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Copy pathOrgKewauneePaper3Data.m
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OrgKewauneePaper3Data.m
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function [sSsRpathname,szS3,szSuse,jtog, szRt3]=OrgKewauneePaper3Data(pathname,sSsRpathname)
%% sS -- can make into cell arrays for option format
rr=sSsRpathname;
if exist(rr)
load(rr)
else
q1=sprintf('%s%s',pathname,'/KewauneeCode/Data/SourceandObservationcopy.mat');
q2=sprintf('%s%s',pathname,'/KewauneeCode/Data/SourceandObservation.mat');
q3=sprintf('%s%s',pathname,'/KewauneeCode/Data/WisclandPolygonFiles.mat');
load(q1)
load(q2)
load(q3)
d1=sprintf('%s%s',pathname,'/KewauneeCode/Data/ManureStorageSimFinal.mat');
d2=sprintf('%s%s',pathname,'/KewauneeCode/Data/WisclandData.mat');
d3=sprintf('%s%s',pathname,'/KewauneeCode/Data/DrainfieldsSimFinal.mat');
d4=sprintf('%s%s',pathname,'/KewauneeCode/Data/SanSystSimFinal.mat');
for i=1:27
SourceCase=i;
switch SourceCase
case 1 % Manure Storages + simulated counts per outer quadrant
load(d1,'zScountOUT','sSOUT')
sS=[sS_CAFO.Xsp sS_CAFO.Ysp;sSOUT];
zS1=sS_CAFO.lntotGal;
zS1(isnan(zS1))=nanmean(zS1);
zScountOUTltg=mean(zS1)*zScountOUT;
zS=[zS1;zScountOUTltg];
zS(isnan(zS))=0;
iS='Manure Storages w Sim Counts per Outer Quadrant';
catS='CAFO';
use=1;
rel='ManureApp';
case 2 % Crop Rotation (Area type)
dat=CropRoationAreas;
zS=lz(dat.Area,2);
sx=dat.Xsp;
sy=dat.Ysp;
sS=[sx sy];
iS='Crop Rotation (Area)';
catS='ManureApp';
use=1;
rel='na';
case 3 % Dairy Rotation Points
load(d2,'sS_CropRota')
idx=sS_CropRota.CLS_DESC_3=='Dairy Rotation';
sx=sS_CropRota.Xsp(idx);
sy=sS_CropRota.Ysp(idx);
sS=[sx sy];
zS=ones(size(sx));
iS='Dairy Rotation (Points)';
catS='ManureApp';
use=0;
rel='na';
case 4 % Manure storages without log total gallons
sS=[sS_CAFO.Xsp sS_CAFO.Ysp];
zS=ones(size(sS_CAFO.Xsp));
iS='Kewaunee Manure Storages (not weighted)';
catS='CAFO';
use=0;
rel='ManureApp';
case 5 % Manure storages without log total gallons real data and simulated outside
load(d1,'zScountOUT','sSOUT')
sS=[sS_CAFO.Xsp sS_CAFO.Ysp;sSOUT];
zS1=ones(size(sS_CAFO.Xsp));
zS=[zS1;zScountOUT];
zS(isnan(zS))=0;
iS='Manure Storages (unweighted) w simulated density outside of Kewaunee';
catS='CAFO';
use=1;
rel='ManureApp';
case 6 % dairy rotation polygon centroid + area
load(d2,'dairy')
sS=[dairy.Xsp dairy.Ysp];
zS=lz(dairy.Area,2);
iS='Dairy Rotation (area type)';
catS='ManureApp';
use=1;
rel='na';
