mapNodeAverageLayerFiles: Generate maps from averaging stochastic DISPLACE spatial...
In frabas/displaceplot: A suite of R routines to treat DISPLACE simulation output files
Description
Usage
Arguments
Examples
View source: R/mapNodeAverageLayerFiles.R
Description
This function generates maps from an average layer as a second step after call to getAggNodesLayerFiles()
Usage
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mapNodeAverageLayerFiles(general, a_type = "cumcatches", a_type2 = "",
func = "ratio", field_pos = 4, a_pop = "",
the_baseline = "svana_baseline",
selected_scenarios_for_plot = general$namefolderoutput,
selected_scenarios_for_table = general$namefolderoutput,
selected_areas_for_table = c("22", "23", "24", "25", "IIIa", "IVa",
"IVb", "IVc"), the_breaks_baseline = c(0.5, 1, round(exp(seq(0.5, 14,
by = 1.2))), 1e+06), the_breaks = c(rev(-round(exp(seq(0, 7, by =
1)))), 0, round(exp(seq(0, 7, by = 1)))), gis_shape = list(),
a_width = 3400, a_height = 3500, xlims = c(-1, 17), ylims = c(53,
60), xcell = 12, ycell = 17,
legend_text1 = "Total Catches kg per ")
Arguments
fname
First name
lname
Last name
Examples
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## Not run:
general <- setGeneralOverallVariable (pathToRawInputs =file.path("C:", "Users", "fbas",
"Documents", "GitHub", paste0("DISPLACE_input_gis_",
"DanishFleet")),
pathToDisplaceInputs = file.path("C:", "Users", "fbas",
"Documents", "GitHub", paste0("DISPLACE_input_", "DanishFleet")),
pathToOutputs =file.path("C:","DISPLACE_outputs"),
caseStudy="DanishFleet",
iGraph=41,
iYear="2015",
iCountry="DEN",
nbPops=39,
nbSzgroup=14,
theScenarios= c("svana_baseline",
"svana_sub1mx20",
"svana_sub4mx20",
"svana_sub4mx5ns20bt",
"svana_sub4mx20ns5bt",
"svana_sub4mx5ns5bt" ),
nbSimus=20,
useSQLite=FALSE
)
# caution: could take a while...
getAggNodeLayerFiles (general, a_type="cumcatches", a_tstep="34321")
getAggNodeLayerFiles (general, a_type="cumsweptarea", a_tstep="34321")
library(maptools)
sh_coastlines <- readShapePoly(file.path('C:','Users','fbas','Documents','GitHub','DISPLACE_input_myfish','graphsspe', 'shp', 'francois_EU'),
proj4string=CRS("+proj=longlat +ellps=WGS84"))
ices_areas <- readShapePoly(file.path('C:','Users','fbas','Documents','GitHub','DISPLACE_input_raw','ices_areas','ices_areas'),
proj4string=CRS("+proj=longlat +ellps=WGS84"))
NSsub1mx20 <- readShapePoly(file.path('C:','Users','fbas','Documents','GitHub',
'DISPLACE_SVANAProject', 'Input for DISPLACE', 'NST2_sub1_mx20_wgs84'),
proj4string=CRS("+proj=longlat +ellps=WGS84"))
BSsub1mx20 <- readShapePoly(file.path('C:','Users','fbas','Documents','GitHub',
'DISPLACE_SVANAProject', 'Input for DISPLACE', 'BHT2_Sub1_Mx_20_wgs84'),
proj4string=CRS("+proj=longlat +ellps=WGS84"))
NSsub4mx20 <- readShapePoly(file.path('C:','Users','fbas','Documents','GitHub',
'DISPLACE_SVANAProject', 'Input for DISPLACE', 'NST2_sub4_mx_20_wgs84'),
proj4string=CRS("+proj=longlat +ellps=WGS84"))
BSsub4mx20 <- readShapePoly(file.path('C:','Users','fbas','Documents','GitHub',
'DISPLACE_SVANAProject', 'Input for DISPLACE', 'BHT2_Sub4_Mx_20LongTailedD_wgs84'),
proj4string=CRS("+proj=longlat +ellps=WGS84"))
