Package: vprr 0.3.0

Emily OGrady

vprr: Processing and Visualization of Video Plankton Recorder Data

An oceanographic data processing package for analyzing and visualizing Video Plankton Recorder data. This package was developed at 'Bedford Institute of Oceanography'. Functions are designed to process automated image classification output and create organized and easily portable data products.

Authors:Emily O'Grady [aut, cre], Kevin Sorochan [aut], Catherine Johnson [aut]

vprr_0.3.0.tar.gz
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vprr_0.3.0.tgz(r-4.4-any)vprr_0.3.0.tgz(r-4.3-any)
vprr_0.3.0.tar.gz(r-4.5-noble)vprr_0.3.0.tar.gz(r-4.4-noble)
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vprr.pdf |vprr.html✨
vprr/json (API)
NEWS

# Install 'vprr' in R:
install.packages('vprr', repos = c('https://eogrady21.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/eogrady21/vprr/issues

Datasets:

On CRAN:

5.11 score 2 stars 16 scripts 96 downloads 27 exports 92 dependencies

Last updated 2 months agofrom:f70ddde7f7. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 27 2024
R-4.5-winNOTEOct 27 2024
R-4.5-linuxNOTEOct 27 2024
R-4.4-winOKOct 27 2024
R-4.4-macOKOct 27 2024
R-4.3-winOKOct 27 2024
R-4.3-macOKOct 27 2024

Exports:bin_calculatebin_castconcentration_categoryctd_castctd_df_colspx_to_mmread_aid_cnnvpr_autoid_checkvpr_autoid_copyvpr_autoid_createvpr_autoid_readvpr_categoryvpr_category_createvpr_ctd_filesvpr_ctd_readvpr_ctd_ymdvpr_ctdroi_mergevpr_dayvpr_dayhourvpr_exportvpr_hourvpr_manual_classificationvpr_oce_createvpr_pred_readvpr_roivpr_roi_concentrationvpr_save

Dependencies:askpassbackportscachemcheckmateclassclassIntclicliprcmoceancolorspacecpp11crayoncredentialscurldata.tableDBIdeldirdescdigestdplyre1071fansifarverfastmapFormulaformula.toolsfsgenericsgertggplot2ghgitcredsgluegridExtragswgtablehttr2iniinterpisobandjsonliteKernSmoothlabelinglatticelifecyclelubridatemagickmagrittrMASSMatrixmemoisemetRmgcvmunsellnlmeoceopenssloperator.toolspillarpkgconfigplyrproxypurrrR6rappdirsRColorBrewerRcppRcppEigenrjsonrlangrprojrootrstudioapis2scalessfstringistringrsystibbletidyrtidyselecttimechangeunitsusethisutf8vctrsviridisLitewhiskerwithrwkyamlzip

Sharing VPR Data

E. O'Grady

Rendered fromsharing_vpr_data.Rmdusingknitr::knitron Oct 27 2024.

Last update: 2024-09-03
Started: 2024-09-03

VPR_processing

Emily O'Grady, Kevin Sorochan, Catherine Johnson

Rendered fromVPR_processing.Rmdusingknitr::knitron Oct 27 2024.

Last update: 2024-09-03
Started: 2020-01-14

Readme and manuals

Help Manual

Help pageTopics
Get bin averages for VPR and CTD databin_calculate
Bin vpr databin_cast
A binned data frame of concentration data per categorycategory_conc_n
Binned concentrationsconcentration_category
Isolate ascending or descending section of ctd castctd_cast
VPR CTD datactd_dat_combine
Read CTD data (SBE49) from CTD- VPR packagectd_df_cols
VPR CTD data combined with tabulated ROIsctd_roi_merge
VPR data including CTD and ROI informationctd_roi_oce
INTERNAL USE ONLY quick data frame function from github to insert row inside dat frameinsertRow
Get vector to draw isopycnal lines on TS plot Used internally to create TS plotsisopycnal_calculate
Normalize a matrixnormalize_matrix
Packagespackage-imports
Get conversion factor for pixels to mm for roi measurementspx_to_mm
Read aid files produced by automated classificationread_aid_cnn
VPR ROI dataroi_dat_combine
VPR measurement data calculated by Visual Planktonroimeas_dat_combine
VPR size information dataframesize_df_f
Checks manually created aid files for errorsvpr_autoid_check
Copy VPR images into foldersvpr_autoid_copy
Modifies aid and aid mea files based on manual reclassificationvpr_autoid_create
Read VPR aid filesvpr_autoid_read
Get category ids from stringvpr_category
Create a new category to be considered for classification after processing with VPvpr_category_create
Create a list of ctd files to be readvpr_ctd_files
Read and format CTD VPR datavpr_ctd_read
Add Year/ month/ day hour:minute:second informationvpr_ctd_ymd
Merge CTD and ROI data from VPRvpr_ctdroi_merge
Format CTD and Size data from VPRvpr_ctdroisize_merge
Get day identifiervpr_day
Find day & hour info to match each station of interest for processingvpr_dayhour
Format and export VPR data for publication (IN DEVELOPMENT) Exports a csv file with standard column names based on British Oceanographic Data Centre, BODC::P01 and DarwinCore (DwC) naming conventions, and a JSON metadata file for station level metadatavpr_export
Get hour identifiervpr_hour
Explore images by depth and classificationvpr_img_category
Remove ROI strings from aid and aidmeas files based on a manually organized folder of imagesvpr_img_check
Image copying function for specific category of interestvpr_img_copy
Explore VPR images by depth binvpr_img_depth
Explore reclassified imagesvpr_img_reclassified
Function to check results of classification manuallyvpr_manual_classification
Create ctd oce object with vpr datavpr_oce_create
Interpolated contour plot of particular variablevpr_plot_contour
Plots VPR profiles of temperature, salinity, density, fluorescence and concentration (by classification group)vpr_plot_profile
Make a balloon plot against a TS plotvpr_plot_TS
Make a balloon plotvpr_plot_TScat
Read prediction output from a CNN modelvpr_pred_read
Get roi ids from stringvpr_roi
Calculate VPR concentrationsvpr_roi_concentration
Save VPR data as an as.oce objectvpr_save
Bin VPR size datavpr_size_bin
Get size data from idsize filesvpr_trrois_size