case 7 % DNR Active CAFO Permit Points (unweighted)
dat=DNRCAFOsubst;
sS=[dat.Xsp dat.Ysp];
zS=ones(size(dat.Xsp));
iS='DNR Active CAFO Permit Points (unweighted)';
catS='CAFO';
use=1;
rel='ManureApp';
case 8 % Drainfields + simulated counts per outer quadrant
load(d3)
sx=sS_Drainfield.Xsp;
sy=sS_Drainfield.Ysp;
sx(isnan(sS_SanSyst.Xsp))=[];
sy(isnan(sS_SanSyst.Xsp))=[];
zS1=ones(size(sx));
sS1=[sx sy];
sS=[sS1;sSOUT];
zScountOUT(isnan(zScountOUT))=0;
zS=[zS1;zScountOUT];
iS='Drainfields w simulated counts per outer quadrant';
catS='Sep';
use=1;
rel='DomLAS';
case 9 % municipal WWTPs
sx=municipalWPDES.Xsp;
sy=municipalWPDES.Ysp;
zS=municipalWPDES.Population;
sS=[sx sy];
iS='Municipal WWTPs';
catS='WWTP';
use=1;
rel='DomLAS';
case 10 % industrial WWTPs
sx=industrialWPDES.Xsp;
sy=industrialWPDES.Ysp;
zS=ones(size(sx));
sS=[sx sy];
iS='Industrial WWTPs';
catS='WWTP';
use=1;
rel='IndLAS';
case 11 % all developed polygon centroid + area
load(d2,'dev')
sS=[dev.Xsp dev.Ysp];
zS=lz(dev.Area,2);
iS='Developed (area type)';
catS='Devel';
use=0;
rel='na';
case 12 %low-intensity developed polygon centroid + area
load(d2,'dev')
sS=[dev.Xsp dev.Ysp];
zS=lz(dev.Area,2);
idx=(dev.type=='Developed, Low Intensity');
sS(~idx,:)=[];
zS(~idx,:)=[];
iS='Low Density Developed (area type)';
catS='LDD';
use=1;
rel='na';
case 13 % high-intensity developed polygon centroid + area
load(d2,'dev')
sS=[dev.Xsp dev.Ysp];
zS=lz(dev.Area,2);
idx=(dev.type=='Developed, High Intensity');
sS(~idx,:)=[];
zS(~idx,:)=[];
iS='High Density Developed (area type)';
catS='HDD';
use=1;
rel='na';
case 14 % sanitary systems + sim
load(d4,'sScomp','zScomp','sSOUT','zSOUT','zScountOUT');
sS=[sS_SanSyst.Xsp sS_SanSyst.Ysp;sSOUT];
zS=[ones(size(sS_SanSyst.Xsp)); zScountOUT];
iS='Sanitary Systems + density per quadrant outside of Door/Kewaunee';
catS='Sep';
use=1;
rel='DomLAS';
case 15 % Developed Low Density (points)
load(d2,'sS_Devel')
dat=sS_Devel;
idx=dat.CLS_DESC_2=='Developed, Low Intensity';
sx=dat.Xsp(idx);
sy=dat.Ysp(idx);
sS=[sx sy];
zS=ones(size(sx));
iS='Low Density Developed (points)';
catS='LDD';
use=1;
rel='na';
case 16 % Developed High Density (points)
load('WisclandData.mat','sS_Devel')
dat=sS_Devel;
idx=dat.CLS_DESC_2=='Developed, High Intensity';
sx=dat.Xsp(idx);
sy=dat.Ysp(idx);
sS=[sx sy];
zS=ones(size(sx));
iS='High Density Developed (points)';
catS='HDD';
use=1;
rel='na';
case 17 % All unweighted wastewater treatment plant locations
