Files in armbrustlab/popcycle
Popcycle: An R package providing reproducible analytical methods to uniformly process and curate SeaFlow data
.Rbuildignore
.dockerignore
.gitignore
DESCRIPTION
Dockerfile
LICENSE
NAMESPACE
R/Load.R
R/calibration.R
R/db.R
R/files.R
R/filter.R
R/gating.R
R/globals.R
R/meta.R
R/plan.R
R/psd.R
R/realtime.R
R/time.R
R/visualization.R
README.md
build-docker.sh
computer/TS_plot.html
computer/div_indices.html
computer/fluo_comp.html
computer/gate.cytogram.html
computer/log_seaflow_stats
computer/vct.cytogram.html
documentation/images/beads-gate.png
documentation/images/fsc_small-chl_small-gates.png
documentation/images/fsc_small-chl_small-vct.png
documentation/images/fsc_small-pe-gates.png
documentation/images/fsc_small-pe-vct.png
documentation/images/seaflow-workflow.png
documentation/user-guide.rmd
executable_scripts/classify_files.R
executable_scripts/filter_and_classify_files.R
executable_scripts/filter_files.R
executable_scripts/psd.R
executable_scripts/update_plan_tables.R
executable_scripts/visualize_reanalysis.R
images/cruise-track.png
inst/abundance/abundance-calibration.csv
inst/extdata/367.evt
inst/extdata/37.evt
inst/extdata/SeaFlow/datafiles/evt/2014_185/2014-07-04T00-00-00+00-00.sfl
inst/extdata/SeaFlow/datafiles/evt/2014_185/2014-07-04T00-00-02+00-00.gz
inst/extdata/SeaFlow/datafiles/evt/2014_185/2014-07-04T00-03-02+00-00.gz
inst/extdata/SeaFlow/logs/SFlog.txt
inst/extdata/par_data.csv
inst/filter/reference_filter_params_130.csv
inst/filter/reference_filter_params_740.csv
inst/filter/seaflow_filter_slopes.csv
inst/flowrate/detectable_region.csv
inst/flowrate/lm_130
inst/flowrate/lm_740
inst/flowrate/lm_751
inst/flowrate/lm_989
inst/par/par-calibration.csv
inst/scatter/RefracIndices_percruise.csv
inst/scatter/calibrated-mie.csv
inst/sql/popcycle.sql
make_docs.R
man/add_abundance.Rd
man/add_auto_classification.Rd
man/add_coord_labels.Rd
man/add_manual_classification.Rd
man/auto_classify.Rd
man/classify_opp.Rd
man/classify_opp_files.Rd
man/clean_file_path.Rd
man/cmap_convert.Rd
man/concatenate.evt.Rd
man/concatenate.opp.Rd
man/copy_outlier_table.Rd
man/copy_tables.Rd
man/create_PSD.Rd
man/create_PSD_one_file.Rd
man/create_breaks.Rd
man/create_filter_params.Rd
man/create_grid.Rd
man/create_meta.Rd
man/create_realtime_bio.Rd
man/create_realtime_meta.Rd
man/create_volume_table.Rd
man/csv_convert.Rd
man/delete_filter_params_by_id.Rd
man/delete_gating_params_by_id.Rd
man/delete_poly_by_id.Rd
man/delete_poly_by_id_pop.Rd
man/empty_evt.Rd
man/empty_opp.Rd
man/filter_evt.Rd
man/filter_evt_files.Rd
man/find_common_dbs.Rd
man/flowrate.Rd
man/from_filename_date_str.Rd
man/get_clean_stat_table.Rd
man/get_cruise.Rd
man/get_evt_by_file.Rd
man/get_evt_files.Rd
man/get_filter_params_by_id.Rd
man/get_filter_plan_table.Rd
man/get_filter_table.Rd
man/get_gating_params_by_id.Rd
man/get_gating_plan_table.Rd
man/get_gating_table.Rd
man/get_inst.Rd
man/get_metadata_table.Rd
