R/aegis_lookup.R
In jae0/aegis: Assessment of ecosystems using GIS
Defines functions
aegis_lookup
# TODO:: tapply can be converted into data.table computations for speed
## WARNING:: if you polygons are misspecified, they can result in some au's being dropped .. check your polygons
aegis_lookup = function(
parameters = NULL,
variable_name=NULL,
LUT = NULL, # look up table from which to obtain results
LOCS = NULL, # look up locations for which results are desired
LUT_AU=NULL, # areal units associated with LUT
LOCS_AU=NULL,
project_class="core", # "project_class" to look up from
DS="aggregated_data", # "DS=.. "
output_format="points",
statvars = c("mean"),
tz="America/Halifax",
FUNC=mean,
returntype = "vector",
space_resolution=NULL, # spatial planar discretization
time_resolution=NULL, # year, seasonal discretization
year.assessment=NULL, ...
) {
if (0) {
# testing usign snow data
p = bio.snowcrab::snowcrab_parameters(
project_class="carstm",
yrs=1999:2021,
areal_units_type="tesselation",
carstm_model_label = "tesselation", # default is the name of areal_units_type
selection = list(type = "number")
)
M = snowcrab.db( p=p, DS="biological_data" )
M = M[ which( M$yr %in% 2011:2015 ) ,] # reduce data size
dim(M)
sppoly = areal_units( p=p ) # poly to estimate a surface
# loadfunctions("aegis")
# debug(aegis_lookup)
if (0) {
# generics
parameters="bathymetry"
variable_name=list( "predictions", c("random", "space", "combined") )
LUT = NULL # look up table from which to obtain results
LOCS = M[, c("lon", "lat", "timestamp")] # look up locations for which results are desired
LUT_AU=NULL # areal units associated with LUT
LOCS_AU=sppoly
project_class="core" # "project_class" to look up from
DS="aggregated_data" # "DS=.. "
output_format="points"
statvars = c("mean")
tz="America/Halifax"
FUNC=mean
space_resolution=1
}
loadfunctions("aegis")
# test raw data lookup
# spatial
o0 = aegis_lookup( parameters="bathymetry", LOCS=M[, c("lon", "lat")],
project_class="core", output_format="points" , DS="aggregated_data", variable_name=c( "z.mean", "z.sd", "z.n"),
returntype="sf"
)
plot(M[["z"]] ~ o0[["z.mean"]])
o1 = aegis_lookup( parameters="bathymetry", LOCS=M[, c("lon", "lat")],
project_class="core", output_format="points" , DS="aggregated_data", variable_name=c( "z.mean" ),
returntype="vector"
)
o2 = aegis_lookup( parameters="bathymetry", LOCS=M[, c("lon", "lat")],
project_class="stmv", output_format="points" , DS="complete", variable_name=c( "z", "dZ", "ddZ")
)
# spatial averaging by areal unit
# this one is slow .. could be sped up if used
o3 = aegis_lookup( parameters="bathymetry", LOCS=M[, c("lon", "lat")], LOCS_AU=sppoly,
project_class="stmv", output_format="areal_units" , DS="complete", variable_name=c( "z", "dZ", "ddZ")
)
# spatial averaging by areal unit
o4 = aegis_lookup( parameters="bathymetry", LOCS=M[, c("lon", "lat")], LOCS_AU=sppoly,
project_class="core", output_format="areal_units" , DS="aggregated_data", variable_name=c( "z.mean", "z.sd", "z.n")
)
# lookup from areal unit predictions
o5 = aegis_lookup( parameters="bathymetry", LOCS=M[, c("lon", "lat")],
project_class="carstm", output_format="points", variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd"), space_resolution=min(p$pres)
)
# slow
o6 = aegis_lookup( parameters="bathymetry", LOCS=M[, c("lon", "lat")], LOCS_AU=sppoly,
project_class="carstm", output_format="areal_units", variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd"), space_resolution=min(p$pres) /2
)
# au to au match (LOCS=NULL)
o7 = aegis_lookup( parameters="bathymetry", LOCS=list(AUID=sppoly$AUID), LOCS_AU=sppoly,
project_class="carstm", output_format="areal_units", variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd"), space_resolution=min(p$pres) /2
)
# au to au match (LOCS=NULL)
o7 = aegis_lookup( parameters="bathymetry", LOCS=sppoly[,"AUID"], LOCS_AU=sppoly,
project_class="carstm", output_format="areal_units", variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd"), space_resolution=min(p$pres) /2
)
# au to au match (LOCS=NULL)
o7 = aegis_lookup( parameters="bathymetry", LOCS=sppoly$AUID, LOCS_AU=sppoly,
project_class="carstm", output_format="areal_units", variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd"), space_resolution=min(p$pres) /2
)
# consistency checks
plot(o1 ~o2$z)
plot(o1 ~o3$z)
plot(o1 ~o4$z)
plot(o1 ~o5$predictions_mean)
plot(o1 ~o6$predictions_mean)
# space-time
o1 = aegis_lookup( parameters="speciescomposition_pca1", LOCS=M[, c("lon", "lat", "timestamp")],
project_class="core", output_format="points" , DS="speciescomposition", variable_name=c( "pca1"), space_resolution=2
)
o2 = aegis_lookup( parameters="speciescomposition_pca1", LOCS=M[, c("lon", "lat", "timestamp")],
project_class="stmv", output_format="points" , DS="complete", variable_name=c( "pca1")
)
o3 = aegis_lookup( parameters="speciescomposition_pca1", LOCS=M[, c("lon", "lat", "timestamp")], LOCS_AU=sppoly,
project_class="core", output_format="areal_units" , variable_name=list( "pca1", "pca2", "ca1", "ca2" )
)
o4 = aegis_lookup( parameters="speciescomposition_pca1", LOCS=M[, c("lon", "lat", "timestamp")],
project_class="carstm", output_format="points", variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd")
)
o5 = aegis_lookup( parameters="speciescomposition_pca1", LOCS=M[, c("lon", "lat", "timestamp")], LOCS_AU=sppoly,
project_class="carstm", output_format="areal_units" , variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd"), space_resolution=min(p$pres)/2
)
mm = expand.grid(AUID=sppoly$AUID, timestamp=lubridate::date_decimal( p$yrs, tz="America/Halifax" ))
mm = expand.grid(AUID=sppoly$AUID, timestamp= p$yrs )
o6 = aegis_lookup( parameters="speciescomposition_pca1", LOCS=mm, LOCS_AU=sppoly,
project_class="carstm", output_format="areal_units" , variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd"), space_resolution=min(p$pres)/2
)
# consistency checks
plot(o1$pca1.mean ~o3$pca1.mean)
plot(o1$pca1.mean ~o4$predictions_mean)
plot(o1$pca1.mean ~o5$predictions_mean)
# space-time-season
o1 = aegis_lookup( parameters="temperature", LOCS=M[, c("lon", "lat", "timestamp")],
project_class="core", output_format="points" , DS="aggregated_data", variable_name=c( "t.mean", "t.sd", "t.n"), space_resolution=2
)
o2 = aegis_lookup( parameters="temperature", LOCS=M[, c("lon", "lat", "timestamp")],
project_class="stmv", output_format="points" , DS="complete", variable_name=c( "t")
)
o3 = aegis_lookup( parameters="temperature", LOCS=M[, c("lon", "lat", "timestamp")], LOCS_AU=sppoly,
project_class="core", output_format="areal_units" , variable_name=list( "t.mean", "t.sd", "t.n" )
)
parameters = list(
temperature = temperature_parameters(
project_class="carstm",
yrs=1970:year.assessment,
carstm_model_label="1970_present"
)
)
o4 = aegis_lookup( parameters=parameters, LOCS=M[, c("lon", "lat", "timestamp")],
project_class="carstm", output_format="points", variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd")
)
o5 = aegis_lookup( parameters=parameters, LOCS=M[, c("lon", "lat", "timestamp")], LOCS_AU=sppoly,
project_class="carstm", output_format="areal_units" , variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd"), space_resolution=min(p$pres)/2
)
# mm = expand.grid(AUID=sppoly$AUID, timestamp=lubridate::date_decimal( p$yrs, tz="America/Halifax" ))
mm = expand.grid(AUID=sppoly$AUID, timestamp= p$yrs )
o6 = aegis_lookup( parameters="temperature", LOCS=mm, LOCS_AU=sppoly,
project_class="carstm", output_format="areal_units" , variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd"), space_resolution=min(p$pres)/2
)
# consistency checks
plot(o1$t.mean ~o3$t.mean)
plot(o1$t.mean ~o4$predictions_mean)
plot(o1$t.mean ~o5$predictions_mean)
if (0) {
p = bathymetry_parameters( project_class="stmv" )
LUT = bathymetry_db ( p=p, DS="complete" )
}
} ## END consistency checks
require(stars)
# -----------
if ( is.null(parameters) ) stop( "parameters is required")
pL = NULL
if ( class(parameters) == "character" ) {
# then use generic defaults
aegis_project = parameters
} else {
aegis_project = names(parameters)
if (length(aegis_project) > 1) {
warning( "more than one parameter list sent, taking the first only")
aegis_project = aegis_project[1]
}
pL = parameters[[aegis_project]]
}
if (is.vector(LOCS)) LOCS = list(AUID=LOCS)
if (!is.null(LOCS)) setDT(LOCS)
crs_lonlat = st_crs(projection_proj4string("lonlat_wgs84"))
# determine LUT (lookup table)
if (is.null(LUT)) {
if ( "bathymetry" %in% aegis_project ) {
if ( is.null(pL) ) pL = bathymetry_parameters( project_class=project_class )
if (is.null(space_resolution)) if (exists( "pres", pL)) space_resolution = pL$pres
if ( project_class %in% c("core" ) ) LUT = bathymetry_db ( p=pL, DS=DS )
if ( project_class %in% c("stmv", "hybrid") ) LUT = bathymetry_db ( p=pL, DS="complete" )
if ( project_class %in% c("carstm" )) {
LUT = carstm_model( p=pL, DS="carstm_modelled_summary" )
LUT$space = LUT$space_id
}
if ( project_class %in% c("core", "stmv", "hybrid") ) {
setDT(LUT)
if ( space_resolution != pL$pres ) {
# regrid to another resolution
LUT$plon = trunc(LUT$plon / space_resolution + 1 ) * space_resolution
LUT$plat = trunc(LUT$plat / space_resolution + 1 ) * space_resolution
LUT = LUT[, setNames(.(mean( get(variable_name), na.rm=TRUE) ), variable_name), by=list(plon, plat) ]
}
setDF(LUT)
}
}
if ( "substrate" %in% aegis_project ) {
if ( is.null(pL) ) pL = substrate_parameters( project_class=project_class )
if (is.null(space_resolution)) if (exists( "pres", pL)) space_resolution = pL$pres
if ( project_class %in% c("core" ) ) LUT = substrate_db ( p=pL, DS=DS )
if ( project_class %in% c("stmv", "hybrid") ) {
LUT = substrate_db ( p=pL, DS="complete" )
pB = bathymetry_parameters( spatial_domain=pL$spatial_domain, project_class=project_class )
BA = bathymetry_db ( p=pB, DS="baseline", varnames=c("lon", "lat") )
LUT = cbind( LUT, BA )
}
if ( project_class %in% c("carstm" )) {
LUT = carstm_model( p=pL, DS="carstm_modelled_summary" )
LUT$space = LUT$space_id
}
if ( project_class %in% c("core", "stmv", "hybrid") ) {
setDT(LUT)
if ( space_resolution != pL$pres ) {
# regrid to another resolution
LUT$plon = trunc(LUT$plon / space_resolution + 1 ) * space_resolution
LUT$plat = trunc(LUT$plat / space_resolution + 1 ) * space_resolution
LUT = LUT[, setNames(.(mean( get(variable_name), na.rm=TRUE) ), variable_name), by=list(plon, plat) ]
}
setDF(LUT)
}
}
if ( "temperature" %in% aegis_project ) {
if (is.null(pL) ) pL = temperature_parameters( project_class=project_class, year.assessment=year.assessment )
if (is.null(space_resolution)) if (exists( "pres", pL)) space_resolution = pL$pres
if (is.null(time_resolution)) if (exists( "tres", pL)) time_resolution = pL$tres
if ( project_class %in% c("core" )) LUT = temperature_db ( p=pL, DS=DS ) # "aggregated_data", "bottom.all"
if ( project_class %in% c("stmv", "hybrid") ) LUT = temperature_db ( p=pL, DS="complete" )
if ( project_class %in% c("carstm" )) {
LUT = carstm_model( p=pL, DS="carstm_modelled_summary" )
LUT$space = LUT$space_id
LUT$time = LUT$time_id
LUT$cyclic = LUT$cyclic_id
}
if ( project_class %in% c("core", "stmv", "hybrid") ) {
setDT(LUT)
if ( time_resolution != pL$tres ) {
LUT$dyear = trunc(LUT$dyear / time_resolution + 1 ) * time_resolution
}
if ( space_resolution != pL$pres ) {
# regrid to another resolution
LUT$plon = trunc(LUT$plon / space_resolution + 1 ) * space_resolution
LUT$plat = trunc(LUT$plat / space_resolution + 1 ) * space_resolution
}
if ( time_resolution != pL$tres | space_resolution != pL$pres ) {
LUT = LUT[, setNames(.(mean( get(variable_name), na.rm=TRUE) ), variable_name), by=list(plon, plat, yr, dyear) ]
LUT$timestamp = lubridate::date_decimal( LUT$yr+LUT$dyear, tz=tz )
}
setDF(LUT)
}
}
if ( grepl("speciescomposition", aegis_project) ) {
if (aegis_project == "speciescomposition_pca1") sc_vn = "pca1"
if (aegis_project == "speciescomposition_pca2") sc_vn = "pca2"
if (aegis_project == "speciescomposition_pca3") sc_vn = "pca3"
if (aegis_project == "speciescomposition_ca1") sc_vn = "ca1"
if (aegis_project == "speciescomposition_ca2") sc_vn = "ca2"
if (aegis_project == "speciescomposition_ca3") sc_vn = "ca3"
if (is.null(pL) ) pL = speciescomposition_parameters( project_class=project_class, variabletomodel=sc_vn , year.assessment=year.assessment )
if (is.null(space_resolution)) if (exists( "pres", pL)) space_resolution = pL$pres
if (is.null(time_resolution)) if (exists( "tres", pL)) time_resolution = pL$tres
if ( project_class %in% c("core" ) ) LUT = speciescomposition_db ( p=pL, DS=DS )
if ( project_class %in% c( "stmv", "hybrid") ) LUT = aegis_db( p=pL, DS="complete" )
if ( project_class %in% c("carstm" )) {
LUT = carstm_model( p=pL, DS="carstm_modelled_summary" )
LUT$space = LUT$space_id
LUT$time = LUT$time_id
LUT$cyclic = LUT$cyclic_id
