Using EDAB Utilities Functions for NE ESPs

EDAB Utilities

This vignette demonstrates use of functions within the EDABUtilities package (https://github.com/NEFSC/READ_EDAB_Utilities/tree/main) in examining ecosystem data for ESPs. The example functions here apply input data (as .nc files) and shape files utilized in the golden tilefish ESP.

Crop netCDFs of bottom temperature and bottom salinity to shape file of BTS strata

Crops a 2D netCDF based on the extent of a shape file.

crop_bottomT <- EDABUtilities::crop_nc_2d(data.in = c(here::here('data','glorys_bottomT.nc')),
                            output.files = c(here::here('data','crop_glorys_bottomT.nc')),
                            shp.file = here::here('shapefiles','BTS_STRATA.shp'),
                            #area.names = c('01030'),
                            var.name = 'bottomT',
                            write.out = F)

terra::plot(crop_bottomT[[1]])

crop_bottomS <- EDABUtilities::crop_nc_2d(data.in = c(here::here('data','glorys_bottomS.nc')),
                            output.files = c(here::here('data','crop_glorys_bottomS.nc')),
                            shp.file = here::here('shapefiles','BTS_STRATA.shp'),
                            var.name = 'bottomS',
                            write.out = F)

terra::plot(crop_bottomS[[1]])

Make 2d summary time series: mean monthly bottom temperature in golden tilefish BTS strata

Provides summary statistics of 2d gridded data as time series by area.

monthly_bt <- EDABUtilities::make_2d_summary_ts(data.in = c(here::here('data','glorys_bottomT.nc')),
                            output.files = c(here::here('data','GLORYS_monthly_bottomT.nc')),
                            shp.file = here::here('shapefiles','BTS_STRATA.shp'),
                            var.name = 'bottomT',
                            area.names = c('01030', '01040', '01070', '01080', '01110', '01120', 
                                           '01140', '01150', '01670', '01680', '01710', '01720', 
                                           '01750', '01760'),
                            statistic = 'mean',
                            agg.time = 'days',
                            tz = NA,
                            touches = TRUE,
                            write.out = F)

ggplot2::ggplot(monthly_bt[[1]],ggplot2::aes(x = time, y= value))+
  ggplot2::geom_line(lwd = 1)+ 
  ggplot2::labs(title = 'Monthly Bottom Temperature in GTF Strata') +
  ggplot2::xlab('Month') +
  ggplot2::ylab('Bottom Temperature') +
  ggplot2::theme_bw() +
  ggplot2::facet_wrap(~area)

Make 2d summary time series: mean daily bottom salinity in golden tilefish BTS strata

Provides summary statistics of 2d gridded data as time series by area.

daily_bS <- EDABUtilities::make_2d_summary_ts(data.in = c(here::here('data','glorys_bottomS.nc')),
                   output.files = c(here::here('data','GLORYS_daily_bottomS.nc')),
                   shp.file = here::here('shapefiles','BTS_STRATA.shp'),
                   var.name = 'bottomS',
                   area.names = c('01030', '01040', '01070', '01080', '01110', '01120', 
                                           '01140', '01150', '01670', '01680', '01710', '01720', 
                                           '01750', '01760'),
                   statistic = 'mean',
                   agg.time = 'days',
                   tz = NA,
                   touches = TRUE,
                   write.out = F)

ggplot2::ggplot(daily_bS[[1]],ggplot2::aes(x = time, y= value))+
  ggplot2::geom_line(lwd = 1)+ 
  ggplot2::labs(title = 'Daily Bottom Salinity in GTF Strata') +
  ggplot2::xlab('Days') +
  ggplot2::ylab('Bottom Salinity') +
  ggplot2::theme_bw() +
  ggplot2::facet_wrap(~area)

Make 2d gridded time series: calculate number of days (nd) above a bottom temperature threshold (14C) in the golden tilefish BTS strata

Provides a data frame of degree-day family statistics

dd <- EDABUtilities::make_2d_deg_day_ts(data.in = c(here::here('data','glorys_bottomT.nc')),
                              output.files = c(here::here('data','GLORYS_monthly_bottomT.nc')),
                              shp.file = here::here('shapefiles','BTS_STRATA.shp'),
                              var.name = 'bottomT',
                              area.names = c('01030', '01040', '01070', '01080', '01110', '01120', 
                                            '01140', '01150', '01670', '01680', '01710', '01720', 
                                            '01750', '01760'),
                   ref.value = 14,
                   type = 'above',
                   statistic = 'nd',
                   write.out = F)

dd_df = dplyr::bind_rows(dd)

ggplot2::ggplot(dd_df,ggplot2::aes(x = ls.id, y = value, fill = area))+
  ggplot2::geom_bar(stat = 'identity', position = ggplot2::position_dodge(width = 1.0))+
  ggplot2::labs(title = 'Number of days above 14C', fill = "Strata Number") +
  ggplot2::xlab('GTF Strata') +
  ggplot2::ylab('Days') +
  ggplot2::theme_bw()