NSsub4mx5 <- readShapePoly(file.path('C:','Users','fbas','Documents','GitHub',
'DISPLACE_SVANAProject', 'Input for DISPLACE', 'NST2_sub4_mx05_wgs84'),
proj4string=CRS("+proj=longlat +ellps=WGS84"))
BSsub4mx5 <- readShapePoly(file.path('C:','Users','fbas','Documents','GitHub',
'DISPLACE_SVANAProject', 'Input for DISPLACE', 'BHT2_Sub4_Mx_5LgtailedD_wgs84'),
proj4string=CRS("+proj=longlat +ellps=WGS84"))
mapNodeAverageLayerFiles (general, a_type="cumcatches", a_type2="", field_pos=4, the_baseline= "svana_baseline",
selected_scenarios_for_plot=general$namefolderoutput,
selected_scenarios_for_table=general$namefolderoutput,
selected_areas_for_table=c("22", "23", "24", "25", "IIIa", "IVa", "IVb", "IVc"),
the_breaks_baseline= c(0.5, 1, round(exp(seq(0.5, 14, by=1.1))), 1000000),
the_breaks=c(rev(-round(exp(seq(0, 7, by=1)))), 0, round(exp(seq(0, 7, by=1)))),
gis_shape=list(svana_baseline= list(sh_coastlines), # ices_areas),
svana_sub1mx20= list(NSsub1mx20, BSsub1mx20),
svana_sub4mx20= list(NSsub4mx20, BSsub4mx20),
svana_sub4mx5ns20bt= list(NSsub4mx5, BSsub4mx20),
svana_sub4mx20ns5bt= list(NSsub4mx20, BSsub4mx5),
svana_sub4mx5ns5bt= list(NSsub4mx5, BSsub4mx5)),
a_width= 3400, a_height =3500, xlims = c(-1, 17), ylims = c(53,60), xcell=12, ycell=17,
legend_text1="Total Catches kg per "
)
mapNodeAverageLayerFiles (general, a_type="cumcatches", a_type2="cumsweptarea", field_pos=4, the_baseline= "svana_baseline",
selected_scenarios_for_plot=general$namefolderoutput,
selected_scenarios_for_table=general$namefolderoutput,
selected_areas_for_table=c("22", "23", "24", "25", "IIIa", "IVa", "IVb", "IVc"),
the_breaks_baseline= c(0.5, 1, round(exp(seq(0.5, 14, by=1.1))), 1000000),
the_breaks=c(rev(-round(exp(seq(0, 7, by=1)))), 0, round(exp(seq(0, 7, by=1)))),
gis_shape=list(svana_baseline= list(sh_coastlines), # ices_areas),
svana_sub1mx20= list(NSsub1mx20, BSsub1mx20),
svana_sub4mx20= list(NSsub4mx20, BSsub4mx20),
svana_sub4mx5ns20bt= list(NSsub4mx5, BSsub4mx20),
svana_sub4mx20ns5bt= list(NSsub4mx20, BSsub4mx5),
svana_sub4mx5ns5bt= list(NSsub4mx5, BSsub4mx5)),
a_width= 3400, a_height =3500, xlims = c(-1, 17), ylims = c(53,60), xcell=12, ycell=17,
legend_text1="Total Catches kg per Swept Area km2 per "
)
mapNodeAverageLayerFiles (general, a_type="cumdiscards", a_type2="cumcatches", func="rate", field_pos=4, the_baseline= "svana_baseline",
selected_scenarios_for_plot=general$namefolderoutput,
selected_scenarios_for_table=general$namefolderoutput,
selected_areas_for_table=c("22", "23", "24", "25", "IIIa", "IVa", "IVb", "IVc"),
the_breaks_baseline= c(round((exp(seq(0.00, 0.6, by=0.04))-1),3), 1.1),
the_breaks=c(rev(-round(exp(seq(0, 7, by=1)))), 0, round(exp(seq(0, 7, by=1)))),
gis_shape=list(svana_baseline= list(sh_coastlines), # ices_areas),
svana_sub1mx20= list(NSsub1mx20, BSsub1mx20),
svana_sub4mx20= list(NSsub4mx20, BSsub4mx20),
svana_sub4mx5ns20bt= list(NSsub4mx5, BSsub4mx20),
svana_sub4mx20ns5bt= list(NSsub4mx20, BSsub4mx5),
svana_sub4mx5ns5bt= list(NSsub4mx5, BSsub4mx5)),
a_width= 3400, a_height =3500, xlims = c(-1, 17), ylims = c(53,60), xcell=12, ycell=17,
legend_text1="Discarded proportion"
)
## End(Not run)
frabas/displaceplot documentation built on May 3, 2019, 4:06 p.m.
