NEWS.md
offhab.duckdb with script inst/_import_duckdb.R to re-import in forward compatible duckdb version 1.0.0-1.oh_map_zone_score_dev() and oh_tbl_zone_score_dev(), to show block type (Lease; Planning Area) along with relevant information (Lease #, Company and Lease Term, Date; Plan).oh_blocks to contain latest BOEM wind planning areas (2023-10-06), whereas previously mistakenly only included BOEM wind lease areas (old: 2022-06-30; new: 2023-09-27) due to bug (incorrectly used dplyr::bind_rows() vs correct sf::rbind() to combine layers).Added reporting functions (with concept report and new Report reference header) oh_tbl_zone_score_dev(), dt_color_fld(), link_caption() for use in generating table outputs in report source.
Modified oh_map() with additional arguments (defaulting to TRUE|FALSE according to knitr::is_html_output()) for zoomControl, attributionControl and fullScreenControl in case of screenshot captures into static report.docx.
oh_zones with oa_rgns to further differentiate portions of zones with and without bottom trawl models.oh_zones to having two zone_version values for with (2) and without (1) OceanAdapt regions for using and skipping bottom trawl data.Added oa_regions (Ocean Adapt regions) to map limits of interpolated bottom trawl model results.
Renamed:
boem_blocks -> oh_blocks
boem_blocks -> blocks
Added hydrothermal vents (InterRidge Global Database of Active Submarine Hydrothermal Vent Fields Version 3.4) with data-raw/mdls_ve.R, which for US are only in Northern California (n=3) and Washington/Oregon (n=4) with a 12 km radius zone of influence based on splitting the difference between studies showing biogeographic influence out to 100 km^2 (Haymon et al., 1990) and 200 km^2 (Van Dover et al., 2002) [round(sqrt(mean(c(200,100)))) = 12].
Added seamounts (Global Seamount Database) with data-raw/mdls_sm.R, which for US are in Central California (n=3), North Atlantic (n=4), Northern California (n=4), Southern California (n=14), and Washington/Oregon (n=18). Created circles of influence based on area (calculated from major and minor axes of ellipse). All summit depths were greater than 800 m, the third class of biogeographic distinction (Clark et al, 2011).
Added productivity (Ocean Productivity from Oregon State) with data-raw/mdls_vg.R for the entire US OffHab study area. Averaged the 12 monthly products using the Vertically Generalized Production Model (VGPM) algorithm (Behrenfeld & Falkowski, 1997a).
Fixed missing data from earlier ingestion of bottom trawl (data-raw/mdls_oa.R) when cell_id was not saving raster in format, creating duplicates.
data-raw/mdls_oa.R with multidplyr parallel processing to speed up raster generation of interpolated biomass survey points. These are the bottom trawl models from OceanAdapt that have been ported to NOAA Distribution Mapping and Analysis Portal (DisMAP).data-raw/mdls_gm.R
Added searching for non-marine taxa with wm_add_aphia_id() and allowance for extra query parameters with wm_rest(), e.g. wm_rest(tbl, fld, operation = "AphiaRecordsByNames", marine_only = F)
Added seabird “NCCOS Assessments Modeling At-Sea Density of Marine Birds” for Atlantic and Pacific with data-raw/mdls_nc.R
Added Habitat-based Marine Mammal Density Models for the U.S. Atlantic: Latest Versions with data-raw/mdsl_du.R
Added operation="AphiaRecordsByVernacular" option to wm_rest() for searching common names.
Added oh_rast() for fetching OffHab reference raster by cell_id, zone_id or all NA and optionally trimming to zone_id
Fixed wm_add_aphia_id() which wasn’t properly including fuzzy matches and updated wm_rest_params with practical values to fetch all data (versus theoretical maxima which bonked when URL of request got too long)
Intersected AquaMaps with new OffHab reference raster in data-raw/am_cells_ply.R
Imported marine IUCN range maps into the OffHab database with data-raw/mdls_rl.R using new rl_pg_con() to import the full set of data before clipping to the OffHab zones into the OffHab database (oh_pg_con()).
Imported Predictive Models of Cetacean Densities in the California Current Ecosystem, 2020b | InPort with data-raw/mdsl_sw.R
zone_id column to oh_zones and block_id column to boem_blocks for integer referencing with rasterswm_add_aphia_id() (now with Roxygen: list(markdown = TRUE) turned on)Added wm_add_aphia_id() to match and prepend aphia_id from WoRMS REST services using new wm_rest() helper function, which uses new dataset wm_rest_params
Added dataset mdls_sw table into db (see data-raw/mdls_sw.R on Github): Predictive Models of Cetacean Densities in the California Current Ecosystem, 2020b | InPort.
data-raw/taxa_worrms.R for matching so far am_spp.{genus} {species} with “WoRMS - World Register of Marine Species” MarineSpecies.org using its API web service marinespecies.org/rest and the R package worrms.oh_map_ply() to oh_map() and added oh_add_ply() to accomodate adding multiple layers of polygons, eg blocks on top of zones.Added oh_map_ply() to map polygons, possibly with divergent midpoint in the color scheme using div_mid argument.
Added oh_zones_s1k: simplified version of oh_zones to 1 km for faster rendering of smaller output files
am_cell_blocks dataset from intersecting OffHab zone x AquaMaps cell x BOEM block; + corresponding raster with get_am_cell_blocks_grd(); + database helper function create_index()
aquamaps postgres database (+ am_pg_con(); for calculating range size of each species) and used cross-database querying to extract subset of cells and species within oh_zones to into offhab postgres database with am_* prefix (see data-raw/aquamaps_db.R).am_meta into database.NEWS.md file to track changes to the package.get_am_cells_grd(), oh_pg_con(); datasets: am_cells_ply, boem_blocks, oh_zones