sS=[industrialWPDES.Xsp industrialWPDES.Ysp;municipalWPDES.Xsp municipalWPDES.Ysp];
zS=ones(size(sS(:,1)));
iS='All Unweighted Wastewater Treatment Plants';
catS='WWTP';
use=1;
rel='LAS';
case 18 % ORR Sites No Weighting Points
dat=ORRSITES;
sS=[dat.Xsp dat.Ysp];
zS=ones(size(dat.Xsp));
idxIN=inpolygon(sS(:,1),sS(:,2),maskshapeX,maskshapeY);
sS=sS(idxIN,:);
zS=zS(idxIN);
iS='DNR ORR Sites No Weighting';
catS='LAS';
use=1;
rel='na';
case 19 % ORR Sites Weighted by Acrage
dat=ORRSITES;
sS=[dat.Xsp dat.Ysp];
idxnan=isnan(ORRSITES.ApprovedAcres);
idx0=ORRSITES.ApprovedAcres==0;
zS=ORRSITES.ApprovedAcres;
zS(idxnan|idx0)=min(zS(zS~=0));
zS=lz(zS,2);
idxIN=inpolygon(sS(:,1),sS(:,2),maskshapeX,maskshapeY);
sS=sS(idxIN,:);
zS=zS(idxIN);
iS='DNR ORR Sites Weighted By Acrage';
catS='LAS';
use=1;
rel='na';
case 20 % ORR Sites with Industrial Sludge
dat=ORRSITES;
sS=[dat.Xsp dat.Ysp];
idxnan=isnan(ORRSITES.ApprovedAcres);
idx0=ORRSITES.ApprovedAcres==0;
zS=ORRSITES.ApprovedAcres;
zS(idxnan|idx0)=min(zS(zS~=0));
zS=lz(zS,2);
idx=dat.IndustrialSludge=='N';
sS(idx,:)=[];
zS(idx)=[];
idxIN=inpolygon(sS(:,1),sS(:,2),maskshapeX,maskshapeY);
sS=sS(idxIN,:);
zS=zS(idxIN);
iS='DNR ORR Sites from Industrial Sludge';
catS='IndLAS';
use=1;
rel='na';
case 21 % ORR Sites with Papermill Sludge
dat=ORRSITES;
sS=[dat.Xsp dat.Ysp];
idxnan=isnan(ORRSITES.ApprovedAcres);
idx0=ORRSITES.ApprovedAcres==0;
zS=ORRSITES.ApprovedAcres;
zS(idxnan|idx0)=min(zS(zS~=0));
zS=lz(zS,2);
idx=dat.Papermill=='N';
sS(idx,:)=[];
zS(idx)=[];
idxIN=inpolygon(sS(:,1),sS(:,2),maskshapeX,maskshapeY);
sS=sS(idxIN,:);
zS=zS(idxIN);
iS='DNR ORR Sites from Papermill Sludge';
catS='IndLAS';
use=1;
rel='na';
case 22 % ORR Sites with food processing
dat=ORRSITES;
sS=[dat.Xsp dat.Ysp];
idxnan=isnan(ORRSITES.ApprovedAcres);
idx0=ORRSITES.ApprovedAcres==0;
zS=ORRSITES.ApprovedAcres;
zS(idxnan|idx0)=min(zS(zS~=0));
zS=lz(zS,2);
idx=dat.FoodProcessing=='N';
sS(idx,:)=[];
zS(idx)=[];
idxIN=inpolygon(sS(:,1),sS(:,2),maskshapeX,maskshapeY);
sS=sS(idxIN,:);
zS=zS(idxIN);
iS='DNR ORR Sites from Food Processing';
catS='IndLAS';
use=1;
rel='na';
case 23 % ORR Sites with Septage
dat=ORRSITES;
sS=[dat.Xsp dat.Ysp];
idxnan=isnan(ORRSITES.ApprovedAcres);
idx0=ORRSITES.ApprovedAcres==0;
zS=ORRSITES.ApprovedAcres;
zS(idxnan|idx0)=min(zS(zS~=0));
zS=lz(zS,2);
idx=dat.Septage=='N';
sS(idx,:)=[];
zS(idx)=[];
idxIN=inpolygon(sS(:,1),sS(:,2),maskshapeX,maskshapeY);
sS=sS(idxIN,:);
zS=zS(idxIN);
iS='DNR ORR Sites from Septage';
catS='DomLAS';
use=1;