}
if ( project_class %in% c("core", "stmv", "hybrid") ) {
setDT(LUT)
if ( time_resolution != pL$tres ) {
LUT$dyear = trunc(LUT$dyear / time_resolution + 1 ) * time_resolution
}
if ( space_resolution != pL$pres ) {
# regrid to another resolution
LUT$plon = trunc(LUT$plon / space_resolution + 1 ) * space_resolution
LUT$plat = trunc(LUT$plat / space_resolution + 1 ) * space_resolution
}
if ( time_resolution != pL$tres | space_resolution != pL$pres ) {
LUT = LUT[, setNames(.(mean( get(sc_vn), na.rm=TRUE) ), sc_vn), by=list(plon, plat, yr, dyear) ]
LUT$timestamp = lubridate::date_decimal( LUT$yr+LUT$dyear, tz=tz )
}
setDF(LUT)
}
}
if ( grepl("snowcrab", aegis_project) ) {
if (aegis_project == "snowcrab_number") sc_vn = "number"
if (aegis_project == "snowcrab_biomass") sc_vn = "biomass"
if (aegis_project == "snowcrab_meansize") sc_vn = "meansize"
if (aegis_project == "snowcrab_pa") sc_vn = "pa"
if (is.null(pL) ) {
if ( sc_vn == "number" ) {
pL = snowcrab_parameters(
project_class="carstm",
yrs=1999:year.assessment,
areal_units_type="tesselation",
family="poisson",
carstm_model_label = "1999_present", # 1999_present is the default anything else and you are on your own
selection = list(type = "number")
)
} else if ( sc_vn == "biomass" ) {
pL = snowcrab_parameters(
project_class="carstm",
yrs=1999:year.assessment,
areal_units_type="tesselation",
carstm_model_label = "1999_present", # 1999_present is the default anything else and you are on your own
# carstm_model_label = paste( carstm_model_label, variabletomodel, sep="_")
family = "gaussian" ,
selection = list(type = "biomass")
)
} else if ( sc_vn == "meansize" ) {
pL = snowcrab_parameters(
project_class="carstm",
yrs=1999:year.assessment,
areal_units_type="tesselation",
carstm_model_label = "1999_present", # 1999_present is the default anything else and you are on your own
# carstm_model_label = paste( carstm_model_label, variabletomodel, sep="_")
family = "gaussian" ,
selection = list(type = "meansize")
)
} else if ( sc_vn == "pa" ) {
pL = snowcrab_parameters(
project_class="carstm",
yrs=1999:year.assessment,
areal_units_type="tesselation",
carstm_model_label = "1999_present", # 1999_present is the default anything else and you are on your own
# carstm_model_label = paste( carstm_model_label, variabletomodel, sep="_")
family = "gaussian" ,
selection = list(type = "presence_absence")
)
} else {
pL = p = bio.snowcrab::load.environment( year.assessment=year.assessment )
}
}
if (is.null(space_resolution)) if (exists( "pres", pL)) space_resolution = pL$pres
if (is.null(time_resolution)) if (exists( "tres", pL)) time_resolution = pL$tres
if ( project_class %in% c("core" ) ) LUT = snowcrab.db ( p=pL, DS=DS )
if ( project_class %in% c( "stmv", "hybrid") ) LUT = aegis_db( p=pL, DS="complete" )
if ( project_class %in% c("carstm" )) {
LUT = carstm_model( p=pL, DS="carstm_modelled_summary" )
LUT$space = LUT$space_id
LUT$time = LUT$time_id
LUT$cyclic = LUT$cyclic_id
}
if ( project_class %in% c("core", "stmv", "hybrid") ) {
setDT(LUT)
if ( time_resolution != pL$tres ) {
LUT$dyear = trunc(LUT$dyear / time_resolution + 1 ) * time_resolution
}
if ( space_resolution != pL$pres ) {
# regrid to another resolution
LUT$plon = trunc(LUT$plon / space_resolution + 1 ) * space_resolution
LUT$plat = trunc(LUT$plat / space_resolution + 1 ) * space_resolution
}
if ( time_resolution != pL$tres | space_resolution != pL$pres ) {
LUT = LUT[, setNames(.(mean( get(sc_vn), na.rm=TRUE) ), sc_vn), by=list(plon, plat, yr, dyear) ]
LUT$timestamp = lubridate::date_decimal( LUT$yr+LUT$dyear, tz=tz )
}
setDF(LUT)
}
}
}
if (is.null(LUT)) stop( "lookup data not found nor given")
if (is.null(variable_name)) {
if ( project_class %in% c("carstm" )) {
variable_name = LUT$fm$dependent_variable
} else {
variable_name = setdiff( names(LUT), c("plon", "plat", "lon", "lat", "timestamp", "year", "dyear", "yr" ))
}
}
# ------------------
if (pL$dimensionality =="space" ) {
if ( project_class %in% c("core", "stmv", "hybrid") & output_format == "points" ) {
if (!exists("plon", LUT)) LUT = lonlat2planar(LUT, proj.type=pL$aegis_proj4string_planar_km)
if (!exists("plon", LOCS)) LOCS = lonlat2planar(LOCS, proj.type=pL$aegis_proj4string_planar_km) # get planar projections of lon/lat in km
LOCS$tplon = trunc(LOCS$plon / space_resolution + 1 ) * space_resolution
LOCS$tplat = trunc(LOCS$plat / space_resolution + 1 ) * space_resolution
plon_range = range( LUT$plon )
plat_range = range( LUT$plat )
plons = seq(plon_range[1], plon_range[2], by=space_resolution)
plats = seq(plat_range[1], plat_range[2], by=space_resolution)
Sdims = c(length(plons), length(plats))
Sres = c(space_resolution, space_resolution)
Sorigin = c( plon_range[1], plat_range[1] )
ii = match(
array_map( "xy->1", LOCS[, c("tplon","tplat")], dims=Sdims, res=Sres, origin=Sorigin ),
array_map( "xy->1", LUT[,c("plon","plat")], dims=Sdims, res=Sres, origin=Sorigin )
)
LOCS$tplon = LOCS$tplat = NULL
gc()
for (vnm in variable_name) {
if ( vnm %in% names(LUT )) {
LOCS[[vnm]] = NA
LOCS[[vnm]] = LUT[ ii, vnm ]
}
}
}
if ( project_class %in% c("core", "stmv", "hybrid") & output_format == "areal_units" ) {
LOCS0 = NULL
if (exists("AUID", LOCS)) {
# this is a special class of lookup taking LUT (usually empirical or aggregated data) and estimating from it for an areal unit (via rasterization)
LOCS0 = LOCS # store as modifications will be made to LOCS
# next, get a x-y coordinate for each LOC by rasterizing to LOCS_AU
LOCS_AU = st_make_valid(LOCS_AU)
LOCS_AU = sf::st_transform( LOCS_AU, crs=st_crs(pL$aegis_proj4string_planar_km) )
LOCS_AU$au_index = 1:nrow(LOCS_AU)
LOCS_AU_raster = stars::st_rasterize( LOCS_AU["au_index"], dx=space_resolution, dy=space_resolution )
# overwrite LOCS with discretized points
LOCS = sf::st_as_sf( LOCS_AU_raster, as_points=TRUE, na.rm=FALSE )
st_crs(LOCS) = st_crs( LOCS_AU )
LOCS$AUID = LOCS_AU$AUID[ st_extract(LOCS_AU_raster, LOCS )$au_index ]
} else {
if (exists("lon", LOCS)) {
LOCS = sf::st_as_sf( LOCS, coords=c("lon", "lat") )
st_crs(LOCS) = st_crs( projection_proj4string("lonlat_wgs84") )
} else if (exists("plon", LOCS)) {
LOCS = sf::st_as_sf( LOCS, coords=c("plon", "plat") )
st_crs(LOCS) = st_crs(pL$aegis_proj4string_planar_km)
}
}
if (exists("lon", LUT)) {
LUT = sf::st_as_sf( LUT, coords=c("lon", "lat") )
st_crs(LUT) = st_crs( projection_proj4string("lonlat_wgs84") )
} else if (exists("plon", LUT)) {
LUT = sf::st_as_sf( LUT, coords=c("plon", "plat") )
st_crs(LUT) = st_crs(pL$aegis_proj4string_planar_km)
}
if (!exists("AUID", LOCS_AU)) {
message ("AUID not found in the polygons, setting AUID as row number of polygons")
LOCS_AU$AUID = as.character(1:nrow(LOCS_AU))
}
LOCS_AU = sf::st_transform( LOCS_AU, crs=st_crs(LUT) ) #
variable_name = intersect( names(LUT), variable_name )
LUT = LUT[, variable_name]
LU_map = st_points_in_polygons( pts=LUT, polys=LOCS_AU[, "AUID"], varname= "AUID" )
if (!exists("AUID", LOCS )) LOCS[["AUID"]] = st_points_in_polygons( pts=LOCS, polys=LOCS_AU[, "AUID"], varname= "AUID" )
st_geometry(LUT) = NULL
setDT(LUT)
for (vnm in variable_name) {
if ( vnm %in% names(LUT )) {
# LUT_regridded = tapply( st_drop_geometry(LUT)[, vnm], LU_map, FUN=FUNC, na.rm=TRUE )
LUT_regridded = LUT[, setNames(.(mean( get(vnm), na.rm=TRUE) ), vnm), by=.(LU_map) ]
LOCS[[ vnm ]] = LUT_regridded[ match( LOCS$AUID, LUT_regridded$LU_map ), vnm, with=FALSE ]
}
}
# revert LOCS to original structure and add the vars to it
if (!is.null(LOCS0)) {
# summarize LOCS to to original AUID's
if ( "sf" %in% class(LOCS) ) st_geometry(LOCS) = NULL
LOCS = as.data.table( LOCS )
# o = LOCS[, lapply(.SD, mean, na.rm=TRUE), by=AUID, .SDcols=variable_name]
o = LOCS[, setNames(.(mean( get(variable_name), na.rm=TRUE) ), variable_name), by=AUID ]
LOCS0[,variable_name] = o[ match( LOCS0$AUID, o$AUID), .SD, .SDcols=variable_name ]
LOCS = LOCS0
}
}
if ( project_class %in% c("carstm" ) & output_format == "points" ) {
if (is.null(LUT_AU)) LUT_AU = LUT$sppoly
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = st_cast( LUT_AU, "MULTIPOLYGON")
# LUT_AU = st_cast(LUT_AU, "POLYGON" )
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = sf::st_transform( LUT_AU, crs=st_crs(pL$aegis_proj4string_planar_km) )
if (!exists("AUID", LUT_AU)) {
message ("AUID not found in LOCS_AU polygons, setting AUID as row number of polygons")
LUT_AU$AUID = as.character(LUT_AU$au_index)
}
bm = match( LUT_AU$AUID, LUT$space )
if (exists("lon", LOCS)) {
LOCS = sf::st_as_sf( LOCS, coords=c("lon", "lat") )
st_crs(LOCS) = st_crs( projection_proj4string("lonlat_wgs84") )
LOCS = sf::st_transform( LOCS, crs=st_crs(pL$aegis_proj4string_planar_km) )
} else if (exists("plon", LOCS)) {
LOCS = sf::st_as_sf( LOCS, coords=c("lon", "lat") )
st_crs(LOCS) = st_crs(pL$aegis_proj4string_planar_km)
}
LOCS$AUID = st_points_in_polygons( pts=LOCS, polys = LUT_AU[, "AUID"], varname= "AUID" )
ii = match( LOCS$AUID, LUT$space[bm] )
for (g in 1:length(statvars)) {
stat_var = statvars[g]
for (h in 1:length(variable_name) ) {
vnh = variable_name[[h]]
if (exists(vnh[[1]], LUT)) {
vnm = paste( paste0(vnh, collapse="_"), stat_var, sep="_" )
LUT_AU[[vnm]] = carstm_results_unpack( LUT, vnh ) [ bm, stat_var ]
LOCS[[vnm]] = LUT_AU[[vnm]] [ ii ]
}
}
}
}
if ( project_class %in% c("carstm") & output_format == "areal_units" ) {
if (is.null(LUT_AU)) LUT_AU = LUT$sppoly
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = st_cast( LUT_AU, "MULTIPOLYGON")
# LUT_AU = st_cast(LUT_AU, "POLYGON" )
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = sf::st_transform( LUT_AU, crs=st_crs(pL$aegis_proj4string_planar_km) )
if (!exists("AUID", LUT_AU)) LUT_AU$AUID = as.character(1:nrow(LUT_AU))
bm = match( LUT_AU$AUID, LUT$space ) # should not be required but just in case things are subsetted
# lut_uid is A LOCAL index of LUT_AU /LUT .. rasterize it
LUT_AU$lut_uid = 1:nrow(LUT_AU)
LUT_AU_raster = stars::st_rasterize( LUT_AU["lut_uid"], dx=space_resolution, dy=space_resolution )
LUT_AU_pts = sf::st_as_sf( LUT_AU_raster, as_points=TRUE, na.rm=FALSE )
st_crs(LUT_AU_pts) = st_crs( LUT_AU )
# format output polygon structure
LOCS_AU = sf::st_transform( LOCS_AU, crs=st_crs(LUT_AU) ) # LOCS_AU .... must be sent ... <---------
LOCS_AU = st_make_valid(LOCS_AU)
LOCS_AU = st_buffer( LOCS_AU, 0 )
LOCS_AU = st_cast( LOCS_AU, "MULTIPOLYGON")
# LOCS_AU = st_cast( LOCS_AU, "POLYGON")
if (!exists("AUID", LOCS_AU)) {
message ("AUID not found in the polygons, setting AUID as row number of polygons")
LOCS_AU$AUID = as.character(1:nrow(LOCS_AU))
}
if (! inherits(LOCS, "sf") ) {
if (exists("lon", LOCS )) {
LOCS = st_as_sf( LOCS, coords=c("lon","lat"), crs=st_crs(projection_proj4string("lonlat_wgs84")) )
LOCS = sf::st_transform( LOCS, crs=st_crs(pL$aegis_proj4string_planar_km) )
if (!exists("AUID", LOCS )) LOCS[["AUID"]] = st_points_in_polygons( pts=LOCS, polys=LOCS_AU[, "AUID"], varname= "AUID" )
}
}
# covert LUT_AU to LOCS_AU
# id membership of LOCS in LOCS_AU
# id membership of LUT raster in LOCS_AU
LUT_AU_pts_LOCS_AU_AUID = st_points_in_polygons( pts=LUT_AU_pts, polys=LOCS_AU[,"AUID"], varname="AUID" )
pts_AU = match(LUT_AU_pts$lut_uid, LUT_AU$lut_uid[match(LUT$space, LUT_AU$AUID)] ) ## (layer==lut_uid) -- to -- LUT
aggFUN = function( LUV ) tapply(X=LUV, INDEX=LUT_AU_pts_LOCS_AU_AUID, FUN=FUNC, na.rm=TRUE)
for (g in 1:length(statvars)) {
stat_var = statvars[g]
for (h in 1:length(variable_name) ) {
vnh = variable_name[[h]]
if (exists(vnh[[1]], LUT)) {
vnm = paste( paste0(vnh, collapse="_"), stat_var, sep="_" )
o = carstm_results_unpack( LUT, vnh )
kk = length(dim(o))
if (kk == 2) {
ov = o[ pts_AU, which(dimnames(o)$stat == stat_var) ]
LUT_as_LOCS_AU = aggFUN( ov)
space_index = match( as.character(LOCS$AUID), as.character(dimnames(LUT_as_LOCS_AU )[[1]] ) ) # AUID of LOCS_AU (from LUT_AU_pts_AUID)
if (all(is.na(space_index))) {
LOCS[,vnm] = LUT_as_LOCS_AU # fiddling required when only 1 AU
} else {
LOCS[,vnm] = LUT_as_LOCS_AU[ space_index ]
}
}
}
}
}
}
}
######################################################
if (pL$dimensionality =="space-time" ) {
if ( project_class %in% c("core", "stmv", "hybrid") & output_format == "points" ) {
if (!exists("plon", LUT)) LUT = lonlat2planar(LUT, proj.type=pL$aegis_proj4string_planar_km)
if (!exists("plon", LOCS)) LOCS = lonlat2planar(LOCS, proj.type=pL$aegis_proj4string_planar_km) # get planar projections of lon/lat in km
if (!exists("dyear", LOCS) | (!exists("yr", LOCS)) ) {
LOCS$tiyr = lubridate::decimal_date( LOCS$timestamp )
LOCS$yr = trunc( LOCS$tiyr )
LOCS$dyear = LOCS$tiyr - LOCS$yr
}
LOCS$tplon = trunc(LOCS$plon / space_resolution + 1 ) * space_resolution
LOCS$tplat = trunc(LOCS$plat / space_resolution + 1 ) * space_resolution
LOCS$tdyear = trunc(LOCS$dyear / time_resolution + 1 ) * time_resolution
nY = diff( range(LUT$yr) )
nW = round(1/time_resolution)
Tdims = c( nY, nW )
