Files in armbrustlab/popcycle
Popcycle: A R package providing reproducible analytical methods to uniformly process and curate SeaFlow data

.gitignore
DESCRIPTION
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/pipeline.R R/visualization.R README.md
computer/Crontab.sh
computer/RT_analysis.log
computer/RT_analysis.sh
computer/TS_plot.html
computer/cron_job.out
computer/div_indices.html
computer/fluo_comp.html
computer/gate.cytogram.html
computer/log_seaflow_stats
computer/mountSeaFlowDisk.sh
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
executable_scripts/.Rapp.history
executable_scripts/copy_file.R executable_scripts/cron_job.R executable_scripts/filter_files.R executable_scripts/merge_and_reanalyze.R
executable_scripts/reset_realtime.sh
executable_scripts/visualize_reanalysis.R
images/cruise-track.png
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/seaflow_filter_slopes.csv
inst/flowrate/detectable_region.csv
inst/flowrate/lm_740
inst/flowrate/lm_751
inst/flowrate/lm_989
inst/scatter/calibrated-mie.csv
inst/sql/popcycle.sql
make_docs.R man/POSIXct.to.db.date.Rd man/RFC3339.now.Rd man/add.auto.classification.Rd man/add.manual.classification.Rd man/auto.classify.Rd man/check.for.populated.sfl.Rd man/classify.opp.Rd man/classify.opp.files.Rd man/clean.file.path.Rd man/concatenate.evt.Rd man/concatenate.opp.Rd man/copy_outlier_table.Rd man/copy_tables.Rd man/csv_convert.Rd man/date.to.db.date.Rd man/delete.filter.params.by.id.Rd man/delete.gating.params.by.id.Rd man/delete.opp.by.file.Rd man/delete.opp.stats.by.file.Rd man/delete.outliers.by.file.Rd man/delete.poly.by.id.Rd man/delete.poly.by.id.pop.Rd man/delete.vct.by.file.Rd man/delete.vct.stats.by.file.Rd man/empty_evt.Rd man/empty_opp.Rd man/endswith.Rd man/evaluate.evt.Rd man/file_transfer.Rd man/filter.evt.Rd man/filter.evt.files.Rd man/filter.notch.Rd man/find_common_dbs.Rd man/flowrate.Rd man/gating.csv.to.poly.log.Rd man/get.cruise.Rd man/get.evt.by.file.Rd man/get.evt.files.Rd man/get.evt.files.by.date.Rd man/get.filter.params.by.id.Rd man/get.filter.params.latest.Rd man/get.filter.table.Rd man/get.gating.params.by.id.Rd man/get.gating.params.latest.Rd man/get.gating.table.Rd man/get.inst.Rd man/get.latest.evt.Rd man/get.meta.table.Rd man/get.opp.by.date.Rd man/get.opp.by.file.Rd man/get.opp.dates.Rd man/get.opp.files.Rd man/get.opp.gates.Rd man/get.opp.stats.by.date.Rd man/get.opp.stats.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.raw.stat.table.Rd man/get.sfl.by.date.Rd man/get.sfl.table.Rd man/get.stat.table.Rd man/get.vct.by.file.Rd man/get.vct.stats.by.date.Rd man/get.vct.stats.by.file.Rd man/get.vct.table.Rd man/make.popcycle.db.Rd man/manual.classify.Rd man/merge_and_reanalyze.Rd man/opp_quantile_inner_join_clause.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/reset.db.Rd man/reset.db.except.params.Rd man/reset.filter.table.Rd man/reset.gating.table.Rd man/reset.opp.stats.table.Rd man/reset.outlier.table.Rd man/reset.poly.table.Rd man/reset.sfl.table.Rd man/reset.table.Rd man/reset.vct.stats.table.Rd man/rle_starts.Rd man/save.filter.params.Rd man/save.gating.params.Rd man/save.opp.file.Rd man/save.opp.stats.Rd man/save.outliers.Rd man/save.poly.Rd man/save.sfl.Rd man/save.vct.file.Rd man/save.vct.stats.Rd man/select_files_in.Rd man/set.gating.params.Rd man/sfl_date_where_clause.Rd man/size.carbon.conversion.Rd man/sql.dbExecute.Rd man/sql.dbGetQuery.Rd man/sql.dbWriteTable.Rd man/string.to.POSIXct.Rd man/transformData.Rd man/untransformData.Rd man/writeSeaflow.Rd scratch.R setup.R tests/README.md
tests/params.RData
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_185/2014-07-04T00-15-02+00-00.gz
tests/testdata/evt/2014_185/2014-07-04T00-17-02+00-00.gz
tests/testdata/evt/2014_185/2014-07-04T00-21-02+00-00
tests/testdata/evt/2014_185/2014-07-04T00-27-02+00-00
tests/testdata/evt/2014_185/README.md
tests/testdata/opp/2014_185/2014-07-04T00-00-02+00-00.opp.gz
tests/testdata/opp/2014_185/2014-07-04T00-03-02+00-00.opp.gz
tests/testdata/recreate_derived_test_data.R
tests/testdata/seaflow_filter_slopes.csv
tests/testdata/testcruise_bare.db
tests/testdata/testcruise_full.db
tests/testdata/vct/2.5/2014_185/2014-07-04T00-00-02+00-00.vct.gz
tests/testdata/vct/2.5/2014_185/2014-07-04T00-03-02+00-00.vct.gz
tests/testdata/vct/50/2014_185/2014-07-04T00-00-02+00-00.vct.gz
tests/testdata/vct/50/2014_185/2014-07-04T00-03-02+00-00.vct.gz
tests/testdata/vct/97.5/2014_185/2014-07-04T00-00-02+00-00.vct.gz
tests/testdata/vct/97.5/2014_185/2014-07-04T00-03-02+00-00.vct.gz
tests/testthat.R tests/testthat/helper.R tests/testthat/test_db.R tests/testthat/test_evaluate_last_file.R tests/testthat/test_files.R tests/testthat/test_filter.R tests/testthat/test_gating.R
wiki/D1_cut.png
wiki/bad_align.png
wiki/good_align.png
wiki/notch1_auto.png
wiki/notch1_corrected.png
wiki/notch_0.8.png
wiki/notch_1.png
wiki/notch_OPP_after.png
wiki/notch_OPP_before.png
wiki/offset_OPP_after.png
wiki/offset_OPP_before.png
wiki/offset_auto.png
wiki/offset_corrected.png
wiki/origin_OPP_after.png
wiki/origin_OPP_before.png
wiki/origin_auto.png
wiki/origin_corrected.png
wiki/width_OPP_after.png
wiki/width_OPP_before.png
wiki/width_auto.png
wiki/width_corrected.png
armbrustlab/popcycle documentation built on Aug. 8, 2020, 1:08 a.m.