# Processing and Visualization of Visual Plankton Recorder Data

## Documentation for package ‘vprr’ version 0.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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_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