rel='na';
case 24 % Acid Whey Land Application
dat=ORRSITES;
sS=[dat.Xsp dat.Ysp];
idxnan=isnan(ORRSITES.ApprovedAcres);
idx0=ORRSITES.ApprovedAcres==0;
zS=ORRSITES.ApprovedAcres;
zS(idxnan|idx0)=min(zS(zS~=0));
zS=lz(zS,2);
idx=dat.Whey=='N';
sS(idx,:)=[];
zS(idx)=[];
idxIN=inpolygon(sS(:,1),sS(:,2),maskshapeX,maskshapeY);
sS=sS(idxIN,:);
zS=zS(idxIN);
iS='DNR ORR Sites from Acid Whey';
catS='IndLAS';
use=1;
rel='na';
case 25 % Industrial WW and Industrial Sludge (From Dairy or Meat Production)
dat=ORRSITES;
sS=[dat.Xsp dat.Ysp];
idxnan=isnan(ORRSITES.ApprovedAcres);
idx0=ORRSITES.ApprovedAcres==0;
zS=ORRSITES.ApprovedAcres;
zS(idxnan|idx0)=min(zS(zS~=0));
zS=lz(zS,2);
idx=(dat.IndustrialWW=='N')&(dat.IndustrialSludge=='N');
sS(idx,:)=[];
zS(idx)=[];
idxIN=inpolygon(sS(:,1),sS(:,2),maskshapeX,maskshapeY);
sS=sS(idxIN,:);
zS=zS(idxIN);
iS='DNR ORR Sites from Industrial WW and Industrial Sludge';
catS='IndLAS';
use=1;
rel='na';
case 26 % Municipal WW Treatment
dat=ORRSITES;
sS=[dat.Xsp dat.Ysp];
idxnan=isnan(ORRSITES.ApprovedAcres);
idx0=ORRSITES.ApprovedAcres==0;
zS=ORRSITES.ApprovedAcres;
zS(idxnan|idx0)=min(zS(zS~=0));
zS=lz(zS,2);
idx=(dat.MunicipalWW=='N');
sS(idx,:)=[];
zS(idx)=[];
idxIN=inpolygon(sS(:,1),sS(:,2),maskshapeX,maskshapeY);
sS=sS(idxIN,:);
zS=zS(idxIN);
iS='DNR ORR Sites from Municipal WW Treatment';
catS='DomLAS';
use=1;
rel='na';
case 27 % Municipal WW Treatment or Septage
dat=ORRSITES;
sS=[dat.Xsp dat.Ysp];
idxnan=isnan(ORRSITES.ApprovedAcres);
idx0=ORRSITES.ApprovedAcres==0;
zS=ORRSITES.ApprovedAcres;
zS(idxnan|idx0)=min(zS(zS~=0));
zS=lz(zS,2);
idx=(dat.MunicipalWW=='N')&(dat.Septage=='N') ;
sS(idx,:)=[];
zS(idx)=[];
idxIN=inpolygon(sS(:,1),sS(:,2),maskshapeX,maskshapeY);
sS=sS(idxIN,:);
zS=zS(idxIN);
iS='DNR ORR Sites from Municipal WW Treatment or Septage';
catS='DomLAS';
use=1;
rel='na';
case 28 % DNR Active CAFO Permit Points (weighted by animal units)
dat=DNRCAFOsubst;
sS=[dat.Xsp dat.Ysp];
zS=dat.AU;
iS='DNR Active CAFO Permit Points (weighted by AUs)';
catS='CAFO';
use=1;
rel='ManureApp';
end
idxIN=inpolygon(sS(:,1),sS(:,2),maskS(:,1),maskS(:,2)); % only within a certain area
szS3{i,1}=[sS(idxIN,:) zS(idxIN)];
szS3{i,2}=iS;
szS3{i,3}=catS;
szSuse(i)=use;
jtog{i}=rel;
end
%% sR -- can make into cell arrays for option format
%load the river network snap the observation/response points to the river network
q4=sprintf('%s%s',pathname,'/KewauneeCode/Results/FinalRiverNetworkSep2020_250m.mat');
load(q4)
