Man pages for armbrustlab/popcycle
Popcycle: A R package providing reproducible analytical methods to uniformly process and curate SeaFlow data polygons for manual population gating.
add.manual.classificationDefine polygons for manual population gating.
auto.classifyClassify particles based on semisupervized clustering method...
check.for.populated.sflCheck if SFL table is populated.
classify.oppClassify particles from an OPP dataframe.
classify.opp.filesClassify particles for a list of OPP files.
clean.file.pathClean a file path.
concatenate.evtConcatenate EVT files
concatenate.oppConcatenate OPP files
copy_outlier_tableCopy outlier entries from src_db to dest_db.
copy_tablesCopy tables from one popcycle database to another.
csv_convertConvert data from sqlite3 database into a csv file of curated... a date string to format suitable for popcycle db date... DB filter parameters by ID. DB gating parameters by gating ID. an OPP binary file by file name. entries in the opp table by file name. entries in the outlier table by file name. DB poly parameters by gating ID. DB poly parameters by gating ID and population a VCT text file by file name. an entry in the vct table by file name.
empty_evtCreate an empty EVT data frame
empty_oppCreate an empty OPP data frame
endswithCheck if file path ends with suffix
evaluate.evtFilter and classify one EVT file.
filter.evtFilter EVT particles with a generic filter function.
filter.evt.filesFilter a list of EVT files.
filter.notchFilter EVT particles.
find_common_dbsFind common database files between two directories.
flowrateCalculation of flow rate based on stream pressure measured by... old popcycle gating logs.
get.cruiseGet cruise name EVT data frame by file.
get.evt.filesFind EVT files with a recursive search down a directory tree. a list of EVT files by date range. filter parameters by id.
get.filter.params.latestGet the latest filter parameters.
get.filter.tableReturn a data frame for the filter table. gating parameters by ID.
get.gating.params.latestGet the latest gating parameters.
get.gating.tableReturn a data frame for the gating table.
get.instGet instrument serial number
get.latest.evtFind the most recent EVT file.
get.meta.tableGet instrument serial number and cruise name OPP data frame by date and quantile OPP data frame by file and quantile.
get.opp.datesGet ISO8601 datetime strings (e.g. 2018-07-13T22:24:40+00:00)...
get.opp.filesGet OPP file names for data with focused particles in all...
get.opp.gatesGet per file gating IDs to use for regating based on previous... OPP aggregated filtered particle statistics by date. OPP aggregated filtered particle statistics by file.
get.opp.tableReturn a data frame for the opp table.
get.outlier.tableGet list of outliers. a gating polygon list for pop combo
get.poly.tableReturn a data frame for the poly table.
get.raw.stat.tableGet aggregate statistics data frame joining sfl, opp, and vct... SFL rows >= and <=
get.sfl.tableReturn a data frame for the sfl table.
get.stat.tableGet aggregate statistics data frame along with estimates of... data frame of per particle population classifications by... VCT aggregated per population statistics by date. VCT aggregated per population statistics by file.
get.vct.tableReturn a data frame for the vct table.
make.popcycle.dbCreate a new, empty sqlite3 popcycle database.
manual.classifyClassify particles based on manually defined population...
merge_and_reanalyzeMerge databases after refiltering and reanalyze OPP.
opp_quantile_inner_join_clauseAdd an INNER JOIN to only select OPP files with data in all...
plot_cruisetrackPlot cruise track on a map.
plot_cytPlot EVT or OPP cytogram with only builtin R graphics.
plot_cytogramPlot EVT or OPP cytogram.
plot_filter_cytogramPlot cytograms for exploring filtering parameters.
plot_histogramPlot histogram.
plot_mapPlot population distribution on a map.
plot_timeplot population dynamics over time
plot_vct_cytogramPlot cytogram with particles colored by population. a POSIXct date objectformat suitable for popcycle db...
readSeaflowRead an EVT or OPP binary file.
reset.dbRemove entries for all tables.
reset.db.except.paramsRemove entries for all tables except in filter, gating, and...
reset.filter.tableDelete all rows in filter table.
reset.gating.tableDelete all rows in gating table.
reset.opp.stats.tableDelete all rows in opp table.
reset.outlier.tableDelete all rows in Outlier table.
reset.poly.tableDelete all rows in poly table.
reset.sfl.tableDelete all rows in sfl table.
reset.tableDelete all rows in an arbitrary SQLite3 DB table.
reset.vct.stats.tableDelete all rows in vct table.
RFC3339.nowGet current UTC datetime as RFC3339 string suitable for entry...
rle_startsGet start indexes for run length encoding results.
save.filter.paramsSave filter parameters to the filter table.
save.gating.paramsSave gating parameters.
save.opp.fileSave OPP as a gzipped LabView format binary file
save.opp.statsSave OPP aggregate statistics for one file/quantile combo to...
save.outliersSave Outliers in the database
save.polySave gating polygon coordinates in the poly table.
save.sflImport SFL files to the database.
save.vct.fileSave VCT per particle population classification.
save.vct.statsSave VCT aggregate population statistics for one file to vct...
select_files_inSelect SeaFlow files based on presence in a second vector
set.gating.paramsDefine polygons for population gating.
sfl_date_where_clauseAdd a WHERE clause with date conditionals to SQL statement.
size.carbon.conversionEstimate cell diameter and carbon cell quotas and biomass of...
sql.dbExecuteWrapper to run dbExecute and clean up connection on error.
sql.dbGetQueryWrapper to run dbGetQuery and clean up connection on error.
sql.dbWriteTableWrapper to run dbWriteTable and clean up connection on error. a POSIXct object for a human readable date string.
transformDataExponentiate SeaFlow log data
untransformDataLog SeaFlow linear data
writeSeaflowWrite an EVT or OPP binary file.
armbrustlab/popcycle documentation built on Aug. 8, 2020, 1:08 a.m.