# Read in callibration data rm(list=ls()) layout(matrix(c(1,2), 1, 1, byrow = TRUE)) opar<- par(mar=c(5, 3, 4, 3) + 0.1) # Adjust skip to get Conc and V(Conc) headers. # Calibration File: Z<- read.table("Lobster012.TXT", header=TRUE, skip=4, nrows=1, sep=' ') # Data File: filnam<-"Lobster010.TXT" Conditions<- "Lobster 2c-scan-1; H-LIX in sea water pH 7.5" # Adjust multiplier to make iConc<-7:9 iVconc<-10:12 Conc<-as.real(Z[iConc])/1000 Vconc<-as.real(Z[iVconc]) Lconc<-log10(Conc) ELconc<-predict(lm(Lconc~Vconc)) plot(Vconc, ELconc, ty='b', main="-pH vs mV CALLIBRATION") points(Vconc, Lconc,col='red') points(90, -5.25, col='red') text(93, -5.25, "Obs[-pH]", col='red', pos=4) points(90, -5.35, col='black') text(93, -5.35, "E[-pH]", col='black', pos=4) points(90, -5.45, col='blue', cex=2) text(93, -5.45, "New E[-pH]", col='blue', pos=4) NewVC <- data.frame(Vconc = c(60, 80, 100, 120, 140, 160)) points(t(NewVC), predict(lm(Lconc~Vconc), newdata=NewVC), cex=2, col='blue') browser() layout(matrix(c(1:6), 2, 3, byrow = TRUE)) # was 2 by 4 XX<-read.table(filnam, header=TRUE, skip=19, nrows=-1, sep=',') print(names(XX)) attach(XX) Origin.Z.1.uV <- - Origin.Z.1.uV Origin.X..1.uV <- - Origin.X..1.uV Origin.Y.1.uV <- - Origin.Y.1.uV Origin.Z.2.uV <- - Origin.Z.2.uV Origin.X..2.uV <- - Origin.X..2.uV Origin.Y.2.uV <- - Origin.Y.2.uV Origin.Z.3.uV <- - Origin.Z.3.uV Origin.X..3.uV <- - Origin.X..3.uV Origin.Y.3.uV <- - Origin.Y.3.uV AvgOrigin.ZuV <- - AvgOrigin.ZuV AvgOrigin.X.uV <- - AvgOrigin.X.uV AvgOrigin.YuV <- - AvgOrigin.YuV minAll<-min(min(AvgOrigin.X.uV),min(AvgOrigin.YuV),min(AvgOrigin.ZuV)) maxAll<-max(max(AvgOrigin.X.uV),max(AvgOrigin.YuV),max(AvgOrigin.ZuV)) Ypos<- ProbeY- sum(ProbeY)/length(ProbeY) Xpos<- ProbeX- sum(ProbeX)/length(ProbeY) Zpos<- ProbeZ- sum(ProbeZ)/length(ProbeY) plot(c(min(Xpos),max(Xpos)), c(minAll,maxAll), ty='n', main=paste(filnam, 'Obs[uVdiff]')) mtext("Observed uV difference (xyz) = (rgb)", line=-1.5) lines(Xpos, AvgOrigin.X.uV, col="red") lines(Xpos, AvgOrigin.YuV, col="green") lines(Xpos, AvgOrigin.ZuV, col="blue") browser() minAll<-min(Origin.1.mV) maxAll<-max(Origin.1.mV) # plot(c(min(Ypos),max(Ypos)), c(minAll,maxAll), # ty='n', # main=paste(filnam, 'Obs[mV]')) # mtext("Observed mV at probe origin", line=-1.5) # lines(Ypos, Origin.1.mV, col="black") NewV0 <- data.frame(Vconc = Origin.1.mV) plot(Xpos, predict(lm(Lconc~Vconc), newdata=NewV0), ty='b', main=paste(filnam, 'E[-pH]')) mtext("E[-pH] = by callibration", line=-1.5) mtext(Conditions, line=-3) Oconc<- 10^(predict(lm(Lconc~Vconc), newdata=NewV0)) browser() plot(Xpos, Oconc, ty='b', main=paste(filnam, 