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Description Usage Arguments Examples
View source: R/mapNodeAverageLayerFiles.R
Description
This function generates maps from an average layer as a second step after call to getAggNodesLayerFiles()
Usage
1 2 3 4 5 6 7 8 9 10 11 12 | mapNodeAverageLayerFiles(general, a_type = "cumcatches", a_type2 = "",
func = "ratio", field_pos = 4, a_pop = "",
the_baseline = "svana_baseline",
selected_scenarios_for_plot = general$namefolderoutput,
selected_scenarios_for_table = general$namefolderoutput,
selected_areas_for_table = c("22", "23", "24", "25", "IIIa", "IVa",
"IVb", "IVc"), the_breaks_baseline = c(0.5, 1, round(exp(seq(0.5, 14,
by = 1.2))), 1e+06), the_breaks = c(rev(-round(exp(seq(0, 7, by =
1)))), 0, round(exp(seq(0, 7, by = 1)))), gis_shape = list(),
a_width = 3400, a_height = 3500, xlims = c(-1, 17), ylims = c(53,
60), xcell = 12, ycell = 17,
legend_text1 = "Total Catches kg per ")
|
Arguments
fname |
First name |
lname |
Last name |
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 | ## Not run:
general <- setGeneralOverallVariable (pathToRawInputs =file.path("C:", "Users", "fbas",
"Documents", "GitHub", paste0("DISPLACE_input_gis_",
"DanishFleet")),
pathToDisplaceInputs = file.path("C:", "Users", "fbas",
"Documents", "GitHub", paste0("DISPLACE_input_", "DanishFleet")),
pathToOutputs =file.path("C:","DISPLACE_outputs"),
caseStudy="DanishFleet",
iGraph=41,
iYear="2015",
iCountry="DEN",
nbPops=39,
nbSzgroup=14,
theScenarios= c("svana_baseline",
"svana_sub1mx20",
"svana_sub4mx20",
"svana_sub4mx5ns20bt",
"svana_sub4mx20ns5bt",
"svana_sub4mx5ns5bt" ),
nbSimus=20,
useSQLite=FALSE
)
# caution: could take a while...
getAggNodeLayerFiles (general, a_type="cumcatches", a_tstep="34321")
getAggNodeLayerFiles (general, a_type="cumsweptarea", a_tstep="34321")
library(maptools)
sh_coastlines <- readShapePoly(file.path('C:','Users','fbas','Documents','GitHub','DISPLACE_input_myfish','graphsspe', 'shp', 'francois_EU'),
proj4string=CRS("+proj=longlat +ellps=WGS84"))
ices_areas <- readShapePoly(file.path('C:','Users','fbas','Documents','GitHub','DISPLACE_input_raw','ices_areas','ices_areas'),
proj4string=CRS("+proj=longlat +ellps=WGS84"))
NSsub1mx20 <- readShapePoly(file.path('C:','Users','fbas','Documents','GitHub',
'DISPLACE_SVANAProject', 'Input for DISPLACE', 'NST2_sub1_mx20_wgs84'),
proj4string=CRS("+proj=longlat +ellps=WGS84"))
BSsub1mx20 <- readShapePoly(file.path('C:','Users','fbas','Documents','GitHub',
'DISPLACE_SVANAProject', 'Input for DISPLACE', 'BHT2_Sub1_Mx_20_wgs84'),
proj4string=CRS("+proj=longlat +ellps=WGS84"))
NSsub4mx20 <- readShapePoly(file.path('C:','Users','fbas','Documents','GitHub',
'DISPLACE_SVANAProject', 'Input for DISPLACE', 'NST2_sub4_mx_20_wgs84'),
proj4string=CRS("+proj=longlat +ellps=WGS84"))
BSsub4mx20 <- readShapePoly(file.path('C:','Users','fbas','Documents','GitHub',
'DISPLACE_SVANAProject', 'Input for DISPLACE', 'BHT2_Sub4_Mx_20LongTailedD_wgs84'),
proj4string=CRS("+proj=longlat +ellps=WGS84"))
NSsub4mx5 <- readShapePoly(file.path('C:','Users','fbas','Documents','GitHub',