Tres = c(1, time_resolution)
Torigin = c( min(LUT$yr), 0)
plon_range = range( LUT$plon )
plat_range = range( LUT$plat )
plons = seq(plon_range[1], plon_range[2], by=space_resolution)
plats = seq(plat_range[1], plat_range[2], by=space_resolution)
Sdims = c(length(plons), length(plats))
Sres = c(space_resolution, space_resolution)
Sorigin = c( plon_range[1], plat_range[1] )
ii = match(
paste(
array_map( "xy->1", LOCS[, c("tplon","tplat")], dims=Sdims, res=Sres, origin=Sorigin ),
array_map( "ts->1", LOCS[, c("yr", "tdyear")], dims=Tdims, res=Tres, origin=Torigin ),
sep="_"
),
paste(
array_map( "xy->1", LUT[,c("plon","plat")], dims=Sdims, res=Sres, origin=Sorigin ),
array_map( "ts->1", LUT[,c("yr", "dyear")], dims=Tdims, res=Tres, origin=Torigin ),
sep="_"
)
)
LOCS$tplon = LOCS$tplat = LOCS$tdyear = NULL
gc()
for (vnm in variable_name) {
if ( vnm %in% names(LUT )) {
LOCS[[vnm]] = NA
LOCS[[vnm]] = LUT[ ii, vnm ]
}
}
}
if ( project_class %in% c("core", "stmv", "hybrid") & output_format == "areal_units" ) {
if (exists("lon", LUT)) {
LUT = sf::st_as_sf( LUT, coords=c("lon", "lat") )
st_crs(LUT) = st_crs( projection_proj4string("lonlat_wgs84") )
} else if (exists("plon", LUT)) {
LUT = sf::st_as_sf( LUT, coords=c("plon", "plat") )
st_crs(LUT) = st_crs(pL$aegis_proj4string_planar_km)
}
Tdims = c( diff( range(LUT$yr) ), pL$nw )
Tres = c(1, pL$tres)
Torigin = c( min(LUT$yr), 0 )
Sdims = c( pL$nplons, pL$nplats )
Sres = c( pL$pres, pL$pres )
Sorigin = pL$origin
if (!exists("AUID", LOCS_AU)) {
message ("AUID not found in LOCS_AU polygons, setting AUID as row number of polygons")
LOCS_AU$AUID = as.character(1:nrow(LOCS_AU))
}
if ( ! "sf" %in% class(LOCS) ) {
LOCS = st_as_sf( LOCS, coords=c("lon","lat"), crs=st_crs(projection_proj4string("lonlat_wgs84")) )
}
LOCS_AU = sf::st_transform( LOCS_AU, crs=st_crs(LUT) )
if (! inherits(LOCS$timestamp, "POSIXct") ) LOCS$timestamp = lubridate::date_decimal( LOCS$timestamp, tz=tz )
if (! exists("yr", LOCS) ) LOCS$yr = lubridate::year(LOCS$timestamp)
LU_map = paste(
st_points_in_polygons( pts=LUT, polys=LOCS_AU[, "AUID"], varname= "AUID" ),
array_map( "ts->1", LUT[,c("yr", "dyear")], dims=Tdims, res=Tres, origin=Torigin ),
sep="_"
)
LOCS_map = paste(
st_points_in_polygons( pts=LOCS, polys = LOCS_AU[, "AUID"], varname= "AUID" ),
array_map( "ts->1", LOCS[, c("yr", "tdyear")], dims=Tdims, res=Tres, origin=Torigin ),
sep="_"
)
LUT = setDT(st_drop_geometry(LUT))
for (vnm in variable_name) {
if ( vnm %in% names(LUT )) {
# LUT_regridded = tapply( st_drop_geometry(LUT)[, vnm], LU_map, FUN=FUNC, na.rm=TRUE )
LUT_regridded = LUT[, setNames(.(mean( get(vnm), na.rm=TRUE) ), vnm), by=.(LU_map) ]
LOCS[[ vnm ]] = LUT_regridded[ match( LOCS$AUID, LUT_regridded$LU_map ), vnm, with=FALSE ]
}
}
}
if ( project_class %in% c("carstm" ) & output_format == "points" ) {
# discretize LUT_AU to LOCS_AU and then re-estimate means by LOCS_AU$AUID then tag each estimate to AUID of LOCS
ny = length(LUT$time)
yr0 = min(as.numeric(LUT$time))
if (is.null(LUT_AU)) LUT_AU = LUT$sppoly
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = st_cast( LUT_AU, "MULTIPOLYGON")
# LUT_AU = st_cast(LUT_AU, "POLYGON" )
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = sf::st_transform( LUT_AU, crs=st_crs(pL$aegis_proj4string_planar_km) )
LUT_AU$au_index = 1:nrow(LUT_AU)
if (!exists("AUID", LUT_AU)) {
message ("AUID not found in LOCS_AU polygons, setting AUID as row number of polygons")
LUT_AU$AUID = as.character(LUT_AU$au_index)
}
bm = match( LUT_AU$AUID, LUT$space )
if (exists("lon", LOCS)) {
LOCS = sf::st_as_sf( LOCS, coords=c("lon", "lat") )
st_crs(LOCS) = st_crs( projection_proj4string("lonlat_wgs84") )
LOCS = sf::st_transform( LOCS, crs=st_crs(pL$aegis_proj4string_planar_km) )
} else if (exists("plon", LOCS)) {
LOCS = sf::st_as_sf( LOCS, coords=c("lon", "lat") )
st_crs(LOCS) = st_crs(pL$aegis_proj4string_planar_km)
}
LOCS$AUID = st_points_in_polygons( pts=LOCS, polys = LUT_AU[, "AUID"], varname= "AUID" )
if (! inherits(LOCS$timestamp, "POSIXct") ) LOCS$timestamp = lubridate::date_decimal( LOCS$timestamp, tz=tz )
if (! exists("yr", LOCS) ) LOCS$yr = lubridate::year(LOCS$timestamp)
ii = cbind( match( LOCS$AUID, LUT$space[bm] ) )
jj = cbind(
ii,
array_map( "ts->year_index", LOCS[["yr"]], dims=c(ny ), res=c( 1 ), origin=c( yr0 ) )
)
for (g in 1:length(statvars)) {
stat_var = statvars[g]
for (h in 1:length(variable_name) ) {
vnh = variable_name[[h]]
if (exists(vnh[[1]], LUT)) {
vnm = paste( paste0(vnh, collapse="_"), stat_var, sep="_" )
o = carstm_results_unpack( LUT, vnh )
kk = length(dim(o))
if (kk == 2) LOCS[[vnm]] = o[ cbind(ii, which(dimnames(o)$stat == stat_var) ) ]
if (kk == 3) LOCS[[vnm]] = o[ cbind(jj, which(dimnames(o)$stat == stat_var) ) ]
}
}
}
}
if ( project_class %in% c("carstm") & output_format == "areal_units" ) {
# discretize LUT_AU to LOCS_AU and then re-estimate means by LOCS_AU$AUID then tag each estimate to AUID of LOCS
# from source data: LUT = modelled predictions; LUT_AU are associated areal units linked by "AUID"
# nw = length(LUT$dyear)
# format coordinate systems
if (is.null(LUT_AU)) LUT_AU = LUT$sppoly
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = st_cast( LUT_AU, "MULTIPOLYGON")
# LUT_AU = st_cast(LUT_AU, "POLYGON" )
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = sf::st_transform( LUT_AU, crs=st_crs(pL$aegis_proj4string_planar_km) )
# dims
ny = length(LUT$time)
yr0 = min(as.numeric(LUT$time))
if (!exists("AUID", LUT_AU)) LUT_AU$AUID = as.character(1:nrow(LUT_AU))
bm = match( LUT_AU$AUID, LUT$space ) # should not be required but just in case things are subsetted
# lut_uid is A LOCAL index of LUT_AU /LUT .. rasterize it
LUT_AU$lut_uid = 1:nrow(LUT_AU)
LUT_AU_raster = stars::st_rasterize( LUT_AU["lut_uid"], dx=space_resolution, dy=space_resolution )
LUT_AU_pts = sf::st_as_sf( LUT_AU_raster, as_points=TRUE, na.rm=FALSE )
st_crs(LUT_AU_pts) = st_crs( LUT_AU )
# format output polygon structure
LOCS_AU = sf::st_transform( LOCS_AU, crs=st_crs(LUT_AU) ) # LOCS_AU .... must be sent ... <---------
LOCS_AU = st_make_valid(LOCS_AU)
LOCS_AU = st_buffer( LOCS_AU, 0 )
LOCS_AU = st_cast( LOCS_AU, "MULTIPOLYGON")
# LOCS_AU = st_cast( LOCS_AU, "POLYGON")
if (!exists("AUID", LOCS_AU)) {
message ("AUID not found in the LOCS_AU polygons, setting AUID as row number of polygons")
LOCS_AU$AUID = as.character(1:nrow(LOCS_AU))
}
if (! inherits(LOCS, "sf") ) {
if (exists("lon", LOCS )) {
LOCS = st_as_sf( LOCS, coords=c("lon","lat"), crs=st_crs(projection_proj4string("lonlat_wgs84")) )
LOCS = sf::st_transform( LOCS, crs=st_crs(pL$aegis_proj4string_planar_km) )
if (!exists("AUID", LOCS )) LOCS[["AUID"]] = st_points_in_polygons( pts=LOCS, polys=LOCS_AU[, "AUID"], varname= "AUID" )
}
}
if (! inherits(LOCS$timestamp, "POSIXct") ) LOCS$timestamp = lubridate::date_decimal( LOCS$timestamp, tz=tz )
if (! exists("yr", LOCS) ) LOCS$yr = lubridate::year(LOCS$timestamp)
TIMESTAMP_index1 = array_map( "ts->year_index", LOCS[["yr"]], dims=c(ny ), res=c( 1 ), origin=c( yr0 ) )
if (any( TIMESTAMP_index1 < 0)) {
TIMESTAMP_index1[ which( TIMESTAMP_index1 <= 0 ) ] = NA
}
# id membership of LUT raster in LOCS_AU
LUT_AU_pts_LOCS_AU_AUID = st_points_in_polygons( pts=LUT_AU_pts, polys=LOCS_AU[,"AUID"], varname="AUID" )
pts_AU = match(LUT_AU_pts$lut_uid, LUT_AU$lut_uid[match(LUT$space, LUT_AU$AUID)] ) ## (layer==lut_uid) -- to -- LUT
aggFUN = function( LUV ) {
tapply(X=LUV, INDEX=LUT_AU_pts_LOCS_AU_AUID, FUN=FUNC, na.rm=TRUE)
}
for (g in 1:length(statvars)) {
stat_var = statvars[g]
for (h in 1:length(variable_name) ) {
vnh = variable_name[[h]]
if (exists(vnh[[1]], LUT)) {
vnm = paste( paste0(vnh, collapse="_"), stat_var, sep="_" )
o = carstm_results_unpack( LUT, vnh )
kk = length(dim(o))
if (kk == 2) {
ov = o[ pts_AU, which(dimnames(o)$stat == stat_var) ]
LUT_as_LOCS_AU = aggFUN( ov)
space_index = match( as.character(LOCS$AUID), as.character(dimnames(LUT_as_LOCS_AU )[[1]] ) ) # AUID of LOCS_AU (from LUT_AU_pts_AUID)
if (all(is.na(space_index))) {
LOCS[,vnm] = LUT_as_LOCS_AU # fiddling required when only 1 AU
} else {
LOCS[,vnm] = LUT_as_LOCS_AU[ space_index ]
}
}
if (kk == 3) {
ov = o[ pts_AU,, which(dimnames(o)$stat == stat_var) ]
LUT_as_LOCS_AU = apply( ov, MARGIN=c(2), FUN=aggFUN )
space_index = match( as.character(LOCS$AUID), as.character(dimnames(LUT_as_LOCS_AU )[[1]] ) ) # AUID of LOCS_AU (from LUT_AU_pts_AUID)
if (all(is.na(space_index))) {
LOCS[,vnm] = LUT_as_LOCS_AU[ TIMESTAMP_index1 ] # fiddling required when only 1 AU
} else {
LOCS[,vnm] = LUT_as_LOCS_AU[ cbind( space_index, TIMESTAMP_index1 ) ]
}
}
}
}
}
}
} # end dimension
######################################################
if (pL$dimensionality =="space-time-cyclic" ) {
if ( project_class %in% c("core", "stmv", "hybrid") & output_format == "points" ) {
if (!exists("plon", LOCS)) LOCS = lonlat2planar(LOCS, proj.type=pL$aegis_proj4string_planar_km) # get planar projections of lon/lat in km
if (!exists("plon", LUT)) LUT = lonlat2planar(LUT, proj.type=pL$aegis_proj4string_planar_km)
if (! inherits(LOCS$timestamp, "POSIXct") ) LOCS$timestamp = lubridate::date_decimal( LOCS$timestamp, tz=tz )
if (!exists("dyear", LOCS) | (!exists("yr", LOCS)) ) {
LOCS$tiyr = lubridate::decimal_date( LOCS$timestamp )
LOCS$yr = trunc( LOCS$tiyr )
LOCS$dyear = LOCS$tiyr - LOCS$yr
}
LOCS$tplon = trunc(LOCS$plon / space_resolution + 1 ) * space_resolution
LOCS$tplat = trunc(LOCS$plat / space_resolution + 1 ) * space_resolution
LOCS$tdyear = trunc(LOCS$dyear / time_resolution + 1 ) * time_resolution
nY = diff( range(LUT$yr) )
nW = round(1/time_resolution)
Tdims = c( nY, nW )
Tres = c(1, time_resolution)
Torigin = c( min(LUT$yr), 0)
plon_range = range( LUT$plon )
plat_range = range( LUT$plat )
plons = seq(plon_range[1], plon_range[2], by=space_resolution)
plats = seq(plat_range[1], plat_range[2], by=space_resolution)
Sdims = c(length(plons), length(plats))
Sres = c(space_resolution, space_resolution)
Sorigin = c( plon_range[1], plat_range[1] )
ii = match(
paste(
array_map( "xy->1", LOCS[, c("tplon","tplat")], dims=Sdims, res=Sres, origin=Sorigin ),
array_map( "ts->1", LOCS[, c("yr", "tdyear")], dims=Tdims, res=Tres, origin=Torigin ),
sep="_"
),
paste(
array_map( "xy->1", LUT[,c("plon","plat")], dims=Sdims, res=Sres, origin=Sorigin ),
array_map( "ts->1", LUT[,c("yr", "dyear")], dims=Tdims, res=Tres, origin=Torigin ),
sep="_"
)
)
LOCS$tplon = LOCS$tplat = LOCS$tdyear = NULL
gc()
for (vnm in variable_name) {
if ( vnm %in% names(LUT )) {
LOCS[[vnm]] = NA
LOCS[[vnm]] = LUT[ ii, vnm ]
}
}
}
if ( project_class %in% c("core", "stmv", "hybrid") & output_format == "areal_units" ) {
if (exists("lon", LUT)) {
LUT = sf::st_as_sf( LUT, coords=c("lon", "lat") )
st_crs(LUT) = st_crs( projection_proj4string("lonlat_wgs84") )
} else if (exists("plon", LUT)) {
LUT = sf::st_as_sf( LUT, coords=c("plon", "plat") )
st_crs(LUT) = st_crs(pL$aegis_proj4string_planar_km)
}
Tdims = c( diff( range(LUT$yr) ), pL$nw )
Tres = c(1, pL$tres)
Torigin = c( min(LUT$yr), 0 )
Sdims = c( pL$nplons, pL$nplats )
Sres = c( pL$pres, pL$pres )
Sorigin = pL$origin
if (!exists("AUID", LOCS_AU)) {
message ("AUID not found in LOCS_AU polygons, setting AUID as row number of polygons")
LOCS_AU$AUID = as.character(1:nrow(LOCS_AU))
}
if ( ! "sf" %in% class(LOCS) ) {
LOCS = st_as_sf( LOCS, coords=c("lon","lat"), crs=st_crs(projection_proj4string("lonlat_wgs84")) )
}
LOCS_AU = sf::st_transform( LOCS_AU, crs=st_crs(LUT) )
if (! inherits(LOCS$timestamp, "POSIXct") ) LOCS$timestamp = lubridate::date_decimal( LOCS$timestamp, tz=tz )
if (! exists("yr", LOCS) )LOCS$yr = lubridate::year(LOCS$timestamp)
if (! exists("dyear", LOCS) ) LOCS$dyear = lubridate::decimal_date( LOCS$timestamp ) - LOCS$yr
LU_map = paste(
st_points_in_polygons( pts=LUT, polys=LOCS_AU[, "AUID"], varname= "AUID" ),
array_map( "ts->1", st_drop_geometry( LUT) [,c("yr", "dyear")], dims=Tdims, res=Tres, origin=Torigin),
sep="_"
)
LOCS_map = paste(
st_points_in_polygons( pts=LOCS, polys = LOCS_AU[, "AUID"], varname= "AUID" ),
array_map( "ts->1", st_drop_geometry(LOCS)[ , c("yr", "dyear") ], dims=Tdims, res=Tres, origin=Torigin),
sep="_"
)
LUT = setDT(st_drop_geometry(LUT))
for (vnm in variable_name) {
if ( vnm %in% names(LUT )) {
# LUT_regridded = tapply( st_drop_geometry(LUT)[, vnm], LU_map, FUN=FUNC, na.rm=TRUE )
LUT_regridded = LUT[, setNames(.(mean( get(vnm), na.rm=TRUE) ), vnm), by=.(LU_map) ]
LOCS[[ vnm ]] = LUT_regridded[ match( LOCS$AUID, LUT_regridded$LU_map ), vnm, with=FALSE ]
}
}
}
if ( project_class %in% c("carstm" ) & output_format == "points" ) {
# areal unit (LUT) to points (LOCS)
nw = length(LUT$cyclic)
ny = length(LUT$time)
yr0 = min(as.numeric(LUT$time))
if (is.null(LUT_AU)) LUT_AU = LUT$sppoly
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = st_cast( LUT_AU, "MULTIPOLYGON") # causes additional polys ..
