Files in LEEF-UZH/LEEF.analysis
Access Functions, Tests and Basic Analysis of the RRD Data from the LEEF Project

.Rbuildignore

.gitignore

.lintr

.vscode/launch.json

DESCRIPTION

LEEF.analyLEEF.analysis.code-workspace

LEEF.analysis.Rproj

LICENSE

Makefile

NAMESPACE

R/LEEF.analysis-package.R R/LEEF_1_biomass_bemovi_16.R R/LEEF_1_biomass_bemovi_25.R R/LEEF_1_biomass_bemovi_25_cropped.R R/LEEF_1_biomass_bemovi_25_non_cropped.R R/LEEF_1_biomass_flowcam.R R/LEEF_1_biomass_flowcytometer.R R/LEEF_2.classify_bemovi_archive.R R/LEEF_2_add_experiment_tables.R R/LEEF_2_biomass_bemovi.R

R/LEEF_2_biomass_bemovi_16.R.DEL

R/LEEF_2_biomass_bemovi_25.R.DEL

R/LEEF_2_biomass_bemovi_25_cropped.R.DEL

R/LEEF_2_biomass_flowcam.R R/LEEF_2_classify_bemovi_files.R R/LEEF_2_classify_flowcam_archive.R R/LEEF_2_classify_flowcam_files.R R/LEEF_2_density_flowcytometer_archive.R R/LEEF_2_extract_traits_flowcytometer_archive.R R/LEEF_2_make_view_density.R R/LEEF_2_make_view_o2.R R/LEEF_2_make_view_toc.R R/LEEF_2_plot_bottles_per_timestamp_per_timestamp.R R/LEEF_2_plot_conductivity_per_bottle_per_timestamp.R R/LEEF_2_plot_density_species_per_bottle.R R/LEEF_2_plot_flowcytometer_individual_per_bottle.R R/LEEF_2_plot_o2s_per_bottle_per_timestamp.R R/LEEF_2_plot_response_incubator.R R/LEEF_2_plot_tocs_per_bottle.R R/LEEF_2_renamer.R R/LEEF_2_report_diagnostic.R R/RRD_LEEF_1_rename.R R/RRD_create_indices.R R/RRD_new.R R/UD_CalculateDensities.R R/UD_SetNotFoundSpeciesTo0.R R/add_experiment_tables.R R/add_extracted_csv_to_db.R R/add_reclassified_to_db.R R/add_to_db.R R/arrow.R R/arrow_read_conductivity.R R/arrow_read_density.R R/arrow_read_o2.R R/arrow_read_table.R R/arrow_read_toc.R R/classify_bemovi_archive.R R/classify_bemovi_files.R R/classify_flowcam_archive.R R/classify_flowcam_files.R R/config_helper.R R/create_metadata_files.R R/create_rrd_trimmed.R R/db_disconnect.R R/db_read_conductivity.R R/db_read_density.R R/db_read_immigration.R R/db_read_light_decline.R R/db_read_o2.R R/db_read_stressor_levels.R R/db_read_table.R R/db_read_toc.R R/density_flowcytometer_archive.R R/extract_timestamps.R R/extract_traits_flowcytometer_archive.R R/generate_overlays.R R/helper.R R/make_view_conductivity.R R/make_view_density.R R/make_view_immigration.R R/make_view_light.R R/make_view_o2.R R/make_view_toc.R R/make_views.R R/overlays.R R/overlays_from_folders.R R/overlays_from_reclassification.R R/plot_bottles_per_timestamp_per_timestamp.R R/plot_density_species_per_bottle.R R/plot_no_species_per_bottle_per_timestamp.R R/plot_o2s_per_bottle_per_timestamp.R R/plot_response_incubator.R R/plot_species_per_timestamp_per_measure.R R/plot_tocs_per_bottle.R R/prepare_rrd.R R/read_sql.R R/render_quarto_temp.R R/report_diagnostic.R R/report_flowcytometer.R R/report_interactive.R R/report_reclassification.R R/report_sanity_check.R R/sanitychecks.R R/traits_flowcytometer_archive.R