'DISPLACE_SVANAProject', 'Input for DISPLACE', 'NST2_sub4_mx05_wgs84'),
proj4string=CRS("+proj=longlat +ellps=WGS84"))
BSsub4mx5 <- readShapePoly(file.path('C:','Users','fbas','Documents','GitHub',
'DISPLACE_SVANAProject', 'Input for DISPLACE', 'BHT2_Sub4_Mx_5LgtailedD_wgs84'),
proj4string=CRS("+proj=longlat +ellps=WGS84"))
mapNodeAverageLayerFiles (general, a_type="cumcatches", a_type2="", field_pos=4, the_baseline= "svana_baseline",
selected_scenarios_for_plot=general$namefolderoutput,
selected_scenarios_for_table=general$namefolderoutput,
selected_areas_for_table=c("22", "23", "24", "25", "IIIa", "IVa", "IVb", "IVc"),
the_breaks_baseline= c(0.5, 1, round(exp(seq(0.5, 14, by=1.1))), 1000000),
the_breaks=c(rev(-round(exp(seq(0, 7, by=1)))), 0, round(exp(seq(0, 7, by=1)))),
gis_shape=list(svana_baseline= list(sh_coastlines), # ices_areas),
svana_sub1mx20= list(NSsub1mx20, BSsub1mx20),
svana_sub4mx20= list(NSsub4mx20, BSsub4mx20),
svana_sub4mx5ns20bt= list(NSsub4mx5, BSsub4mx20),
svana_sub4mx20ns5bt= list(NSsub4mx20, BSsub4mx5),
svana_sub4mx5ns5bt= list(NSsub4mx5, BSsub4mx5)),
a_width= 3400, a_height =3500, xlims = c(-1, 17), ylims = c(53,60), xcell=12, ycell=17,
legend_text1="Total Catches kg per "
)
mapNodeAverageLayerFiles (general, a_type="cumcatches", a_type2="cumsweptarea", field_pos=4, the_baseline= "svana_baseline",
selected_scenarios_for_plot=general$namefolderoutput,
selected_scenarios_for_table=general$namefolderoutput,
selected_areas_for_table=c("22", "23", "24", "25", "IIIa", "IVa", "IVb", "IVc"),
the_breaks_baseline= c(0.5, 1, round(exp(seq(0.5, 14, by=1.1))), 1000000),
the_breaks=c(rev(-round(exp(seq(0, 7, by=1)))), 0, round(exp(seq(0, 7, by=1)))),
gis_shape=list(svana_baseline= list(sh_coastlines), # ices_areas),
svana_sub1mx20= list(NSsub1mx20, BSsub1mx20),
svana_sub4mx20= list(NSsub4mx20, BSsub4mx20),
svana_sub4mx5ns20bt= list(NSsub4mx5, BSsub4mx20),
svana_sub4mx20ns5bt= list(NSsub4mx20, BSsub4mx5),
svana_sub4mx5ns5bt= list(NSsub4mx5, BSsub4mx5)),
a_width= 3400, a_height =3500, xlims = c(-1, 17), ylims = c(53,60), xcell=12, ycell=17,
legend_text1="Total Catches kg per Swept Area km2 per "
)
mapNodeAverageLayerFiles (general, a_type="cumdiscards", a_type2="cumcatches", func="rate", field_pos=4, the_baseline= "svana_baseline",
selected_scenarios_for_plot=general$namefolderoutput,
selected_scenarios_for_table=general$namefolderoutput,
selected_areas_for_table=c("22", "23", "24", "25", "IIIa", "IVa", "IVb", "IVc"),
the_breaks_baseline= c(round((exp(seq(0.00, 0.6, by=0.04))-1),3), 1.1),
the_breaks=c(rev(-round(exp(seq(0, 7, by=1)))), 0, round(exp(seq(0, 7, by=1)))),
gis_shape=list(svana_baseline= list(sh_coastlines), # ices_areas),
svana_sub1mx20= list(NSsub1mx20, BSsub1mx20),
svana_sub4mx20= list(NSsub4mx20, BSsub4mx20),
svana_sub4mx5ns20bt= list(NSsub4mx5, BSsub4mx20),
svana_sub4mx20ns5bt= list(NSsub4mx20, BSsub4mx5),
svana_sub4mx5ns5bt= list(NSsub4mx5, BSsub4mx5)),
a_width= 3400, a_height =3500, xlims = c(-1, 17), ylims = c(53,60), xcell=12, ycell=17,
legend_text1="Discarded proportion"
)
## End(Not run)
|
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