# LUT_AU = st_cast( LUT_AU, "POLYGON" )
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = sf::st_transform( LUT_AU, crs=st_crs(pL$aegis_proj4string_planar_km) )
LUT_AU$au_index = 1:nrow(LUT_AU)
if (!exists("AUID", LUT_AU)) {
message ("AUID not found in LOCS_AU polygons, setting AUID as row number of polygons")
LUT_AU$AUID = as.character(LUT_AU$au_index)
}
bm = match( LUT_AU$AUID, LUT$space )
if (exists("lon", LOCS)) {
LOCS = sf::st_as_sf( LOCS, coords=c("lon", "lat") )
st_crs(LOCS) = st_crs( projection_proj4string("lonlat_wgs84") )
LOCS = sf::st_transform( LOCS, crs=st_crs(pL$aegis_proj4string_planar_km) )
} else if (exists("plon", LOCS)) {
LOCS = sf::st_as_sf( LOCS, coords=c("lon", "lat") )
st_crs(LOCS) = st_crs(pL$aegis_proj4string_planar_km)
}
LOCS$AUID = st_points_in_polygons( pts=LOCS, polys = LUT_AU[, "AUID"], varname= "AUID" )
if (! inherits(LOCS$timestamp, "POSIXct") ) LOCS$timestamp = lubridate::date_decimal( LOCS$timestamp, tz=tz )
if (! exists("yr", LOCS) ) LOCS$yr = lubridate::year(LOCS$timestamp)
if (! exists("dyear", LOCS) ) LOCS$dyear = lubridate::decimal_date( LOCS$timestamp ) - LOCS$yr
ii = cbind( match( LOCS$AUID, LUT$space[bm] ) )
jj = cbind(
ii,
array_map( "ts->year_index", LOCS[["yr"]], dims=c(ny ), res=c( 1 ), origin=c( yr0 ) )
)
LOCS_DF = LOCS
if (inherits(LOCS_DF, "sf")) LOCS_DF = st_drop_geometry(LOCS_DF)
ll = cbind(
ii,
array_map( "ts->2", LOCS_DF[, c("yr", "dyear")], dims=c(ny, nw), res=c( 1, 1/nw ), origin=c( yr0, 0) )
)
LOCS_DF = NULL
for (g in 1:length(statvars)) {
stat_var = statvars[g]
for (h in 1:length(variable_name) ) {
vnh = variable_name[[h]]
if (exists(vnh[[1]], LUT)) {
vnm = paste( paste0(vnh, collapse="_"), stat_var, sep="_" )
o = carstm_results_unpack( LUT, vnh )
kk = length(dim(o))
if (kk == 2) LOCS[[vnm]] = o[ cbind(ii, which(dimnames(o)$stat == stat_var) ) ]
if (kk == 3) LOCS[[vnm]] = o[ cbind(jj, which(dimnames(o)$stat == stat_var) ) ]
if (kk == 4) LOCS[[vnm]] = o[ cbind(ll, which(dimnames(o)$stat == stat_var) ) ]
}
}
}
}
if ( project_class %in% c("carstm") & output_format == "areal_units" ) {
# areal unit (LUT) to areal units (LUT_AU/LOCS)
# from source data: LUT = modelled predictions; LUT_AU are associated areal units linked by "AUID"
# format coordinate systems
if (is.null(LUT_AU)) LUT_AU = LUT$sppoly
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = st_cast( LUT_AU, "MULTIPOLYGON")
# LUT_AU = st_cast (LUT_AU, "POLYGON" )
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = sf::st_transform( LUT_AU, crs=st_crs(pL$aegis_proj4string_planar_km) )
nw = length(LUT$cyclic)
ny = length(LUT$time)
yr0 = min(as.numeric(LUT$time))
if (!exists("AUID", LUT_AU)) LUT_AU$AUID = as.character(1:nrow(LUT_AU))
bm = match( LUT_AU$AUID, LUT$space ) # should not be required but just in case things are subsetted
# lut_uid is A LOCAL index of LUT_AU /LUT .. rasterize it
LUT_AU$lut_uid = 1:nrow(LUT_AU)
LUT_AU_raster = stars::st_rasterize( LUT_AU["lut_uid"], dx=space_resolution, dy=space_resolution )
LUT_AU_pts = sf::st_as_sf( LUT_AU_raster, as_points=TRUE, na.rm=FALSE )
st_crs(LUT_AU_pts) = st_crs( LUT_AU )
# format output polygon structure
LOCS_AU = sf::st_transform( LOCS_AU, crs=st_crs(LUT_AU) ) # LOCS_AU .... must be sent ... <---------
LOCS_AU = st_make_valid(LOCS_AU)
LOCS_AU = st_buffer( LOCS_AU, 0 )
LOCS_AU = st_cast( LOCS_AU, "MULTIPOLYGON")
# LOCS_AU = st_cast( LOCS_AU, "POLYGON")
if (!exists("AUID", LOCS_AU)) {
message ("AUID not found in the LOCS_AU polygons, setting AUID as row number of polygons")
LOCS_AU$AUID = as.character(1:nrow(LOCS_AU))
}
if (! inherits(LOCS, "sf") ) {
if (exists("lon", LOCS )) {
LOCS = st_as_sf( LOCS, coords=c("lon","lat"), crs=st_crs(projection_proj4string("lonlat_wgs84")) )
LOCS = sf::st_transform( LOCS, crs=st_crs(pL$aegis_proj4string_planar_km) )
if (!exists("AUID", LOCS )) LOCS[["AUID"]] = st_points_in_polygons( pts=LOCS, polys=LOCS_AU[, "AUID"], varname= "AUID" )
}
}
if (! inherits(LOCS$timestamp, "POSIXct") ) LOCS$timestamp = lubridate::date_decimal( LOCS$timestamp, tz=tz )
if (! exists("yr", LOCS) ) LOCS$yr = lubridate::year(LOCS$timestamp)
if (! exists("dyear", LOCS) ) LOCS$dyear = lubridate::decimal_date( LOCS$timestamp ) - LOCS$yr
LOCS_DF = LOCS
if (inherits(LOCS_DF, "sf")) LOCS_DF = st_drop_geometry(LOCS_DF)
TIMESTAMP_index1 = array_map( "ts->year_index", LOCS_DF[, "yr"], dims=c(ny ), res=c( 1 ), origin=c( yr0 ) )
TIMESTAMP_index2 = array_map( "ts->2", LOCS_DF[, c("yr", "dyear")], dims=c(ny, nw), res=c( 1, 1/nw ), origin=c( yr0, 0) )
if (any( TIMESTAMP_index1 < 0)) {
TIMESTAMP_index1[ which( TIMESTAMP_index1 <= 0 ) ] = NA
}
if (any( TIMESTAMP_index2 < 0)) {
warning ("cyclic time index is negative: lookup table does not contain data to lookup ... \n
lookup data needs to be expanded or time periods reduced in model")
TIMESTAMP_index2[ which( TIMESTAMP_index2 <= 0 ) ] = NA
}
LOCS_DF = NULL
# id membership of LUT raster in LOCS_AU
LUT_AU_pts_LOCS_AU_AUID = st_points_in_polygons( pts=LUT_AU_pts, polys=LOCS_AU[,"AUID"], varname="AUID" )
pts_AU = match(LUT_AU_pts$lut_uid, LUT_AU$lut_uid[match(LUT$space, LUT_AU$AUID)] ) ## (layer==lut_uid) -- to -- LUT
aggFUN = function( LUV ) {
tapply(X=LUV, INDEX=LUT_AU_pts_LOCS_AU_AUID, FUN=FUNC, na.rm=TRUE)
}
for (g in 1:length(statvars)) {
stat_var = statvars[g]
for (h in 1:length(variable_name) ) {
vnh = variable_name[[h]]
if (exists(vnh[[1]], LUT)) {
vnm = paste( paste0(vnh, collapse="_"), stat_var, sep="_" )
o = carstm_results_unpack( LUT, vnh )
kk = length(dim(o))
if (kk == 2) {
ov = o[ pts_AU, which(dimnames(o)$stat == stat_var) ]
LUT_as_LOCS_AU = aggFUN( ov)
space_index = match( as.character(LOCS$AUID), as.character(dimnames(LUT_as_LOCS_AU )[[1]] ) ) # AUID of LOCS_AU (from LUT_AU_pts_AUID)
if (all(is.na(space_index))) {
LOCS[,vnm] = LUT_as_LOCS_AU # fiddling required when only 1 AU
} else {
LOCS[,vnm] = LUT_as_LOCS_AU[ space_index ]
}
}
if (kk == 3) {
ov = o[ pts_AU,, which(dimnames(o)$stat == stat_var) ]
LUT_as_LOCS_AU = apply( ov, MARGIN=c(2), FUN=aggFUN )
space_index = match( as.character(LOCS$AUID), as.character(dimnames(LUT_as_LOCS_AU )[[1]] ) ) # AUID of LOCS_AU (from LUT_AU_pts_AUID)
if (all(is.na(space_index))) {
LOCS[,vnm] = LUT_as_LOCS_AU[ TIMESTAMP_index1 ] # fiddling required when only 1 AU
} else {
LOCS[,vnm] = LUT_as_LOCS_AU[ cbind( space_index, TIMESTAMP_index1 ) ]
}
}
if (kk == 4) {
ov = o[ pts_AU,,, which(dimnames(o)$stat == stat_var) ]
LUT_as_LOCS_AU = apply( ov, MARGIN=c(2,3), FUN=aggFUN )
space_index = match( as.character(LOCS$AUID), as.character(dimnames(LUT_as_LOCS_AU )[[1]] ) ) # AUID of LOCS_AU (from LUT_AU_pts_AUID)
if (all(is.na(space_index))) {
LOCS[,vnm] = LUT_as_LOCS_AU[ TIMESTAMP_index2 ] # fiddling required when only 1 AU
} else {
LOCS[,vnm] = LUT_as_LOCS_AU[ cbind( space_index, TIMESTAMP_index2 ) ]
}
}
}
}
}
}
} # end space-time-cyclic
if (returntype =="sf" ) {
if (! inherits(LOCS, "sf")) LOCS = st_as_sf( LOCS, coords=c("lon","lat"), crs=st_crs(projection_proj4string("lonlat_wgs84")) )
}
if (returntype =="data.frame" ) {
if (! inherits(LOCS, "data.frame")) LOCS = as.data.frame(LOCS)
}
if (returntype =="data.table" ) {
if (! inherits(LOCS, "data.table")) setDT(LOCS)
}
if (returntype =="vector" ) {
if (length(variable_name) == 1) {
if (project_class=="carstm") {
variable_name = paste( paste0(variable_name[[1]], collapse="_"), statvars[1], sep="_" )
}
if (exists( variable_name, LOCS)) {
LOCS = LOCS[[variable_name]]
} else {
LOCS = rep(NA, nrow(LOCS))
}
}
}
return(LOCS)
}
jae0/aegis documentation built on April 4, 2024, 2:40 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions aegis_lookup
# TODO:: tapply can be converted into data.table computations for speed
## WARNING:: if you polygons are misspecified, they can result in some au's being dropped .. check your polygons
aegis_lookup = function(
parameters = NULL,
variable_name=NULL,
LUT = NULL, # look up table from which to obtain results
LOCS = NULL, # look up locations for which results are desired
LUT_AU=NULL, # areal units associated with LUT
LOCS_AU=NULL,
project_class="core", # "project_class" to look up from
DS="aggregated_data", # "DS=.. "
output_format="points",
statvars = c("mean"),
tz="America/Halifax",
FUNC=mean,
returntype = "vector",
space_resolution=NULL, # spatial planar discretization
time_resolution=NULL, # year, seasonal discretization
year.assessment=NULL, ...
