Processing and Visualization of Video Plankton Recorder Data

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Documentation for package ‘vprr’ version 0.2.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

bin_calculate	Get bin averages for VPR and CTD data
bin_cast	Bin vpr data
concentration_category	Binned concentrations
ctd_cast	Isolate ascending or descending section of ctd cast
ctd_dat_combine	VPR CTD data
ctd_df_cols	Read CTD data (SBE49) and Fluorometer data from CTD- VPR package
ctd_roi_merge	VPR CTD data combined with tabulated ROIs
ctd_roi_oce	VPR data including CTD and ROI information
getRoiMeasurements	THIS FUNCTION HAS BEEN DEPRECATED
insertRow	INTERNAL USE ONLY quick data frame function from github to insert row inside dat frame
isopycnal_calculate	Get vector to draw isopycnal lines on TS plot Used internally to create TS plots
normalize_matrix	Normalize a matrix
px_to_mm	Get conversion factor for pixels to mm for roi measurements
roimeas_dat_combine	VPR measurement data calculated by Visual Plankton
roi_dat_combine	VPR ROI data
size_df_f	VPR size information dataframe
taxa_conc_n	A binned data frame of concentration data per category
vpr_autoid_check	Checks manually created aid files for errors
vpr_autoid_copy	Copy VPR images into folders
vpr_autoid_create	Modifies aid and aid mea files based on manual reclassification
vpr_autoid_read	Read VPR aid files
vpr_category	Get taxa ids from string
vpr_category_create	Create a new taxa to be considered for classification after processing with VP
vpr_ctdroisize_merge	Format CTD and Size data from VPR
vpr_ctdroi_merge	Merge CTD and ROI data from VPR
vpr_ctd_files	Create a list of ctd files to be read
vpr_ctd_read	Read and format CTD VPR data
vpr_ctd_ymd	Add Year/ month/ day hour:minute:second information
vpr_day	Get day identifier
vpr_dayhour	Find day & hour info to match each station of interest for processing
vpr_hour	Get hour identifier
vpr_img_category	Explore images by depth and classification
vpr_img_check	Remove ROI strings from aid and aidmeas files based on a manually organized folder of images
vpr_img_copy	Image copying function for specific taxa of interest
vpr_img_depth	Explore VPR images by depth bin
vpr_img_reclassified	Explore reclassified images
vpr_manual_classification	Function to check results of classification manually
vpr_oce_create	Create ctd oce object with vpr data
vpr_plot_contour	Interpolated contour plot of particular variable
vpr_plot_histsize	Plot size frequency histogram
vpr_plot_profile	Plots VPR profiles of temperature, salinity, density, fluorescence and concentration (by classification group)
vpr_plot_sizefreq	Size Frequency plots for VPR data
vpr_plot_TS	Make a balloon plot against a TS plot
vpr_plot_TScat	Make a balloon plot
vpr_pred_read	Read prediction output from a CNN model
vpr_roi	Get roi ids from string
vpr_roi_concentration	Calculate VPR concentrations
vpr_save	Save VPR data as an as.oce object
vpr_size_bin	Bin VPR size data
vpr_summary	Data Summary Report
vpr_trrois_size	Get size data from idsize files
vp_plot_matrix	Plots normalized confusion matrix
vp_plot_unkn	Function to visualize losses to unknown category due to disagreement in Dual classifier