man/get_opp_by_date.Rd
man/get_opp_by_file.Rd
man/get_opp_table.Rd
man/get_outlier_table.Rd
man/get_poly_log_by_gating_id_pop.Rd
man/get_poly_table.Rd
man/get_processed_particles.Rd
man/get_raw_stat_table.Rd
man/get_sfl_table.Rd
man/get_stat_table.Rd
man/get_vct_by_date.Rd
man/get_vct_by_file.Rd
man/get_vct_quantile_range.Rd
man/get_vct_range.Rd
man/get_vct_range_one_file.Rd
man/get_vct_table.Rd
man/grid_labels.Rd
man/group_psd_by_time.Rd
man/identify_noise.Rd
man/identify_saturated.Rd
man/inflection_point.Rd
man/is_transformed.Rd
man/make_popcycle_db.Rd
man/manual_classify.Rd
man/migrate_tables.Rd
man/mktempname.Rd
man/plan_from_table.Rd
man/plot_cruisetrack.Rd
man/plot_cyt.Rd
man/plot_cytogram.Rd
man/plot_filter_cytogram.Rd
man/plot_histogram.Rd
man/plot_map.Rd
man/plot_time.Rd
man/plot_vct_cytogram.Rd
man/readSeaflow.Rd
man/read_calib_csv.Rd
man/read_mie_csv.Rd
man/read_par_csv.Rd
man/read_parquet_one_quantile.Rd
man/read_reference_filter_params.Rd
man/read_refraction_csv.Rd
man/read_sfl_tsv.Rd
man/remove_boundary_points.Rd
man/reset_filter_plan_table.Rd
man/reset_filter_table.Rd
man/reset_gating_plan_table.Rd
man/reset_gating_table.Rd
man/reset_metadata_table.Rd
man/reset_opp_table.Rd
man/reset_outlier_table.Rd
man/reset_poly_table.Rd
man/reset_sfl_table.Rd
man/reset_table.Rd
man/reset_vct_table.Rd
man/save_filter_params.Rd
man/save_filter_plan.Rd
man/save_gating_params.Rd
man/save_gating_plan.Rd
man/save_metadata.Rd
man/save_opp_stats.Rd
man/save_outliers.Rd
man/save_poly.Rd
man/save_sfl.Rd
man/save_vct_stats.Rd
man/set_gating_params.Rd
man/size_carbon_conversion.Rd
man/sql_dbExecute.Rd
man/sql_dbGetQuery.Rd
man/sql_dbWriteTable.Rd
man/stat_calibration.Rd
man/to_date_str.Rd
man/to_filename_date_str.Rd
man/transformData.Rd
man/untransformData.Rd
man/update_plan_table.Rd
man/validate_psd.Rd
man/writeSeaflow.Rd
man/write_realtime_bio_tsdata.Rd
man/write_realtime_meta_tsdata.Rd
setup.R
tests/README.md
tests/params.RData
tests/testdata/calibrated-mie.de77773.2020-10-23.csv
tests/testdata/evt/2014_185/2014-07-04T00-00-00+00-00.sfl
tests/testdata/evt/2014_185/2014-07-04T00-00-02+00-00
tests/testdata/evt/2014_185/2014-07-04T00-00-02+00-00.notransform.rds
tests/testdata/evt/2014_185/2014-07-04T00-00-02+00-00.transform.rds
tests/testdata/evt/2014_185/2014-07-04T00-03-02+00-00.gz
tests/testdata/evt/2014_185/2014-07-04T00-03-02+00-00.notransform.rds
tests/testdata/evt/2014_185/2014-07-04T00-03-02+00-00.transform.rds
tests/testdata/evt/2014_185/2014-07-04T00-06-02+00-00.gz
tests/testdata/evt/2014_185/2014-07-04T00-09-02+00-00
tests/testdata/evt/2014_185/2014-07-04T00-12-02+00-00
tests/testdata/evt/2014_185/2014-07-04T01-15-02+00-00.gz
tests/testdata/evt/2014_185/2014-07-04T01-17-02+00-00.gz
tests/testdata/evt/2014_185/2014-07-04T01-21-02+00-00
tests/testdata/evt/2014_185/2014-07-04T01-27-02+00-00
tests/testdata/evt/2014_185/2014-07-04T01-30-02+00-00
tests/testdata/evt/2014_185/README.md