codemeta.json

inst/.gitignore

inst/Assessment Size Standard Small Beads.qmd

inst/Assessment Size Standard.qmd

inst/Bemovi_timestamp_missing_search.qmd

inst/Flowcytometer Biomass Calculation log10.qmd

inst/Flowcytometer Biomass Calculation.html

inst/Flowcytometer Biomass Calculation.qmd

inst/InteractiveReport.Rmd

inst/LEEF-1/.gitignore

inst/LEEF-1/Biomass over time per bottle.qmd

inst/LEEF-1/DiagnosticReport.Rmd

inst/LEEF-1/Differences_Bottles.qmd

inst/LEEF-1/FSC.A.density.qmd

inst/LEEF-1/Flowcytometer_Report.qmd

inst/LEEF-1/RRD.empty.sql

inst/LEEF-1/RRD.indices.sql

inst/LEEF-1/RRDReadyCheckJune23.R

inst/LEEF-1/RRDReadyCheckJune23.qmd

inst/LEEF-1/Reclassification_and_Data_Cleaning.qmd

inst/LEEF-1/TMP_fixed_eawag_flowcytometer.qmd

inst/LEEF-1/Verify Data Cleaning.qmd

inst/LEEF-2/.gitignore

inst/LEEF-2/DiagnosticReport.Rmd

inst/LEEF-2/Flowcytometer_Report.qmd

inst/LEEF-2/Flowcytometer_plates.qmd

inst/LEEF-2/LEEF-2 Reclassification_and_Data_Cleaning.qmd

inst/LEEF-2/ScriptsByUriah/LEEF2_RRDReadyCheck.html

inst/LEEF-2/ScriptsByUriah/LEEF2_RRDReadyCheck.qmd

inst/LEEF-2/ScriptsByUriah/LEEF2_RRDReadyCheck_local.qmd

inst/LEEF-2/ScriptsByUriah/LEEF2_RRD_PostPipelineCleaning.qmd

inst/LEEF-2/ScriptsByUriah/LEEF2_RRD_PostPipelineCleaning_local.qmd

inst/LEEF-2/ScriptsByUriah/VideoChecks/FirstMethodCheck/tocheck_1stmethod.csv

inst/LEEF-2/ScriptsByUriah/VideoChecks/SecondMethodCheck/tocheck_2ndmethod.csv

inst/LEEF-2/ScriptsByUriah/VideoChecks/SecondMethodCheck/tocheck_2ndmethod_MissingTimestamps.csv

inst/LEEF-2/ScriptsByUriah/VideoChecks/ThirdMethodCheck/videos_16x.csv

inst/LEEF-2/ScriptsByUriah/VideoChecks/ThirdMethodCheck/videos_25x.csv

inst/LEEF-2/ScriptsByUriah/VideoChecks/new_densities_for_doublecheck.csv

inst/LEEF-2/ScriptsByUriah/biomass20221107_doubleCheck.csv

inst/LEEF-2/ScriptsByUriah/microscopic_checks_ciliates.csv

inst/LEEF-2/ScriptsByUriah/microscopic_checks_ciliates.xlsx

inst/LEEF-2/ScriptsByUriah/new_PCaudatum_densities_for_doublecheck.csv

toc.rds

LEEF-UZH/LEEF.analysis documentation built on Feb. 8, 2025, 11:18 a.m.

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

Files in LEEF-UZH/LEEF.analysis
Access Functions, Tests and Basic Analysis of the RRD Data from the LEEF Project

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

Files in LEEF-UZH/LEEF.analysis Access Functions, Tests and Basic Analysis of the RRD Data from the LEEF Project

R Package Documentation

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

Files in LEEF-UZH/LEEF.analysis
Access Functions, Tests and Basic Analysis of the RRD Data from the LEEF Project