bottle_per_timestamp
FUNCTION_TITLELEEF_2_rename_composition
FUNCTION_TITLELEEF_2_rename_species
FUNCTION_TITLELEEF_2_rename_species_prob_columns
FUNCTION_TITLELEEF_2_rename_toc
Report for checking pipeline and samplingLEEF_2_report_diagnostic
Create 'o2' view wgich contains selected fields from the conductivity measurementmake_view_conductivity
Create 'density' view wgich contains all density data from all measurementsmake_view_density
Create 'immigration_event' view which adds the experimental daymake_view_immigration_event
Create 'light_decline' view which adds the experimental daymake_view_light_decline
Create 'o2' view wgich contains selected fields from the os measurementmake_view_o2
Create 'toc' view wich contains selected fields from the toc__toc measurementmake_view_toc
Create all viewsmake_views
Create overlaysoverlays
Create overlaysoverlays_from_folders
Create overlaysoverlays_from_reclassification
FUNCTION_TITLEobject_to_parquet parquet_add_bemovi_16 parquet_add_bemovi_25 parquet_add_bemovi_25_cropped parquet_add_conductivity parquet_add_flowcam parquet_add_flowcytometer parquet_add_manualcount parquet_add_o2 parquet_add_toc
Plot diagnostic plot to check bottles per timestampplot_bottles_per_timestamp
Plot diagnostic plot to check number of species per timestampplot_density_species_per_bottle_per_timestamp
Plot diagnostic plot to check number of species per timestampplot_no_species_per_bottle_per_timestamp
Plot diagnostic plot to check number of species per timestampplot_o2s_per_bottle_per_timestamp
Plot diagnostic plot to check number of species per timestampplot_response_incubator
Plot diagnostic plot to check species per timestamp per methodplot_species_per_timestamp_per_measure
Plot diagnostic plot to check number of species per timestampplot_tocs_per_bottle_per_timestamp
Prepare the RRD database for usage with the other functions in this package.prepare_rrd
Read data from the RRD databaseread_sql
Render a quarto file in a temporary directory and copy the resulting files back to the working directoryrender_quarto_temp
Report for checking pipeline and samplingreport_diagnostic
Report for checking pipeline and samplingreport_flowcytometer
Run interactive reportreport_interactive
Do the reclassification and create a reportreport_reclassification
Report for the sanity check of the data for submission to the pipelinereport_sanity_check
Create indices in RRD databaseRRD_create_indices
Rename columns and species in the RRDRRD_LEEF_1_rename
Create new RRD databaseRRD_new
Sanity check data for pipelinesanity_check
Sanity check for bemovi.mag.16sanity_check_bemovi.mag.16
Sanity check for bemovi.mag.25sanity_check_bemovi.mag.25
Sanity check for flowcamsanity_check_flowcam
Sanity check for flowcytometersanity_check_flowcytometer
Sanity check for 0.general.datasanity_check_general.data
Sanity check for manualcountsanity_check_manualcount
Sanity check for o2metersanity_check_o2meter
Extract timestamp from 'sample_metadata.yml' filesanity_get_timestamp
Set number of Not Found species to 0SetNotFoundSpeciesTo0
Defines sets of speciesspecies_set
Gate and extract densities from flowcytometer data by using the archived datatraits_flowcytometer_archive