'E[H+]')) mtext("E[H+] = 10^(E[-pH]) at probe origin", line=-1.5) mtext(Conditions, line=-3) Xconc<- 10^(predict(lm(Lconc~Vconc), newdata=NewV0+AvgOrigin.X.uV/1000)) Yconc<- 10^(predict(lm(Lconc~Vconc), newdata=NewV0+AvgOrigin.YuV/1000)) Zconc<- 10^(predict(lm(Lconc~Vconc), newdata=NewV0+AvgOrigin.ZuV/1000)) dXH<- Xconc-Oconc dYH<- Yconc-Oconc dZH<- Zconc-Oconc minAll<-min(min(dXH),min(dYH),min(dZH)) maxAll<-max(max(dXH),max(dYH),max(dZH)) dHtot<-(dXH^2 + dYH^2 + dZH^2)^0.5 Hflux<- dHtot*10^19 browser() plot(c(min(Xpos),max(Xpos)), c(minAll,maxAll), ty='n', main=paste(filnam, '[H+]dxyz')) mtext("[H+]dxyz", line=-1.5, col='red') mtext(Conditions, line=-3) lines(Xpos, dXH, col="red", ty='b') lines(Xpos, dYH, col="green", ty='b') lines(Xpos, dZH, col="blue", ty='b') # detach(X) require(scatterplot3d) # mul<-2*10^8 mul<-600/maxAll Miny<- min(c(Ypos,Ypos+mul*dYH)) Minz<- min(c(Zpos,Zpos+mul*dZH)) Minx<- min(c(Xpos,Xpos+mul*dXH)) Maxy<- max(c(Ypos,Ypos+mul*dYH)) Maxz<- max(c(Zpos,Zpos+mul*dZH)) Maxx<- max(c(Xpos,Xpos+mul*dXH)) nx<-17 ny<-9 browser() # Left Scat 3D s3d<-scatterplot3d(c(Minx,Maxx), c(Miny,Maxy), c(Minz,Maxz), highlight.3d=TRUE, col.axis="blue", col.grid="lightblue", main="scatterplot3d - L", pch=16, cex.symbols=2, angle= 96, typ='n', axis=FALSE, mar=c(0.5,0.5,0.5,0.5), scale.y=0.25) for(i in (nx*ny):1) { s3d$points3d(Xpos[i], Ypos[i], Zpos[i], col="black", type="b", pch=16) # was b } for(i in (nx*ny):1) { s3d$points3d(Xpos[i]+mul*dXH[i], Ypos[i]+mul*dYH[i], Zpos[i]+mul*dZH[i], col="red", type="b", pch=16) } for(i in (nx*ny):1) { s3d$points3d(c(Xpos[i],Xpos[i]+mul*dXH[i]), c(Ypos[i],Ypos[i]+mul*dYH[i]), c(Zpos[i],Zpos[i]+mul*dZH[i]), col="blue", type="l", pch=16) } # Right Scat 3D browser() s3d<-scatterplot3d(c(Minx,Maxx), c(Miny,Maxy), c(Minz,Maxz), highlight.3d=TRUE, col.axis="blue", col.grid="lightblue", main="scatterplot3d - R", pch=16, cex.symbols=2, angle= 90, typ='n', axis=FALSE, mar=c(0.5,0.5,0.5,0.5), scale.y=0.25) # mar(b,l,t,r) for(i in (nx*ny):1) { s3d$points3d(Xpos[i], Ypos[i], Zpos[i], col="black", type="b", pch=16) } for(i in (nx*ny):1) { s3d$points3d(Xpos[i]+mul*dXH[i], Ypos[i]+mul*dYH[i], Zpos[i]+mul*dZH[i], col="red", type="b", pch=16) } for(i in (nx*ny):1) { s3d$points3d(c(Xpos[i],Xpos[i]+mul*dXH[i]), c(Ypos[i],Ypos[i]+mul*dYH[i]), c(Zpos[i],Zpos[i]+mul*dZH[i]), col="blue", type="l", pch=16) } text(125,10, "Y") browser() opar<- par(mar=c(5, 3, 4, 3) + 0.1) Flux<-matrix(Hflux, ny,nx, byrow=TRUE) for (i in seq(1,ny,2)) {Flux[i,1:nx]<- Flux[i,nx:1] } persp(Flux, theta = 285, phi = 30, expand = 