R/older-functions/PACea_regions.R

In pbs-assess/PACea: An R package of Pacific ecosystem information to help facilitate an ecosystem approach to fisheries management

#' @export
# Script for searching and plotting the available regions
Pacea_regions <- function(regions = NULL, plot=F, return_sf_Polys=F, approximate=F)
{
  if(is.null(regions)){
    print(c('The available regions are called ',
            names(PACea::BC_Partition_Objects$index_vectors)))

    if(return_sf_Polys){
      sf_Polys = vector('list',
                        length(names(PACea::BC_Partition_Objects$index_vectors)))
      names(sf_Polys) <- names(PACea::BC_Partition_Objects$index_vectors)
    }

    if(plot | return_sf_Polys){
      for(i in names(PACea::BC_Partition_Objects$index_vectors)){
        if(approximate==TRUE){
          region_Poly <- PACea::BC_Partition_Objects$BC_Partition %>%
            dplyr::filter(Poly_ID %in%
                          do.call('c',
                                  apply(PACea::BC_Partition_Objects$Mapping_Matrix[,
                                                                                   PACea::BC_Partition_Objects$index_vectors[[i]]
                                                                                   ],
                                        2, FUN=function(x){which(x>0)},
                                        simplify = F))
                          )
          # Which Poly_ID corresponds to which 'exact polygon'?
          region_Poly$Exact_Poly_ID <-
            do.call('c',
                    lapply(FUN=function(x){
                      paste0(PACea::BC_Partition_Objects$index_vectors[[i]][x],
                             collapse=' and ')},
                      apply(PACea::BC_Partition_Objects$Mapping_Matrix[region_Poly$Poly_ID,
                                                                       PACea::BC_Partition_Objects$index_vectors[[i]]],
                            1, FUN=function(x){which(x>0)}, simplify = T)
                      )
                    )
          # And the names?
          region_Poly$Exact_Poly_Name <-
            do.call('c',
                    lapply(FUN=function(x){
                      paste0(PACea::BC_Partition_Objects$BC_Partition$Poly_Name[PACea::BC_Partition_Objects$index_vectors[[i]][x]],
                             collapse=' and ')},
                      apply(PACea::BC_Partition_Objects$Mapping_Matrix[region_Poly$Poly_ID,
                                                                       PACea::BC_Partition_Objects$index_vectors[[i]]],
                            1, FUN=function(x){which(x>0)}, simplify = T)
                      )
                    )

          if(plot){
            if(length(unique(region_Poly$Exact_Poly_Name)) > 10){
              print(
                ggplot2::ggplot(PACea::Coastline_Expanded) +
                ggplot2::geom_sf(fill='lightblue') +
                ggplot2::geom_sf(data=region_Poly,
                                 ggplot2::aes(fill=factor(Exact_Poly_Name,
                                                          ordered = T),
                                              colour=factor(Exact_Poly_Name,
                                                            ordered = T)),
                                 alpha=0.2) +
                ggplot2::geom_sf_label(data=region_Poly,
                                       ggplot2::aes(label=Exact_Poly_ID)) +
                #ggplot2::guides(fill=ggplot2::guide_legend(title='Poly_Name'), colour=ggplot2::guide_legend(title='Poly_Name')) +
                ggplot2::guides(fill="none",
                                colour="none") +
                ggplot2::ggtitle(paste0('PACea-Approximated Polygons Defining Region "',i,'"'),
                                 subtitle = 'Polygons coloured by Poly_Name and labelled by Poly_ID \nWhen numbers are present, they ascend in the same order')
              )
            }