) {
if (0) {
# testing usign snow data
p = bio.snowcrab::snowcrab_parameters(
project_class="carstm",
yrs=1999:2021,
areal_units_type="tesselation",
carstm_model_label = "tesselation", # default is the name of areal_units_type
selection = list(type = "number")
)
M = snowcrab.db( p=p, DS="biological_data" )
M = M[ which( M$yr %in% 2011:2015 ) ,] # reduce data size
dim(M)
sppoly = areal_units( p=p ) # poly to estimate a surface
# loadfunctions("aegis")
# debug(aegis_lookup)
if (0) {
# generics
parameters="bathymetry"
variable_name=list( "predictions", c("random", "space", "combined") )
LUT = NULL # look up table from which to obtain results
LOCS = M[, c("lon", "lat", "timestamp")] # look up locations for which results are desired
LUT_AU=NULL # areal units associated with LUT
LOCS_AU=sppoly
project_class="core" # "project_class" to look up from
DS="aggregated_data" # "DS=.. "
output_format="points"
statvars = c("mean")
tz="America/Halifax"
FUNC=mean
space_resolution=1
}
loadfunctions("aegis")
# test raw data lookup
# spatial
o0 = aegis_lookup( parameters="bathymetry", LOCS=M[, c("lon", "lat")],
project_class="core", output_format="points" , DS="aggregated_data", variable_name=c( "z.mean", "z.sd", "z.n"),
returntype="sf"
)
plot(M[["z"]] ~ o0[["z.mean"]])
o1 = aegis_lookup( parameters="bathymetry", LOCS=M[, c("lon", "lat")],
project_class="core", output_format="points" , DS="aggregated_data", variable_name=c( "z.mean" ),
returntype="vector"
)
o2 = aegis_lookup( parameters="bathymetry", LOCS=M[, c("lon", "lat")],
project_class="stmv", output_format="points" , DS="complete", variable_name=c( "z", "dZ", "ddZ")
)
# spatial averaging by areal unit
# this one is slow .. could be sped up if used
o3 = aegis_lookup( parameters="bathymetry", LOCS=M[, c("lon", "lat")], LOCS_AU=sppoly,
project_class="stmv", output_format="areal_units" , DS="complete", variable_name=c( "z", "dZ", "ddZ")
)
# spatial averaging by areal unit
o4 = aegis_lookup( parameters="bathymetry", LOCS=M[, c("lon", "lat")], LOCS_AU=sppoly,
project_class="core", output_format="areal_units" , DS="aggregated_data", variable_name=c( "z.mean", "z.sd", "z.n")
)
# lookup from areal unit predictions
o5 = aegis_lookup( parameters="bathymetry", LOCS=M[, c("lon", "lat")],
project_class="carstm", output_format="points", variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd"), space_resolution=min(p$pres)
)
# slow
o6 = aegis_lookup( parameters="bathymetry", LOCS=M[, c("lon", "lat")], LOCS_AU=sppoly,
project_class="carstm", output_format="areal_units", variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd"), space_resolution=min(p$pres) /2
)
# au to au match (LOCS=NULL)
o7 = aegis_lookup( parameters="bathymetry", LOCS=list(AUID=sppoly$AUID), LOCS_AU=sppoly,
project_class="carstm", output_format="areal_units", variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd"), space_resolution=min(p$pres) /2
)
# au to au match (LOCS=NULL)
o7 = aegis_lookup( parameters="bathymetry", LOCS=sppoly[,"AUID"], LOCS_AU=sppoly,
project_class="carstm", output_format="areal_units", variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd"), space_resolution=min(p$pres) /2
)
# au to au match (LOCS=NULL)
o7 = aegis_lookup( parameters="bathymetry", LOCS=sppoly$AUID, LOCS_AU=sppoly,
project_class="carstm", output_format="areal_units", variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd"), space_resolution=min(p$pres) /2
)
# consistency checks
plot(o1 ~o2$z)
plot(o1 ~o3$z)
plot(o1 ~o4$z)
plot(o1 ~o5$predictions_mean)
plot(o1 ~o6$predictions_mean)
# space-time
o1 = aegis_lookup( parameters="speciescomposition_pca1", LOCS=M[, c("lon", "lat", "timestamp")],
project_class="core", output_format="points" , DS="speciescomposition", variable_name=c( "pca1"), space_resolution=2
)
o2 = aegis_lookup( parameters="speciescomposition_pca1", LOCS=M[, c("lon", "lat", "timestamp")],
project_class="stmv", output_format="points" , DS="complete", variable_name=c( "pca1")
)
o3 = aegis_lookup( parameters="speciescomposition_pca1", LOCS=M[, c("lon", "lat", "timestamp")], LOCS_AU=sppoly,
project_class="core", output_format="areal_units" , variable_name=list( "pca1", "pca2", "ca1", "ca2" )
)
o4 = aegis_lookup( parameters="speciescomposition_pca1", LOCS=M[, c("lon", "lat", "timestamp")],
project_class="carstm", output_format="points", variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd")
)
o5 = aegis_lookup( parameters="speciescomposition_pca1", LOCS=M[, c("lon", "lat", "timestamp")], LOCS_AU=sppoly,
project_class="carstm", output_format="areal_units" , variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd"), space_resolution=min(p$pres)/2
)
mm = expand.grid(AUID=sppoly$AUID, timestamp=lubridate::date_decimal( p$yrs, tz="America/Halifax" ))
mm = expand.grid(AUID=sppoly$AUID, timestamp= p$yrs )
o6 = aegis_lookup( parameters="speciescomposition_pca1", LOCS=mm, LOCS_AU=sppoly,
project_class="carstm", output_format="areal_units" , variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd"), space_resolution=min(p$pres)/2
)
# consistency checks
plot(o1$pca1.mean ~o3$pca1.mean)
plot(o1$pca1.mean ~o4$predictions_mean)
plot(o1$pca1.mean ~o5$predictions_mean)
# space-time-season
o1 = aegis_lookup( parameters="temperature", LOCS=M[, c("lon", "lat", "timestamp")],
project_class="core", output_format="points" , DS="aggregated_data", variable_name=c( "t.mean", "t.sd", "t.n"), space_resolution=2
)
o2 = aegis_lookup( parameters="temperature", LOCS=M[, c("lon", "lat", "timestamp")],
project_class="stmv", output_format="points" , DS="complete", variable_name=c( "t")
)
o3 = aegis_lookup( parameters="temperature", LOCS=M[, c("lon", "lat", "timestamp")], LOCS_AU=sppoly,
project_class="core", output_format="areal_units" , variable_name=list( "t.mean", "t.sd", "t.n" )
)
parameters = list(
temperature = temperature_parameters(
project_class="carstm",
yrs=1970:year.assessment,
carstm_model_label="1970_present"
)
)
o4 = aegis_lookup( parameters=parameters, LOCS=M[, c("lon", "lat", "timestamp")],
project_class="carstm", output_format="points", variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd")
)
o5 = aegis_lookup( parameters=parameters, LOCS=M[, c("lon", "lat", "timestamp")], LOCS_AU=sppoly,
project_class="carstm", output_format="areal_units" , variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd"), space_resolution=min(p$pres)/2
)
# mm = expand.grid(AUID=sppoly$AUID, timestamp=lubridate::date_decimal( p$yrs, tz="America/Halifax" ))
mm = expand.grid(AUID=sppoly$AUID, timestamp= p$yrs )
o6 = aegis_lookup( parameters="temperature", LOCS=mm, LOCS_AU=sppoly,
project_class="carstm", output_format="areal_units" , variable_name=list( "predictions", c("random", "space", "combined") ), statvars=c("mean", "sd"), space_resolution=min(p$pres)/2
)
# consistency checks
plot(o1$t.mean ~o3$t.mean)
plot(o1$t.mean ~o4$predictions_mean)
plot(o1$t.mean ~o5$predictions_mean)
if (0) {
p = bathymetry_parameters( project_class="stmv" )
LUT = bathymetry_db ( p=p, DS="complete" )
}
} ## END consistency checks
require(stars)
# -----------
if ( is.null(parameters) ) stop( "parameters is required")
pL = NULL
if ( class(parameters) == "character" ) {
# then use generic defaults
aegis_project = parameters
} else {
aegis_project = names(parameters)
if (length(aegis_project) > 1) {
warning( "more than one parameter list sent, taking the first only")
aegis_project = aegis_project[1]
}
pL = parameters[[aegis_project]]
}
if (is.vector(LOCS)) LOCS = list(AUID=LOCS)
if (!is.null(LOCS)) setDT(LOCS)
crs_lonlat = st_crs(projection_proj4string("lonlat_wgs84"))
# determine LUT (lookup table)
if (is.null(LUT)) {
if ( "bathymetry" %in% aegis_project ) {
if ( is.null(pL) ) pL = bathymetry_parameters( project_class=project_class )
if (is.null(space_resolution)) if (exists( "pres", pL)) space_resolution = pL$pres
if ( project_class %in% c("core" ) ) LUT = bathymetry_db ( p=pL, DS=DS )
if ( project_class %in% c("stmv", "hybrid") ) LUT = bathymetry_db ( p=pL, DS="complete" )
if ( project_class %in% c("carstm" )) {
LUT = carstm_model( p=pL, DS="carstm_modelled_summary" )
LUT$space = LUT$space_id
}
if ( project_class %in% c("core", "stmv", "hybrid") ) {
setDT(LUT)
if ( space_resolution != pL$pres ) {
# regrid to another resolution
LUT$plon = trunc(LUT$plon / space_resolution + 1 ) * space_resolution
LUT$plat = trunc(LUT$plat / space_resolution + 1 ) * space_resolution
LUT = LUT[, setNames(.(mean( get(variable_name), na.rm=TRUE) ), variable_name), by=list(plon, plat) ]
}
setDF(LUT)
}
}
if ( "substrate" %in% aegis_project ) {
if ( is.null(pL) ) pL = substrate_parameters( project_class=project_class )
if (is.null(space_resolution)) if (exists( "pres", pL)) space_resolution = pL$pres
if ( project_class %in% c("core" ) ) LUT = substrate_db ( p=pL, DS=DS )
if ( project_class %in% c("stmv", "hybrid") ) {
LUT = substrate_db ( p=pL, DS="complete" )
pB = bathymetry_parameters( spatial_domain=pL$spatial_domain, project_class=project_class )
BA = bathymetry_db ( p=pB, DS="baseline", varnames=c("lon", "lat") )
LUT = cbind( LUT, BA )
}
if ( project_class %in% c("carstm" )) {
LUT = carstm_model( p=pL, DS="carstm_modelled_summary" )
LUT$space = LUT$space_id
}
if ( project_class %in% c("core", "stmv", "hybrid") ) {
setDT(LUT)
if ( space_resolution != pL$pres ) {
# regrid to another resolution
LUT$plon = trunc(LUT$plon / space_resolution + 1 ) * space_resolution
LUT$plat = trunc(LUT$plat / space_resolution + 1 ) * space_resolution
LUT = LUT[, setNames(.(mean( get(variable_name), na.rm=TRUE) ), variable_name), by=list(plon, plat) ]
}
setDF(LUT)
}
}
if ( "temperature" %in% aegis_project ) {
if (is.null(pL) ) pL = temperature_parameters( project_class=project_class, year.assessment=year.assessment )
if (is.null(space_resolution)) if (exists( "pres", pL)) space_resolution = pL$pres
if (is.null(time_resolution)) if (exists( "tres", pL)) time_resolution = pL$tres
if ( project_class %in% c("core" )) LUT = temperature_db ( p=pL, DS=DS ) # "aggregated_data", "bottom.all"
if ( project_class %in% c("stmv", "hybrid") ) LUT = temperature_db ( p=pL, DS="complete" )
if ( project_class %in% c("carstm" )) {
LUT = carstm_model( p=pL, DS="carstm_modelled_summary" )
LUT$space = LUT$space_id
LUT$time = LUT$time_id
LUT$cyclic = LUT$cyclic_id
}
if ( project_class %in% c("core", "stmv", "hybrid") ) {
setDT(LUT)
if ( time_resolution != pL$tres ) {
LUT$dyear = trunc(LUT$dyear / time_resolution + 1 ) * time_resolution
}
if ( space_resolution != pL$pres ) {
# regrid to another resolution
LUT$plon = trunc(LUT$plon / space_resolution + 1 ) * space_resolution
LUT$plat = trunc(LUT$plat / space_resolution + 1 ) * space_resolution
}
if ( time_resolution != pL$tres | space_resolution != pL$pres ) {
LUT = LUT[, setNames(.(mean( get(variable_name), na.rm=TRUE) ), variable_name), by=list(plon, plat, yr, dyear) ]
LUT$timestamp = lubridate::date_decimal( LUT$yr+LUT$dyear, tz=tz )
}
setDF(LUT)
}
}
if ( grepl("speciescomposition", aegis_project) ) {
if (aegis_project == "speciescomposition_pca1") sc_vn = "pca1"
if (aegis_project == "speciescomposition_pca2") sc_vn = "pca2"
if (aegis_project == "speciescomposition_pca3") sc_vn = "pca3"
if (aegis_project == "speciescomposition_ca1") sc_vn = "ca1"
if (aegis_project == "speciescomposition_ca2") sc_vn = "ca2"
if (aegis_project == "speciescomposition_ca3") sc_vn = "ca3"
if (is.null(pL) ) pL = speciescomposition_parameters( project_class=project_class, variabletomodel=sc_vn , year.assessment=year.assessment )
if (is.null(space_resolution)) if (exists( "pres", pL)) space_resolution = pL$pres
if (is.null(time_resolution)) if (exists( "tres", pL)) time_resolution = pL$tres
if ( project_class %in% c("core" ) ) LUT = speciescomposition_db ( p=pL, DS=DS )
if ( project_class %in% c( "stmv", "hybrid") ) LUT = aegis_db( p=pL, DS="complete" )
if ( project_class %in% c("carstm" )) {
LUT = carstm_model( p=pL, DS="carstm_modelled_summary" )
LUT$space = LUT$space_id
LUT$time = LUT$time_id
LUT$cyclic = LUT$cyclic_id
}
if ( project_class %in% c("core", "stmv", "hybrid") ) {
setDT(LUT)
if ( time_resolution != pL$tres ) {
LUT$dyear = trunc(LUT$dyear / time_resolution + 1 ) * time_resolution
}
if ( space_resolution != pL$pres ) {
# regrid to another resolution
LUT$plon = trunc(LUT$plon / space_resolution + 1 ) * space_resolution
LUT$plat = trunc(LUT$plat / space_resolution + 1 ) * space_resolution
}
if ( time_resolution != pL$tres | space_resolution != pL$pres ) {
LUT = LUT[, setNames(.(mean( get(sc_vn), na.rm=TRUE) ), sc_vn), by=list(plon, plat, yr, dyear) ]