sRO=[ARGdata.Xsp ARGdata.Ysp];
sRRmat=snapMS2river(FI,sRO,0); %make sure the sampling sites are on the river network
for j=1:8
ObservationCase=j;
switch ObservationCase
case 1 % ermB in sediment
sR=sRRmat(:,1:2); % save river network points for response
rR=sRRmat(:,3:5); % save river network info for response points
zR=ARGdata3.ermB_Sed;
tR=month(datetime(ARGdata.Datnum,'ConvertFrom','datenum'));
idxnan=isnan(zR);
sR(idxnan,:)=[];
zR(idxnan)=[];
tR(idxnan)=[];
rR(idxnan,:)=[];
flowtype=2;
% Euclidean
Ebounds=[50 34000];
% River Distance
Rbounds=[50 3000];
% Overland Flow
Obounds=[2000 20000];
% Ground Transport
Gbounds=[50 34000];
case 2 % ermB in water
sR=sRRmat(:,1:2);
rR=sRRmat(:,3:5);
zR=ARGdata3.ermB_Water;
zR(zR==0)=min(zR(zR>0))/1.09;
zR(zR==-9999)=min(zR(zR>0))/1.05;
tR=month(datetime(ARGdata.Datnum,'ConvertFrom','datenum'));
idxnan=isnan(zR);
zR(idxnan)=[];
sR(idxnan,:)=[];
tR(idxnan)=[];
rR(idxnan,:)=[];
flowtype=2;
Ebounds=[50 10000];
% River Distance
Rbounds=[50 10000];
% Overland Flow
Obounds=[50 10000];
% Ground Transport
Gbounds=[50 34000];
case 3 % tetW in sediment
sR=sRRmat(:,1:2); % save river network points for response
rR=sRRmat(:,3:5); % save river network info for response points
zR=ARGdata3.tetW_Sed;
tR=month(datetime(ARGdata.Datnum,'ConvertFrom','datenum'));
idxnan=isnan(zR);
sR(idxnan,:)=[];
zR(idxnan)=[];
tR(idxnan)=[];
rR(idxnan,:)=[];
flowtype=2;
% Euclidean
Ebounds=[50 34000];
% River Distance
Rbounds=[50 3000];
% Overland Flow
Obounds=[2000 20000];
% Ground Transport
Gbounds=[50 34000];
case 4 % tetW in water
sR=sRRmat(:,1:2);
rR=sRRmat(:,3:5);
zR=ARGdata3.tetW_Water;
zR(zR==0)=min(zR(zR>0))/1.09;
zR(zR==-9999)=min(zR(zR>0))/1.05;
tR=month(datetime(ARGdata.Datnum,'ConvertFrom','datenum'));
idxnan=isnan(zR);
zR(idxnan)=[];
sR(idxnan,:)=[];
tR(idxnan)=[];
rR(idxnan,:)=[];
flowtype=2;
Ebounds=[50 10000];
% River Distance
Rbounds=[50 10000];
% Overland Flow
Obounds=[50 10000];
% Ground Transport
Gbounds=[50 34000];
case 5 % qnrA in sediment
sR=sRRmat(:,1:2); % save river network points for response
rR=sRRmat(:,3:5); % save river network info for response points
zR=ARGdata3.qnrA_Sed;
tR=month(datetime(ARGdata.Datnum,'ConvertFrom','datenum'));
idxnan=isnan(zR);
sR(idxnan,:)=[];
zR(idxnan)=[];
tR(idxnan)=[];
rR(idxnan,:)=[];
flowtype=2;
% Euclidean
Ebounds=[50 34000];
% River Distance
Rbounds=[50 3000];
% Overland Flow
Obounds=[2000 20000];
% Ground Transport
Gbounds=[50 34000];
case 6 % qnrA in water