            if(length(unique(region_Poly$Exact_Poly_Name)) <= 10){
              print(
                ggplot2::ggplot(PACea::Coastline_Expanded) +
                ggplot2::geom_sf(fill='lightblue') +
                ggplot2::geom_sf(data=region_Poly,
                                 ggplot2::aes(fill=factor(Exact_Poly_Name,
                                                          ordered = T),
                                              colour=factor(Exact_Poly_Name,
                                                            ordered = T)),
                                 alpha=0.2) +
                ggplot2::geom_sf_label(data=region_Poly,
                                       ggplot2::aes(label=Exact_Poly_ID)) +
                ggplot2::guides(fill=ggplot2::guide_legend(title='Poly_Name'),
                                colour=ggplot2::guide_legend(title='Poly_Name')) +
                #ggplot2::guides(fill="none", colour="none") +
                ggplot2::ggtitle(paste0('PACea-Approximated Polygons Defining Region "',i,'"'),
                                 subtitle =
                                   'Polygons coloured by Poly_Name and labelled by Poly_ID \nWhen numbers are present, they ascend in the same order')
              )
            }
          }
        }

        if(approximate == FALSE)
        {
          region_Poly <-
            PACea::BC_Partition_Objects$BC_Partition %>%
            dplyr::filter(Poly_ID %in% BC_Partition_Objects$index_vectors[[i]])

          if(plot)
          {
            print(
              ggplot2::ggplot(PACea::Coastline_Expanded) +
              ggplot2::geom_sf(fill='lightblue') +
              ggplot2::geom_sf(data=region_Poly,
                               ggplot2::aes(fill=factor(Poly_Name, levels=Poly_Name, ordered = T),
                                            colour=factor(Poly_Name, levels=Poly_Name, ordered = T)),
                               alpha=0.2) +
              ggplot2::geom_sf_label(data=region_Poly, ggplot2::aes(label=Poly_ID)) +
              ggplot2::guides(fill=ggplot2::guide_legend(title='Poly_Name'), colour=ggplot2::guide_legend(title='Poly_Name')) +
              ggplot2::ggtitle(paste0('Exact Polygons Defining Region "',i,'"'),
                               subtitle = 'Polygons coloured by Poly_Name and labelled by Poly_ID \nWhen numbers are present, they ascend in the same order')
            )
          }
        }
        if(return_sf_Polys){
          sf_Polys[[i]] <- region_Poly
        }
      }
    }
  }

  if(!is.null(regions)){
    if(return_sf_Polys){
      sf_Polys = vector('list',
                        length(regions))
      names(sf_Polys) <- regions
    }

    if(plot | return_sf_Polys){
      for(i in regions){
        if(approximate == TRUE){
          if(!(i %in% names(PACea::BC_Partition_Objects$index_vectors))){
            stop(paste0(i, ' is not a valid region. Please run Pacea_regions() to see the names of all the valid regions'))
          }