LUT$timestamp = lubridate::date_decimal( LUT$yr+LUT$dyear, tz=tz )
}
setDF(LUT)
}
}
if ( grepl("snowcrab", aegis_project) ) {
if (aegis_project == "snowcrab_number") sc_vn = "number"
if (aegis_project == "snowcrab_biomass") sc_vn = "biomass"
if (aegis_project == "snowcrab_meansize") sc_vn = "meansize"
if (aegis_project == "snowcrab_pa") sc_vn = "pa"
if (is.null(pL) ) {
if ( sc_vn == "number" ) {
pL = snowcrab_parameters(
project_class="carstm",
yrs=1999:year.assessment,
areal_units_type="tesselation",
family="poisson",
carstm_model_label = "1999_present", # 1999_present is the default anything else and you are on your own
selection = list(type = "number")
)
} else if ( sc_vn == "biomass" ) {
pL = snowcrab_parameters(
project_class="carstm",
yrs=1999:year.assessment,
areal_units_type="tesselation",
carstm_model_label = "1999_present", # 1999_present is the default anything else and you are on your own
# carstm_model_label = paste( carstm_model_label, variabletomodel, sep="_")
family = "gaussian" ,
selection = list(type = "biomass")
)
} else if ( sc_vn == "meansize" ) {
pL = snowcrab_parameters(
project_class="carstm",
yrs=1999:year.assessment,
areal_units_type="tesselation",
carstm_model_label = "1999_present", # 1999_present is the default anything else and you are on your own
# carstm_model_label = paste( carstm_model_label, variabletomodel, sep="_")
family = "gaussian" ,
selection = list(type = "meansize")
)
} else if ( sc_vn == "pa" ) {
pL = snowcrab_parameters(
project_class="carstm",
yrs=1999:year.assessment,
areal_units_type="tesselation",
carstm_model_label = "1999_present", # 1999_present is the default anything else and you are on your own
# carstm_model_label = paste( carstm_model_label, variabletomodel, sep="_")
family = "gaussian" ,
selection = list(type = "presence_absence")
)
} else {
pL = p = bio.snowcrab::load.environment( year.assessment=year.assessment )
}
}
if (is.null(space_resolution)) if (exists( "pres", pL)) space_resolution = pL$pres
if (is.null(time_resolution)) if (exists( "tres", pL)) time_resolution = pL$tres
if ( project_class %in% c("core" ) ) LUT = snowcrab.db ( p=pL, DS=DS )
if ( project_class %in% c( "stmv", "hybrid") ) LUT = aegis_db( p=pL, DS="complete" )
if ( project_class %in% c("carstm" )) {
LUT = carstm_model( p=pL, DS="carstm_modelled_summary" )
LUT$space = LUT$space_id
LUT$time = LUT$time_id
LUT$cyclic = LUT$cyclic_id
}
if ( project_class %in% c("core", "stmv", "hybrid") ) {
setDT(LUT)
if ( time_resolution != pL$tres ) {
LUT$dyear = trunc(LUT$dyear / time_resolution + 1 ) * time_resolution
}
if ( space_resolution != pL$pres ) {
# regrid to another resolution
LUT$plon = trunc(LUT$plon / space_resolution + 1 ) * space_resolution
LUT$plat = trunc(LUT$plat / space_resolution + 1 ) * space_resolution
}
if ( time_resolution != pL$tres | space_resolution != pL$pres ) {
LUT = LUT[, setNames(.(mean( get(sc_vn), na.rm=TRUE) ), sc_vn), by=list(plon, plat, yr, dyear) ]
LUT$timestamp = lubridate::date_decimal( LUT$yr+LUT$dyear, tz=tz )
}
setDF(LUT)
}
}
}
if (is.null(LUT)) stop( "lookup data not found nor given")
if (is.null(variable_name)) {
if ( project_class %in% c("carstm" )) {
variable_name = LUT$fm$dependent_variable
} else {
variable_name = setdiff( names(LUT), c("plon", "plat", "lon", "lat", "timestamp", "year", "dyear", "yr" ))
}
}
# ------------------
if (pL$dimensionality =="space" ) {
if ( project_class %in% c("core", "stmv", "hybrid") & output_format == "points" ) {
if (!exists("plon", LUT)) LUT = lonlat2planar(LUT, proj.type=pL$aegis_proj4string_planar_km)
if (!exists("plon", LOCS)) LOCS = lonlat2planar(LOCS, proj.type=pL$aegis_proj4string_planar_km) # get planar projections of lon/lat in km
LOCS$tplon = trunc(LOCS$plon / space_resolution + 1 ) * space_resolution
LOCS$tplat = trunc(LOCS$plat / space_resolution + 1 ) * space_resolution
plon_range = range( LUT$plon )
plat_range = range( LUT$plat )
plons = seq(plon_range[1], plon_range[2], by=space_resolution)
plats = seq(plat_range[1], plat_range[2], by=space_resolution)
Sdims = c(length(plons), length(plats))
Sres = c(space_resolution, space_resolution)
Sorigin = c( plon_range[1], plat_range[1] )
ii = match(
array_map( "xy->1", LOCS[, c("tplon","tplat")], dims=Sdims, res=Sres, origin=Sorigin ),
array_map( "xy->1", LUT[,c("plon","plat")], dims=Sdims, res=Sres, origin=Sorigin )
)
LOCS$tplon = LOCS$tplat = NULL
gc()
for (vnm in variable_name) {
if ( vnm %in% names(LUT )) {
LOCS[[vnm]] = NA
LOCS[[vnm]] = LUT[ ii, vnm ]
}
}
}
if ( project_class %in% c("core", "stmv", "hybrid") & output_format == "areal_units" ) {
LOCS0 = NULL
if (exists("AUID", LOCS)) {
# this is a special class of lookup taking LUT (usually empirical or aggregated data) and estimating from it for an areal unit (via rasterization)
LOCS0 = LOCS # store as modifications will be made to LOCS
# next, get a x-y coordinate for each LOC by rasterizing to LOCS_AU
LOCS_AU = st_make_valid(LOCS_AU)
LOCS_AU = sf::st_transform( LOCS_AU, crs=st_crs(pL$aegis_proj4string_planar_km) )
LOCS_AU$au_index = 1:nrow(LOCS_AU)
LOCS_AU_raster = stars::st_rasterize( LOCS_AU["au_index"], dx=space_resolution, dy=space_resolution )
# overwrite LOCS with discretized points
LOCS = sf::st_as_sf( LOCS_AU_raster, as_points=TRUE, na.rm=FALSE )
st_crs(LOCS) = st_crs( LOCS_AU )
LOCS$AUID = LOCS_AU$AUID[ st_extract(LOCS_AU_raster, LOCS )$au_index ]
} else {
if (exists("lon", LOCS)) {
LOCS = sf::st_as_sf( LOCS, coords=c("lon", "lat") )
st_crs(LOCS) = st_crs( projection_proj4string("lonlat_wgs84") )
} else if (exists("plon", LOCS)) {
LOCS = sf::st_as_sf( LOCS, coords=c("plon", "plat") )
st_crs(LOCS) = st_crs(pL$aegis_proj4string_planar_km)
}
}
if (exists("lon", LUT)) {
LUT = sf::st_as_sf( LUT, coords=c("lon", "lat") )
st_crs(LUT) = st_crs( projection_proj4string("lonlat_wgs84") )
} else if (exists("plon", LUT)) {
LUT = sf::st_as_sf( LUT, coords=c("plon", "plat") )
st_crs(LUT) = st_crs(pL$aegis_proj4string_planar_km)
}
if (!exists("AUID", LOCS_AU)) {
message ("AUID not found in the polygons, setting AUID as row number of polygons")
LOCS_AU$AUID = as.character(1:nrow(LOCS_AU))
}
LOCS_AU = sf::st_transform( LOCS_AU, crs=st_crs(LUT) ) #
variable_name = intersect( names(LUT), variable_name )
LUT = LUT[, variable_name]
LU_map = st_points_in_polygons( pts=LUT, polys=LOCS_AU[, "AUID"], varname= "AUID" )
if (!exists("AUID", LOCS )) LOCS[["AUID"]] = st_points_in_polygons( pts=LOCS, polys=LOCS_AU[, "AUID"], varname= "AUID" )
st_geometry(LUT) = NULL
setDT(LUT)
for (vnm in variable_name) {
if ( vnm %in% names(LUT )) {
# LUT_regridded = tapply( st_drop_geometry(LUT)[, vnm], LU_map, FUN=FUNC, na.rm=TRUE )
LUT_regridded = LUT[, setNames(.(mean( get(vnm), na.rm=TRUE) ), vnm), by=.(LU_map) ]
LOCS[[ vnm ]] = LUT_regridded[ match( LOCS$AUID, LUT_regridded$LU_map ), vnm, with=FALSE ]
}
}
# revert LOCS to original structure and add the vars to it
if (!is.null(LOCS0)) {
# summarize LOCS to to original AUID's
if ( "sf" %in% class(LOCS) ) st_geometry(LOCS) = NULL
LOCS = as.data.table( LOCS )
# o = LOCS[, lapply(.SD, mean, na.rm=TRUE), by=AUID, .SDcols=variable_name]
o = LOCS[, setNames(.(mean( get(variable_name), na.rm=TRUE) ), variable_name), by=AUID ]
LOCS0[,variable_name] = o[ match( LOCS0$AUID, o$AUID), .SD, .SDcols=variable_name ]
LOCS = LOCS0
}
}
if ( project_class %in% c("carstm" ) & output_format == "points" ) {
if (is.null(LUT_AU)) LUT_AU = LUT$sppoly
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = st_cast( LUT_AU, "MULTIPOLYGON")
# LUT_AU = st_cast(LUT_AU, "POLYGON" )
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = sf::st_transform( LUT_AU, crs=st_crs(pL$aegis_proj4string_planar_km) )
if (!exists("AUID", LUT_AU)) {
message ("AUID not found in LOCS_AU polygons, setting AUID as row number of polygons")
LUT_AU$AUID = as.character(LUT_AU$au_index)
}
bm = match( LUT_AU$AUID, LUT$space )
if (exists("lon", LOCS)) {
LOCS = sf::st_as_sf( LOCS, coords=c("lon", "lat") )
st_crs(LOCS) = st_crs( projection_proj4string("lonlat_wgs84") )
LOCS = sf::st_transform( LOCS, crs=st_crs(pL$aegis_proj4string_planar_km) )
} else if (exists("plon", LOCS)) {
LOCS = sf::st_as_sf( LOCS, coords=c("lon", "lat") )
st_crs(LOCS) = st_crs(pL$aegis_proj4string_planar_km)
}
LOCS$AUID = st_points_in_polygons( pts=LOCS, polys = LUT_AU[, "AUID"], varname= "AUID" )
ii = match( LOCS$AUID, LUT$space[bm] )
for (g in 1:length(statvars)) {
stat_var = statvars[g]
for (h in 1:length(variable_name) ) {
vnh = variable_name[[h]]
if (exists(vnh[[1]], LUT)) {
vnm = paste( paste0(vnh, collapse="_"), stat_var, sep="_" )
LUT_AU[[vnm]] = carstm_results_unpack( LUT, vnh ) [ bm, stat_var ]
LOCS[[vnm]] = LUT_AU[[vnm]] [ ii ]
}
}
}
}
if ( project_class %in% c("carstm") & output_format == "areal_units" ) {
if (is.null(LUT_AU)) LUT_AU = LUT$sppoly
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = st_cast( LUT_AU, "MULTIPOLYGON")
# LUT_AU = st_cast(LUT_AU, "POLYGON" )
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = sf::st_transform( LUT_AU, crs=st_crs(pL$aegis_proj4string_planar_km) )
if (!exists("AUID", LUT_AU)) LUT_AU$AUID = as.character(1:nrow(LUT_AU))
bm = match( LUT_AU$AUID, LUT$space ) # should not be required but just in case things are subsetted
# lut_uid is A LOCAL index of LUT_AU /LUT .. rasterize it
LUT_AU$lut_uid = 1:nrow(LUT_AU)
LUT_AU_raster = stars::st_rasterize( LUT_AU["lut_uid"], dx=space_resolution, dy=space_resolution )
LUT_AU_pts = sf::st_as_sf( LUT_AU_raster, as_points=TRUE, na.rm=FALSE )
st_crs(LUT_AU_pts) = st_crs( LUT_AU )
# format output polygon structure
LOCS_AU = sf::st_transform( LOCS_AU, crs=st_crs(LUT_AU) ) # LOCS_AU .... must be sent ... <---------
LOCS_AU = st_make_valid(LOCS_AU)
LOCS_AU = st_buffer( LOCS_AU, 0 )
LOCS_AU = st_cast( LOCS_AU, "MULTIPOLYGON")
# LOCS_AU = st_cast( LOCS_AU, "POLYGON")
if (!exists("AUID", LOCS_AU)) {
message ("AUID not found in the polygons, setting AUID as row number of polygons")
LOCS_AU$AUID = as.character(1:nrow(LOCS_AU))
}
if (! inherits(LOCS, "sf") ) {
if (exists("lon", LOCS )) {
LOCS = st_as_sf( LOCS, coords=c("lon","lat"), crs=st_crs(projection_proj4string("lonlat_wgs84")) )
LOCS = sf::st_transform( LOCS, crs=st_crs(pL$aegis_proj4string_planar_km) )
if (!exists("AUID", LOCS )) LOCS[["AUID"]] = st_points_in_polygons( pts=LOCS, polys=LOCS_AU[, "AUID"], varname= "AUID" )
}
}
# covert LUT_AU to LOCS_AU
# id membership of LOCS in LOCS_AU
# id membership of LUT raster in LOCS_AU
LUT_AU_pts_LOCS_AU_AUID = st_points_in_polygons( pts=LUT_AU_pts, polys=LOCS_AU[,"AUID"], varname="AUID" )
pts_AU = match(LUT_AU_pts$lut_uid, LUT_AU$lut_uid[match(LUT$space, LUT_AU$AUID)] ) ## (layer==lut_uid) -- to -- LUT
aggFUN = function( LUV ) tapply(X=LUV, INDEX=LUT_AU_pts_LOCS_AU_AUID, FUN=FUNC, na.rm=TRUE)
for (g in 1:length(statvars)) {
stat_var = statvars[g]
for (h in 1:length(variable_name) ) {
vnh = variable_name[[h]]
if (exists(vnh[[1]], LUT)) {
vnm = paste( paste0(vnh, collapse="_"), stat_var, sep="_" )
o = carstm_results_unpack( LUT, vnh )
kk = length(dim(o))
if (kk == 2) {
ov = o[ pts_AU, which(dimnames(o)$stat == stat_var) ]
LUT_as_LOCS_AU = aggFUN( ov)
space_index = match( as.character(LOCS$AUID), as.character(dimnames(LUT_as_LOCS_AU )[[1]] ) ) # AUID of LOCS_AU (from LUT_AU_pts_AUID)
if (all(is.na(space_index))) {
LOCS[,vnm] = LUT_as_LOCS_AU # fiddling required when only 1 AU
} else {
LOCS[,vnm] = LUT_as_LOCS_AU[ space_index ]
}
}
}
}
}
}
}
######################################################
if (pL$dimensionality =="space-time" ) {
if ( project_class %in% c("core", "stmv", "hybrid") & output_format == "points" ) {
if (!exists("plon", LUT)) LUT = lonlat2planar(LUT, proj.type=pL$aegis_proj4string_planar_km)
if (!exists("plon", LOCS)) LOCS = lonlat2planar(LOCS, proj.type=pL$aegis_proj4string_planar_km) # get planar projections of lon/lat in km
if (!exists("dyear", LOCS) | (!exists("yr", LOCS)) ) {
LOCS$tiyr = lubridate::decimal_date( LOCS$timestamp )
LOCS$yr = trunc( LOCS$tiyr )
LOCS$dyear = LOCS$tiyr - LOCS$yr
}
LOCS$tplon = trunc(LOCS$plon / space_resolution + 1 ) * space_resolution
LOCS$tplat = trunc(LOCS$plat / space_resolution + 1 ) * space_resolution
LOCS$tdyear = trunc(LOCS$dyear / time_resolution + 1 ) * time_resolution
nY = diff( range(LUT$yr) )
nW = round(1/time_resolution)
Tdims = c( nY, nW )
Tres = c(1, time_resolution)
Torigin = c( min(LUT$yr), 0)
plon_range = range( LUT$plon )
plat_range = range( LUT$plat )
plons = seq(plon_range[1], plon_range[2], by=space_resolution)
plats = seq(plat_range[1], plat_range[2], by=space_resolution)
Sdims = c(length(plons), length(plats))