sR=sRRmat(:,1:2);
rR=sRRmat(:,3:5);
zR=ARGdata3.qnrA_Water;
zR(zR==0)=min(zR(zR>0))/1.09;
zR(zR==-9999)=min(zR(zR>0))/1.05;
tR=month(datetime(ARGdata.Datnum,'ConvertFrom','datenum'));
idxnan=isnan(zR);
zR(idxnan)=[];
sR(idxnan,:)=[];
tR(idxnan)=[];
rR(idxnan,:)=[];
flowtype=2;
Ebounds=[50 10000];
% River Distance
Rbounds=[50 10000];
% Overland Flow
Obounds=[50 10000];
% Ground Transport
Gbounds=[50 34000];
case 7 % sul1 in sediment
sR=sRRmat(:,1:2); % save river network points for response
rR=sRRmat(:,3:5); % save river network info for response points
zR=ARGdata3.sul1_Sed;
tR=month(datetime(ARGdata.Datnum,'ConvertFrom','datenum'));
idxnan=isnan(zR);
sR(idxnan,:)=[];
zR(idxnan)=[];
tR(idxnan)=[];
rR(idxnan,:)=[];
flowtype=2;
% Euclidean
Ebounds=[50 34000];
% River Distance
Rbounds=[50 3000];
% Overland Flow
Obounds=[2000 20000];
% Ground Transport
Gbounds=[50 34000];
case 8 % sul1 in water
sR=sRRmat(:,1:2);
rR=sRRmat(:,3:5);
zR=ARGdata3.sul1_Water;
zR(zR==0)=min(zR(zR>0))/1.09;
zR(zR==-9999)=min(zR(zR>0))/1.05;
tR=month(datetime(ARGdata.Datnum,'ConvertFrom','datenum'));
idxnan=isnan(zR);
zR(idxnan)=[];
sR(idxnan,:)=[];
tR(idxnan)=[];
rR(idxnan,:)=[];
flowtype=2;
Ebounds=[50 10000];
% River Distance
Rbounds=[50 10000];
% Overland Flow
Obounds=[50 10000];
% Ground Transport
Gbounds=[50 34000];
case 9 % intI in sediment
sR=sRRmat(:,1:2);
rR=sRRmat(:,3:5);
zR=ARGdata3.intI1_Sed;
zR(zR==0)=min(zR(zR>0))/1.09;
zR(zR==-9999)=min(zR(zR>0))/1.05;
tR=month(datetime(ARGdata.Datnum,'ConvertFrom','datenum'));
idxnan=isnan(zR);
zR(idxnan)=[];
sR(idxnan,:)=[];
tR(idxnan)=[];
rR(idxnan,:)=[];
flowtype=2;
% Euclidean
Ebounds=[50 34000];
% River Distance
Rbounds=[50 3000];
% Overland Flow
Obounds=[2000 20000];
% Ground Transport
Gbounds=[50 34000];
case 10 % intI in water
sR=sRRmat(:,1:2);
rR=sRRmat(:,3:5);
zR=ARGdata3.intI1_Wate;
zR(zR==0)=min(zR(zR>0))/1.09;
zR(zR==-9999)=min(zR(zR>0))/1.05;
tR=month(datetime(ARGdata.Datnum,'ConvertFrom','datenum'));
idxnan=isnan(zR);
zR(idxnan)=[];
sR(idxnan,:)=[];
tR(idxnan)=[];
rR(idxnan,:)=[];
flowtype=2;
Ebounds=[50 10000];
% River Distance
Rbounds=[50 10000];
% Overland Flow
Obounds=[50 10000];
% Ground Transport
Gbounds=[50 34000];
end
szRt3{ObservationCase,1}=[sR zR tR rR];
szRt3{ObservationCase,2}=idxnan;
szRt3{ObservationCase,3}=2;
E{ObservationCase}=Ebounds;
R{ObservationCase}=Rbounds;
O{ObservationCase}=Obounds;
G{ObservationCase}=Gbounds;
end
save(rr,'szS3','szSuse','jtog', 'szRt3','E','R','O','G')