          region_Poly <-
            PACea::BC_Partition_Objects$BC_Partition %>%
            dplyr::filter(Poly_ID %in%
                          do.call('c',
                                  apply(PACea::BC_Partition_Objects$Mapping_Matrix[,
                                                                                   PACea::BC_Partition_Objects$index_vectors[[i]]
                                                                                   ],
                                        2, FUN=function(x){which(x>0)}, simplify = FALSE))
                          )
          # Which Poly_ID corresponds to which 'exact polygon'?
          region_Poly$Exact_Poly_ID <-
            do.call('c',
                    lapply(FUN=function(x){
                      paste0(PACea::BC_Partition_Objects$index_vectors[[i]][x],
                             collapse=' and ')},
                      apply(PACea::BC_Partition_Objects$Mapping_Matrix[region_Poly$Poly_ID,
                                                                       PACea::BC_Partition_Objects$index_vectors[[i]]],
                            1, FUN=function(x){which(x>0)}, simplify = TRUE)
                      )
                    )
          # And the names?
          region_Poly$Exact_Poly_Name <-
            do.call('c',
                    lapply(FUN=function(x){
                      paste0(PACea::BC_Partition_Objects$BC_Partition$Poly_Name[PACea::BC_Partition_Objects$index_vectors[[i]][x]],
                             collapse=' and ')},
                      apply(PACea::BC_Partition_Objects$Mapping_Matrix[region_Poly$Poly_ID,
                                                                       PACea::BC_Partition_Objects$index_vectors[[i]]],
                            1, FUN=function(x){which(x>0)}, simplify = T)
                      )
                    )
          if(plot){
            if(length(unique(region_Poly$Exact_Poly_Name)) > 10){
              print(
                ggplot2::ggplot(PACea::Coastline_Expanded) +
                ggplot2::geom_sf(fill='lightblue') +
                ggplot2::geom_sf(data=region_Poly,
                                 ggplot2::aes(fill=factor(Exact_Poly_Name, ordered = T),
                                              colour=factor(Exact_Poly_Name, ordered = T)),
                                 alpha=0.2) +
                ggplot2::geom_sf_label(data=region_Poly, ggplot2::aes(label=Exact_Poly_ID)) +
                #ggplot2::guides(fill=ggplot2::guide_legend(title='Poly_Name'), colour=ggplot2::guide_legend(title='Poly_Name')) +
                ggplot2::guides(fill="none", colour="none") +
                ggplot2::ggtitle(paste0('PACea-Approximated Polygons Defining Region "',i,'"'),
                                 subtitle = 'Polygons coloured by Poly_Name and labelled by Poly_ID \nWhen numbers are present, they ascend in the same order')
              )
            }
            if(length(unique(region_Poly$Exact_Poly_Name)) <= 10){
              print(
                ggplot2::ggplot(PACea::Coastline_Expanded) +
                ggplot2::geom_sf(fill='lightblue') +
                ggplot2::geom_sf(data=region_Poly,
                                 ggplot2::aes(fill=factor(Exact_Poly_Name, ordered = T),
                                              colour=factor(Exact_Poly_Name, ordered = T)),
                                 alpha=0.2) +
                ggplot2::geom_sf_label(data=region_Poly, ggplot2::aes(label=Exact_Poly_ID)) +
                ggplot2::guides(fill=ggplot2::guide_legend(title='Poly_Name'), colour=ggplot2::guide_legend(title='Poly_Name')) +
                #ggplot2::guides(fill="none", colour="none") +
                ggplot2::ggtitle(paste0('PACea-Approximated Polygons Defining Region "',i,'"'),
                                 subtitle = 'Polygons coloured by Poly_Name and labelled by Poly_ID \nWhen numbers are present, they ascend in the same order')
              )
            }
          }
        }
        if(approximate == FALSE){
          if(!(i %in% names(PACea::BC_Partition_Objects$index_vectors))){
            stop(paste0(i, ' is not a valid region. Please run Pacea_regions() to see the names of all the valid regions'))
          }

          region_Poly <-
            PACea::BC_Partition_Objects$BC_Partition %>%
            dplyr::filter(Poly_ID %in% BC_Partition_Objects$index_vectors[[i]]
                          )

          if(plot){
            print(
              ggplot2::ggplot(PACea::Coastline_Expanded) +
              ggplot2::geom_sf(fill='lightblue') +
              ggplot2::geom_sf(data=region_Poly,
                               ggplot2::aes(fill=factor(Poly_Name, levels=Poly_Name, ordered = T),
                                            colour=factor(Poly_Name, levels=Poly_Name, ordered = T)),
                               alpha=0.2) +
              ggplot2::geom_sf_label(data=region_Poly, ggplot2::aes(label=Poly_ID)) +
              ggplot2::guides(fill=ggplot2::guide_legend(title='Poly_Name'), colour=ggplot2::guide_legend(title='Poly_Name')) +
              ggplot2::ggtitle(paste0('Exact Polygons Defining Region "',i,'"'),
                               subtitle = 'Polygons coloured by Poly_Name and labelled by Poly_ID \nWhen numbers are present, they ascend in the same order')
            )
          }
        }
        if(return_sf_Polys){
          sf_Polys[[i]] <- region_Poly
        }
      }
    }
  }
  if(return_sf_Polys){
    return(sf_Polys)
  }
}