Sres = c(space_resolution, space_resolution)
Sorigin = c( plon_range[1], plat_range[1] )
ii = match(
paste(
array_map( "xy->1", LOCS[, c("tplon","tplat")], dims=Sdims, res=Sres, origin=Sorigin ),
array_map( "ts->1", LOCS[, c("yr", "tdyear")], dims=Tdims, res=Tres, origin=Torigin ),
sep="_"
),
paste(
array_map( "xy->1", LUT[,c("plon","plat")], dims=Sdims, res=Sres, origin=Sorigin ),
array_map( "ts->1", LUT[,c("yr", "dyear")], dims=Tdims, res=Tres, origin=Torigin ),
sep="_"
)
)
LOCS$tplon = LOCS$tplat = LOCS$tdyear = NULL
gc()
for (vnm in variable_name) {
if ( vnm %in% names(LUT )) {
LOCS[[vnm]] = NA
LOCS[[vnm]] = LUT[ ii, vnm ]
}
}
}
if ( project_class %in% c("core", "stmv", "hybrid") & output_format == "areal_units" ) {
if (exists("lon", LUT)) {
LUT = sf::st_as_sf( LUT, coords=c("lon", "lat") )
st_crs(LUT) = st_crs( projection_proj4string("lonlat_wgs84") )
} else if (exists("plon", LUT)) {
LUT = sf::st_as_sf( LUT, coords=c("plon", "plat") )
st_crs(LUT) = st_crs(pL$aegis_proj4string_planar_km)
}
Tdims = c( diff( range(LUT$yr) ), pL$nw )
Tres = c(1, pL$tres)
Torigin = c( min(LUT$yr), 0 )
Sdims = c( pL$nplons, pL$nplats )
Sres = c( pL$pres, pL$pres )
Sorigin = pL$origin
if (!exists("AUID", LOCS_AU)) {
message ("AUID not found in LOCS_AU polygons, setting AUID as row number of polygons")
LOCS_AU$AUID = as.character(1:nrow(LOCS_AU))
}
if ( ! "sf" %in% class(LOCS) ) {
LOCS = st_as_sf( LOCS, coords=c("lon","lat"), crs=st_crs(projection_proj4string("lonlat_wgs84")) )
}
LOCS_AU = sf::st_transform( LOCS_AU, crs=st_crs(LUT) )
if (! inherits(LOCS$timestamp, "POSIXct") ) LOCS$timestamp = lubridate::date_decimal( LOCS$timestamp, tz=tz )
if (! exists("yr", LOCS) ) LOCS$yr = lubridate::year(LOCS$timestamp)
LU_map = paste(
st_points_in_polygons( pts=LUT, polys=LOCS_AU[, "AUID"], varname= "AUID" ),
array_map( "ts->1", LUT[,c("yr", "dyear")], dims=Tdims, res=Tres, origin=Torigin ),
sep="_"
)
LOCS_map = paste(
st_points_in_polygons( pts=LOCS, polys = LOCS_AU[, "AUID"], varname= "AUID" ),
array_map( "ts->1", LOCS[, c("yr", "tdyear")], dims=Tdims, res=Tres, origin=Torigin ),
sep="_"
)
LUT = setDT(st_drop_geometry(LUT))
for (vnm in variable_name) {
if ( vnm %in% names(LUT )) {
# LUT_regridded = tapply( st_drop_geometry(LUT)[, vnm], LU_map, FUN=FUNC, na.rm=TRUE )
LUT_regridded = LUT[, setNames(.(mean( get(vnm), na.rm=TRUE) ), vnm), by=.(LU_map) ]
LOCS[[ vnm ]] = LUT_regridded[ match( LOCS$AUID, LUT_regridded$LU_map ), vnm, with=FALSE ]
}
}
}
if ( project_class %in% c("carstm" ) & output_format == "points" ) {
# discretize LUT_AU to LOCS_AU and then re-estimate means by LOCS_AU$AUID then tag each estimate to AUID of LOCS
ny = length(LUT$time)
yr0 = min(as.numeric(LUT$time))
if (is.null(LUT_AU)) LUT_AU = LUT$sppoly
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = st_cast( LUT_AU, "MULTIPOLYGON")
# LUT_AU = st_cast(LUT_AU, "POLYGON" )
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = sf::st_transform( LUT_AU, crs=st_crs(pL$aegis_proj4string_planar_km) )
LUT_AU$au_index = 1:nrow(LUT_AU)
if (!exists("AUID", LUT_AU)) {
message ("AUID not found in LOCS_AU polygons, setting AUID as row number of polygons")
LUT_AU$AUID = as.character(LUT_AU$au_index)
}
bm = match( LUT_AU$AUID, LUT$space )
if (exists("lon", LOCS)) {
LOCS = sf::st_as_sf( LOCS, coords=c("lon", "lat") )
st_crs(LOCS) = st_crs( projection_proj4string("lonlat_wgs84") )
LOCS = sf::st_transform( LOCS, crs=st_crs(pL$aegis_proj4string_planar_km) )
} else if (exists("plon", LOCS)) {
LOCS = sf::st_as_sf( LOCS, coords=c("lon", "lat") )
st_crs(LOCS) = st_crs(pL$aegis_proj4string_planar_km)
}
LOCS$AUID = st_points_in_polygons( pts=LOCS, polys = LUT_AU[, "AUID"], varname= "AUID" )
if (! inherits(LOCS$timestamp, "POSIXct") ) LOCS$timestamp = lubridate::date_decimal( LOCS$timestamp, tz=tz )
if (! exists("yr", LOCS) ) LOCS$yr = lubridate::year(LOCS$timestamp)
ii = cbind( match( LOCS$AUID, LUT$space[bm] ) )
jj = cbind(
ii,
array_map( "ts->year_index", LOCS[["yr"]], dims=c(ny ), res=c( 1 ), origin=c( yr0 ) )
)
for (g in 1:length(statvars)) {
stat_var = statvars[g]
for (h in 1:length(variable_name) ) {
vnh = variable_name[[h]]
if (exists(vnh[[1]], LUT)) {
vnm = paste( paste0(vnh, collapse="_"), stat_var, sep="_" )
o = carstm_results_unpack( LUT, vnh )
kk = length(dim(o))
if (kk == 2) LOCS[[vnm]] = o[ cbind(ii, which(dimnames(o)$stat == stat_var) ) ]
if (kk == 3) LOCS[[vnm]] = o[ cbind(jj, which(dimnames(o)$stat == stat_var) ) ]
}
}
}
}
if ( project_class %in% c("carstm") & output_format == "areal_units" ) {
# discretize LUT_AU to LOCS_AU and then re-estimate means by LOCS_AU$AUID then tag each estimate to AUID of LOCS
# from source data: LUT = modelled predictions; LUT_AU are associated areal units linked by "AUID"
# nw = length(LUT$dyear)
# format coordinate systems
if (is.null(LUT_AU)) LUT_AU = LUT$sppoly
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = st_cast( LUT_AU, "MULTIPOLYGON")
# LUT_AU = st_cast(LUT_AU, "POLYGON" )
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = sf::st_transform( LUT_AU, crs=st_crs(pL$aegis_proj4string_planar_km) )
# dims
ny = length(LUT$time)
yr0 = min(as.numeric(LUT$time))
if (!exists("AUID", LUT_AU)) LUT_AU$AUID = as.character(1:nrow(LUT_AU))
bm = match( LUT_AU$AUID, LUT$space ) # should not be required but just in case things are subsetted
# lut_uid is A LOCAL index of LUT_AU /LUT .. rasterize it
LUT_AU$lut_uid = 1:nrow(LUT_AU)
LUT_AU_raster = stars::st_rasterize( LUT_AU["lut_uid"], dx=space_resolution, dy=space_resolution )
LUT_AU_pts = sf::st_as_sf( LUT_AU_raster, as_points=TRUE, na.rm=FALSE )
st_crs(LUT_AU_pts) = st_crs( LUT_AU )
# format output polygon structure
LOCS_AU = sf::st_transform( LOCS_AU, crs=st_crs(LUT_AU) ) # LOCS_AU .... must be sent ... <---------
LOCS_AU = st_make_valid(LOCS_AU)
LOCS_AU = st_buffer( LOCS_AU, 0 )
LOCS_AU = st_cast( LOCS_AU, "MULTIPOLYGON")
# LOCS_AU = st_cast( LOCS_AU, "POLYGON")
if (!exists("AUID", LOCS_AU)) {
message ("AUID not found in the LOCS_AU polygons, setting AUID as row number of polygons")
LOCS_AU$AUID = as.character(1:nrow(LOCS_AU))
}
if (! inherits(LOCS, "sf") ) {
if (exists("lon", LOCS )) {
LOCS = st_as_sf( LOCS, coords=c("lon","lat"), crs=st_crs(projection_proj4string("lonlat_wgs84")) )
LOCS = sf::st_transform( LOCS, crs=st_crs(pL$aegis_proj4string_planar_km) )
if (!exists("AUID", LOCS )) LOCS[["AUID"]] = st_points_in_polygons( pts=LOCS, polys=LOCS_AU[, "AUID"], varname= "AUID" )
}
}
if (! inherits(LOCS$timestamp, "POSIXct") ) LOCS$timestamp = lubridate::date_decimal( LOCS$timestamp, tz=tz )
if (! exists("yr", LOCS) ) LOCS$yr = lubridate::year(LOCS$timestamp)
TIMESTAMP_index1 = array_map( "ts->year_index", LOCS[["yr"]], dims=c(ny ), res=c( 1 ), origin=c( yr0 ) )
if (any( TIMESTAMP_index1 < 0)) {
TIMESTAMP_index1[ which( TIMESTAMP_index1 <= 0 ) ] = NA
}
# id membership of LUT raster in LOCS_AU
LUT_AU_pts_LOCS_AU_AUID = st_points_in_polygons( pts=LUT_AU_pts, polys=LOCS_AU[,"AUID"], varname="AUID" )
pts_AU = match(LUT_AU_pts$lut_uid, LUT_AU$lut_uid[match(LUT$space, LUT_AU$AUID)] ) ## (layer==lut_uid) -- to -- LUT
aggFUN = function( LUV ) {
tapply(X=LUV, INDEX=LUT_AU_pts_LOCS_AU_AUID, FUN=FUNC, na.rm=TRUE)
}
for (g in 1:length(statvars)) {
stat_var = statvars[g]
for (h in 1:length(variable_name) ) {
vnh = variable_name[[h]]
if (exists(vnh[[1]], LUT)) {
vnm = paste( paste0(vnh, collapse="_"), stat_var, sep="_" )
o = carstm_results_unpack( LUT, vnh )
kk = length(dim(o))
if (kk == 2) {
ov = o[ pts_AU, which(dimnames(o)$stat == stat_var) ]
LUT_as_LOCS_AU = aggFUN( ov)
space_index = match( as.character(LOCS$AUID), as.character(dimnames(LUT_as_LOCS_AU )[[1]] ) ) # AUID of LOCS_AU (from LUT_AU_pts_AUID)
if (all(is.na(space_index))) {
LOCS[,vnm] = LUT_as_LOCS_AU # fiddling required when only 1 AU
} else {
LOCS[,vnm] = LUT_as_LOCS_AU[ space_index ]
}
}
if (kk == 3) {
ov = o[ pts_AU,, which(dimnames(o)$stat == stat_var) ]
LUT_as_LOCS_AU = apply( ov, MARGIN=c(2), FUN=aggFUN )
space_index = match( as.character(LOCS$AUID), as.character(dimnames(LUT_as_LOCS_AU )[[1]] ) ) # AUID of LOCS_AU (from LUT_AU_pts_AUID)
if (all(is.na(space_index))) {
LOCS[,vnm] = LUT_as_LOCS_AU[ TIMESTAMP_index1 ] # fiddling required when only 1 AU
} else {
LOCS[,vnm] = LUT_as_LOCS_AU[ cbind( space_index, TIMESTAMP_index1 ) ]
}
}
}
}
}
}
} # end dimension
######################################################
if (pL$dimensionality =="space-time-cyclic" ) {
if ( project_class %in% c("core", "stmv", "hybrid") & output_format == "points" ) {
if (!exists("plon", LOCS)) LOCS = lonlat2planar(LOCS, proj.type=pL$aegis_proj4string_planar_km) # get planar projections of lon/lat in km
if (!exists("plon", LUT)) LUT = lonlat2planar(LUT, proj.type=pL$aegis_proj4string_planar_km)
if (! inherits(LOCS$timestamp, "POSIXct") ) LOCS$timestamp = lubridate::date_decimal( LOCS$timestamp, tz=tz )
if (!exists("dyear", LOCS) | (!exists("yr", LOCS)) ) {
LOCS$tiyr = lubridate::decimal_date( LOCS$timestamp )
LOCS$yr = trunc( LOCS$tiyr )
LOCS$dyear = LOCS$tiyr - LOCS$yr
}
LOCS$tplon = trunc(LOCS$plon / space_resolution + 1 ) * space_resolution
LOCS$tplat = trunc(LOCS$plat / space_resolution + 1 ) * space_resolution
LOCS$tdyear = trunc(LOCS$dyear / time_resolution + 1 ) * time_resolution
nY = diff( range(LUT$yr) )
nW = round(1/time_resolution)
Tdims = c( nY, nW )
Tres = c(1, time_resolution)
Torigin = c( min(LUT$yr), 0)
plon_range = range( LUT$plon )
plat_range = range( LUT$plat )
plons = seq(plon_range[1], plon_range[2], by=space_resolution)
plats = seq(plat_range[1], plat_range[2], by=space_resolution)
Sdims = c(length(plons), length(plats))
Sres = c(space_resolution, space_resolution)
Sorigin = c( plon_range[1], plat_range[1] )
ii = match(
paste(
array_map( "xy->1", LOCS[, c("tplon","tplat")], dims=Sdims, res=Sres, origin=Sorigin ),
array_map( "ts->1", LOCS[, c("yr", "tdyear")], dims=Tdims, res=Tres, origin=Torigin ),
sep="_"
),
paste(
array_map( "xy->1", LUT[,c("plon","plat")], dims=Sdims, res=Sres, origin=Sorigin ),
array_map( "ts->1", LUT[,c("yr", "dyear")], dims=Tdims, res=Tres, origin=Torigin ),
sep="_"
)
)
LOCS$tplon = LOCS$tplat = LOCS$tdyear = NULL
gc()
for (vnm in variable_name) {
if ( vnm %in% names(LUT )) {
LOCS[[vnm]] = NA
LOCS[[vnm]] = LUT[ ii, vnm ]
}
}
}
if ( project_class %in% c("core", "stmv", "hybrid") & output_format == "areal_units" ) {
if (exists("lon", LUT)) {
LUT = sf::st_as_sf( LUT, coords=c("lon", "lat") )
st_crs(LUT) = st_crs( projection_proj4string("lonlat_wgs84") )
} else if (exists("plon", LUT)) {
LUT = sf::st_as_sf( LUT, coords=c("plon", "plat") )
st_crs(LUT) = st_crs(pL$aegis_proj4string_planar_km)
}
Tdims = c( diff( range(LUT$yr) ), pL$nw )
Tres = c(1, pL$tres)
Torigin = c( min(LUT$yr), 0 )
Sdims = c( pL$nplons, pL$nplats )
Sres = c( pL$pres, pL$pres )
Sorigin = pL$origin
if (!exists("AUID", LOCS_AU)) {
message ("AUID not found in LOCS_AU polygons, setting AUID as row number of polygons")
LOCS_AU$AUID = as.character(1:nrow(LOCS_AU))
}
if ( ! "sf" %in% class(LOCS) ) {
LOCS = st_as_sf( LOCS, coords=c("lon","lat"), crs=st_crs(projection_proj4string("lonlat_wgs84")) )
}
LOCS_AU = sf::st_transform( LOCS_AU, crs=st_crs(LUT) )
if (! inherits(LOCS$timestamp, "POSIXct") ) LOCS$timestamp = lubridate::date_decimal( LOCS$timestamp, tz=tz )
if (! exists("yr", LOCS) )LOCS$yr = lubridate::year(LOCS$timestamp)
if (! exists("dyear", LOCS) ) LOCS$dyear = lubridate::decimal_date( LOCS$timestamp ) - LOCS$yr
LU_map = paste(
st_points_in_polygons( pts=LUT, polys=LOCS_AU[, "AUID"], varname= "AUID" ),
array_map( "ts->1", st_drop_geometry( LUT) [,c("yr", "dyear")], dims=Tdims, res=Tres, origin=Torigin),
sep="_"
)
LOCS_map = paste(
st_points_in_polygons( pts=LOCS, polys = LOCS_AU[, "AUID"], varname= "AUID" ),
array_map( "ts->1", st_drop_geometry(LOCS)[ , c("yr", "dyear") ], dims=Tdims, res=Tres, origin=Torigin),
sep="_"
)
LUT = setDT(st_drop_geometry(LUT))
for (vnm in variable_name) {
if ( vnm %in% names(LUT )) {
# LUT_regridded = tapply( st_drop_geometry(LUT)[, vnm], LU_map, FUN=FUNC, na.rm=TRUE )
LUT_regridded = LUT[, setNames(.(mean( get(vnm), na.rm=TRUE) ), vnm), by=.(LU_map) ]
LOCS[[ vnm ]] = LUT_regridded[ match( LOCS$AUID, LUT_regridded$LU_map ), vnm, with=FALSE ]
}
}
}
if ( project_class %in% c("carstm" ) & output_format == "points" ) {
# areal unit (LUT) to points (LOCS)
nw = length(LUT$cyclic)
ny = length(LUT$time)
yr0 = min(as.numeric(LUT$time))
if (is.null(LUT_AU)) LUT_AU = LUT$sppoly
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = st_cast( LUT_AU, "MULTIPOLYGON") # causes additional polys ..