tests/testdata/evt_v2/2014_185/2014-07-04T00-00-00+00-00.sfl
tests/testdata/evt_v2/2014_185/2014-07-04T00-00-02+00-00
tests/testdata/evt_v2/2014_185/2014-07-04T00-00-02+00-00.notransform.rds
tests/testdata/evt_v2/2014_185/2014-07-04T00-00-02+00-00.transform.rds
tests/testdata/evt_v2/2014_185/2014-07-04T00-03-02+00-00.gz
tests/testdata/evt_v2/2014_185/2014-07-04T00-03-02+00-00.notransform.rds
tests/testdata/evt_v2/2014_185/2014-07-04T00-03-02+00-00.transform.rds
tests/testdata/evt_v2/2014_185/2014-07-04T00-06-02+00-00
tests/testdata/evt_v2/2014_185/2014-07-04T00-09-02+00-00
tests/testdata/evt_v2/2014_185/2014-07-04T00-12-02+00-00
tests/testdata/evt_v2/2014_185/2014-07-04T01-15-02+00-00.gz
tests/testdata/evt_v2/2014_185/2014-07-04T01-17-02+00-00.gz
tests/testdata/evt_v2/2014_185/2014-07-04T01-21-02+00-00
tests/testdata/evt_v2/2014_185/2014-07-04T01-27-02+00-00
tests/testdata/evt_v2/2014_185/2014-07-04T01-30-02+00-00
tests/testdata/gates1.rds
tests/testdata/gates2.rds
tests/testdata/getvct/2018-06-25T20-00-00+00-00.1H.vct.parquet
tests/testdata/getvct/2018-06-25T21-00-00+00-00.1H.vct.parquet
tests/testdata/getvct/HOT303.db
tests/testdata/opp_one_param/2014-07-04T00-00-00+00-00.1H.opp.parquet
tests/testdata/opp_one_param/2014-07-04T01-00-00+00-00.1H.opp.parquet
tests/testdata/opp_plan/2014-07-04T00-00-00+00-00.1H.opp.parquet
tests/testdata/opp_plan/2014-07-04T01-00-00+00-00.1H.opp.parquet
tests/testdata/psd/SCOPE_19.db
tests/testdata/psd/SCOPE_19_vct/2016-08-08T19-00-00+00-00.1H.vct.parquet
tests/testdata/psd/SCOPE_19_vct/2016-08-08T20-00-00+00-00.1H.vct.parquet
tests/testdata/recreate_derived_test_data.R
tests/testdata/seaflow_filter_slopes.csv
tests/testdata/testcruise_bare.db
tests/testdata/testcruise_full_one_param.db
tests/testdata/testcruise_full_plan.db
tests/testdata/vct_one_param/2014-07-04T00-00-00+00-00.1H.vct.parquet
tests/testdata/vct_one_param/2014-07-04T01-00-00+00-00.1H.vct.parquet
tests/testdata/vct_plan/2014-07-04T00-00-00+00-00.1H.vct.parquet
tests/testdata/vct_plan/2014-07-04T01-00-00+00-00.1H.vct.parquet
tests/testthat.R
tests/testthat/helper.R
tests/testthat/helper_psd.R
tests/testthat/helper_read_parquet.R
tests/testthat/test_db.R
tests/testthat/test_files.R
tests/testthat/test_filter.R
tests/testthat/test_gating.R
tests/testthat/test_plan.R
tests/testthat/test_psd.R
tests/testthat/test_read_parquet.R
tests/testthat/test_time.R
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wiki/good_align.png
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wiki/notch1_corrected.png
wiki/notch_0.8.png
wiki/notch_1.png
wiki/notch_OPP_after.png
wiki/notch_OPP_before.png
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wiki/offset_auto.png
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wiki/origin_OPP_after.png
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wiki/origin_auto.png
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