# LUT_AU = st_cast( LUT_AU, "POLYGON" )
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = sf::st_transform( LUT_AU, crs=st_crs(pL$aegis_proj4string_planar_km) )
LUT_AU$au_index = 1:nrow(LUT_AU)
if (!exists("AUID", LUT_AU)) {
message ("AUID not found in LOCS_AU polygons, setting AUID as row number of polygons")
LUT_AU$AUID = as.character(LUT_AU$au_index)
}
bm = match( LUT_AU$AUID, LUT$space )
if (exists("lon", LOCS)) {
LOCS = sf::st_as_sf( LOCS, coords=c("lon", "lat") )
st_crs(LOCS) = st_crs( projection_proj4string("lonlat_wgs84") )
LOCS = sf::st_transform( LOCS, crs=st_crs(pL$aegis_proj4string_planar_km) )
} else if (exists("plon", LOCS)) {
LOCS = sf::st_as_sf( LOCS, coords=c("lon", "lat") )
st_crs(LOCS) = st_crs(pL$aegis_proj4string_planar_km)
}
LOCS$AUID = st_points_in_polygons( pts=LOCS, polys = LUT_AU[, "AUID"], varname= "AUID" )
if (! inherits(LOCS$timestamp, "POSIXct") ) LOCS$timestamp = lubridate::date_decimal( LOCS$timestamp, tz=tz )
if (! exists("yr", LOCS) ) LOCS$yr = lubridate::year(LOCS$timestamp)
if (! exists("dyear", LOCS) ) LOCS$dyear = lubridate::decimal_date( LOCS$timestamp ) - LOCS$yr
ii = cbind( match( LOCS$AUID, LUT$space[bm] ) )
jj = cbind(
ii,
array_map( "ts->year_index", LOCS[["yr"]], dims=c(ny ), res=c( 1 ), origin=c( yr0 ) )
)
LOCS_DF = LOCS
if (inherits(LOCS_DF, "sf")) LOCS_DF = st_drop_geometry(LOCS_DF)
ll = cbind(
ii,
array_map( "ts->2", LOCS_DF[, c("yr", "dyear")], dims=c(ny, nw), res=c( 1, 1/nw ), origin=c( yr0, 0) )
)
LOCS_DF = NULL
for (g in 1:length(statvars)) {
stat_var = statvars[g]
for (h in 1:length(variable_name) ) {
vnh = variable_name[[h]]
if (exists(vnh[[1]], LUT)) {
vnm = paste( paste0(vnh, collapse="_"), stat_var, sep="_" )
o = carstm_results_unpack( LUT, vnh )
kk = length(dim(o))
if (kk == 2) LOCS[[vnm]] = o[ cbind(ii, which(dimnames(o)$stat == stat_var) ) ]
if (kk == 3) LOCS[[vnm]] = o[ cbind(jj, which(dimnames(o)$stat == stat_var) ) ]
if (kk == 4) LOCS[[vnm]] = o[ cbind(ll, which(dimnames(o)$stat == stat_var) ) ]
}
}
}
}
if ( project_class %in% c("carstm") & output_format == "areal_units" ) {
# areal unit (LUT) to areal units (LUT_AU/LOCS)
# from source data: LUT = modelled predictions; LUT_AU are associated areal units linked by "AUID"
# format coordinate systems
if (is.null(LUT_AU)) LUT_AU = LUT$sppoly
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = st_cast( LUT_AU, "MULTIPOLYGON")
# LUT_AU = st_cast (LUT_AU, "POLYGON" )
LUT_AU = st_make_valid(LUT_AU)
LUT_AU = sf::st_transform( LUT_AU, crs=st_crs(pL$aegis_proj4string_planar_km) )
nw = length(LUT$cyclic)
ny = length(LUT$time)
yr0 = min(as.numeric(LUT$time))
if (!exists("AUID", LUT_AU)) LUT_AU$AUID = as.character(1:nrow(LUT_AU))
bm = match( LUT_AU$AUID, LUT$space ) # should not be required but just in case things are subsetted
# lut_uid is A LOCAL index of LUT_AU /LUT .. rasterize it
LUT_AU$lut_uid = 1:nrow(LUT_AU)
LUT_AU_raster = stars::st_rasterize( LUT_AU["lut_uid"], dx=space_resolution, dy=space_resolution )
LUT_AU_pts = sf::st_as_sf( LUT_AU_raster, as_points=TRUE, na.rm=FALSE )
st_crs(LUT_AU_pts) = st_crs( LUT_AU )
# format output polygon structure
LOCS_AU = sf::st_transform( LOCS_AU, crs=st_crs(LUT_AU) ) # LOCS_AU .... must be sent ... <---------
LOCS_AU = st_make_valid(LOCS_AU)
LOCS_AU = st_buffer( LOCS_AU, 0 )
LOCS_AU = st_cast( LOCS_AU, "MULTIPOLYGON")
# LOCS_AU = st_cast( LOCS_AU, "POLYGON")
if (!exists("AUID", LOCS_AU)) {
message ("AUID not found in the LOCS_AU polygons, setting AUID as row number of polygons")
LOCS_AU$AUID = as.character(1:nrow(LOCS_AU))
}
if (! inherits(LOCS, "sf") ) {
if (exists("lon", LOCS )) {
LOCS = st_as_sf( LOCS, coords=c("lon","lat"), crs=st_crs(projection_proj4string("lonlat_wgs84")) )
LOCS = sf::st_transform( LOCS, crs=st_crs(pL$aegis_proj4string_planar_km) )
if (!exists("AUID", LOCS )) LOCS[["AUID"]] = st_points_in_polygons( pts=LOCS, polys=LOCS_AU[, "AUID"], varname= "AUID" )
}
}
if (! inherits(LOCS$timestamp, "POSIXct") ) LOCS$timestamp = lubridate::date_decimal( LOCS$timestamp, tz=tz )
if (! exists("yr", LOCS) ) LOCS$yr = lubridate::year(LOCS$timestamp)
if (! exists("dyear", LOCS) ) LOCS$dyear = lubridate::decimal_date( LOCS$timestamp ) - LOCS$yr
LOCS_DF = LOCS
if (inherits(LOCS_DF, "sf")) LOCS_DF = st_drop_geometry(LOCS_DF)
TIMESTAMP_index1 = array_map( "ts->year_index", LOCS_DF[, "yr"], dims=c(ny ), res=c( 1 ), origin=c( yr0 ) )
TIMESTAMP_index2 = array_map( "ts->2", LOCS_DF[, c("yr", "dyear")], dims=c(ny, nw), res=c( 1, 1/nw ), origin=c( yr0, 0) )
if (any( TIMESTAMP_index1 < 0)) {
TIMESTAMP_index1[ which( TIMESTAMP_index1 <= 0 ) ] = NA
}
if (any( TIMESTAMP_index2 < 0)) {
warning ("cyclic time index is negative: lookup table does not contain data to lookup ... \n
lookup data needs to be expanded or time periods reduced in model")
TIMESTAMP_index2[ which( TIMESTAMP_index2 <= 0 ) ] = NA
}
LOCS_DF = NULL
# id membership of LUT raster in LOCS_AU
LUT_AU_pts_LOCS_AU_AUID = st_points_in_polygons( pts=LUT_AU_pts, polys=LOCS_AU[,"AUID"], varname="AUID" )
pts_AU = match(LUT_AU_pts$lut_uid, LUT_AU$lut_uid[match(LUT$space, LUT_AU$AUID)] ) ## (layer==lut_uid) -- to -- LUT
aggFUN = function( LUV ) {
tapply(X=LUV, INDEX=LUT_AU_pts_LOCS_AU_AUID, FUN=FUNC, na.rm=TRUE)
}
for (g in 1:length(statvars)) {
stat_var = statvars[g]
for (h in 1:length(variable_name) ) {
vnh = variable_name[[h]]
if (exists(vnh[[1]], LUT)) {
vnm = paste( paste0(vnh, collapse="_"), stat_var, sep="_" )
o = carstm_results_unpack( LUT, vnh )
kk = length(dim(o))
if (kk == 2) {
ov = o[ pts_AU, which(dimnames(o)$stat == stat_var) ]
LUT_as_LOCS_AU = aggFUN( ov)
space_index = match( as.character(LOCS$AUID), as.character(dimnames(LUT_as_LOCS_AU )[[1]] ) ) # AUID of LOCS_AU (from LUT_AU_pts_AUID)
if (all(is.na(space_index))) {
LOCS[,vnm] = LUT_as_LOCS_AU # fiddling required when only 1 AU
} else {
LOCS[,vnm] = LUT_as_LOCS_AU[ space_index ]
}
}
if (kk == 3) {
ov = o[ pts_AU,, which(dimnames(o)$stat == stat_var) ]
LUT_as_LOCS_AU = apply( ov, MARGIN=c(2), FUN=aggFUN )
space_index = match( as.character(LOCS$AUID), as.character(dimnames(LUT_as_LOCS_AU )[[1]] ) ) # AUID of LOCS_AU (from LUT_AU_pts_AUID)
if (all(is.na(space_index))) {
LOCS[,vnm] = LUT_as_LOCS_AU[ TIMESTAMP_index1 ] # fiddling required when only 1 AU
} else {
LOCS[,vnm] = LUT_as_LOCS_AU[ cbind( space_index, TIMESTAMP_index1 ) ]
}
}
if (kk == 4) {
ov = o[ pts_AU,,, which(dimnames(o)$stat == stat_var) ]
LUT_as_LOCS_AU = apply( ov, MARGIN=c(2,3), FUN=aggFUN )
space_index = match( as.character(LOCS$AUID), as.character(dimnames(LUT_as_LOCS_AU )[[1]] ) ) # AUID of LOCS_AU (from LUT_AU_pts_AUID)
if (all(is.na(space_index))) {
LOCS[,vnm] = LUT_as_LOCS_AU[ TIMESTAMP_index2 ] # fiddling required when only 1 AU
} else {
LOCS[,vnm] = LUT_as_LOCS_AU[ cbind( space_index, TIMESTAMP_index2 ) ]
}
}
}
}
}
}
} # end space-time-cyclic
if (returntype =="sf" ) {
if (! inherits(LOCS, "sf")) LOCS = st_as_sf( LOCS, coords=c("lon","lat"), crs=st_crs(projection_proj4string("lonlat_wgs84")) )
}
if (returntype =="data.frame" ) {
if (! inherits(LOCS, "data.frame")) LOCS = as.data.frame(LOCS)
}
if (returntype =="data.table" ) {
if (! inherits(LOCS, "data.table")) setDT(LOCS)
}
if (returntype =="vector" ) {
if (length(variable_name) == 1) {
if (project_class=="carstm") {
variable_name = paste( paste0(variable_name[[1]], collapse="_"), statvars[1], sep="_" )
}
if (exists( variable_name, LOCS)) {
LOCS = LOCS[[variable_name]]
} else {
LOCS = rep(NA, nrow(LOCS))
}
}
}
return(LOCS)
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.