1.2, col = "lightblue", zlab="H-flux", xlab="Z-axis", ylab="Y-axis") browser() persp(Flux, theta = 288, phi = 30, expand = 1.2, col = "lightblue", zlab="H-flux", xlab="Z-axis", ylab="Y-axis") browser() xmed<-ymed<-zmed<- rep(0,nx*ny) for(i in 1:(nx*ny)) { xmed[i]<-median(c(Origin.X..1.uV[i],Origin.X..2.uV[i],Origin.X..3.uV[i])) ymed[i]<-median(c(Origin.Y.1.uV[i],Origin.Y.2.uV[i],Origin.Y.3.uV[i])) zmed[i]<-median(c(Origin.Z.1.uV[i],Origin.Z.2.uV[i],Origin.Z.3.uV[i])) } dVtotmed<-(xmed^2 + ymed^2 + zmed^2)^0.5 mV<-matrix(dVtotmed, ny,nx, byrow=TRUE) for (i in seq(1,ny,2)) {mV[i,1:nx]<- mV[i,nx:1] } persp(mV, theta = 285, phi = 30, expand = 1.2, col = "lightblue", zlab="mV", xlab="Z-axis", ylab="Y-axis") xmed<-matrix(xmed, ny,nx, byrow=TRUE) for (i in seq(1,ny,2)) {xmed[i,1:nx]<- xmed[i,nx:1] } persp(xmed, theta = 285, phi = 30, expand = 1.2, col = "lightblue", zlab="Xmed", xlab="Z-axis", ylab="Y-axis") ymed<-matrix(ymed, ny,nx, byrow=TRUE) for (i in seq(1,ny,2)) {ymed[i,1:nx]<- ymed[i,nx:1] } persp(ymed, theta = 285, phi = 30, expand = 1.2, col = "lightblue", zlab="Ymed", xlab="Z-axis", ylab="Y-axis") zmed<-matrix(zmed, ny,nx, byrow=TRUE) for (i in seq(1,ny,2)) {zmed[i,1:nx]<- zmed[i,nx:1] } persp(zmed, theta = 285, phi = 30, expand = 1.2, col = "lightblue", zlab="Zmed", xlab="Z-axis", ylab="Y-axis") browser() layout(matrix(1:4, 2, 2, byrow = TRUE)) # was 2 by 4 contour(zmed, main="Z median") contour(xmed, col='red', main="X median") contour(ymed, col='blue', main="Y median") contour(zmed, main="Z, X and Y median") contour(xmed, add=TRUE, col='red') contour(ymed, add=TRUE, col='blue') layout(matrix(1:4, 2, 2, byrow = TRUE)) # was 2 by 4 MinZ<- min(c(Origin.Z.1.uV, Origin.Z.2.uV, Origin.Z.3.uV)) MinX<- min(c(Origin.X..1.uV, Origin.X..2.uV, Origin.X..3.uV)) MinY<- min(c(Origin.Y.1.uV, Origin.Y.2.uV, Origin.Y.3.uV)) MaxZ<- max(c(Origin.Z.1.uV, Origin.Z.2.uV, Origin.Z.3.uV)) MaxX<- max(c(Origin.X..1.uV, Origin.X..2.uV, Origin.X..3.uV)) MaxY<- max(c(Origin.Y.1.uV, Origin.Y.2.uV, Origin.Y.3.uV)) MinMed<- min(c(xmed,ymed,zmed)) MaxMed<- max(c(xmed,ymed,zmed)) indy<- 1:(ll<-length(Origin.Z.1.uV) ) # AvgOrigin.ZuV AvgOrigin.X.uV AvgOrigin.YuV plot(c(1,ll),c(MinX,MaxX), typ='n', main=paste(filnam,"X: 1st=red, 2nd=blue, 3rd=green, Avg=black")) points(indy,Origin.X..1.uV, typ='b', col='red') points(indy,Origin.X..2.uV, typ='b', col='green') points(indy,Origin.X..3.uV, typ='b', col='blue') points(indy,AvgOrigin.X.uV, typ='b', col='black', lwd=2) plot(c(1,ll),c(MinY,MaxY), typ='n', main=paste(filnam,"Y: 1st=red, 2nd=blue, 3rd=green, Avg=black")) points(indy,Origin.Y.1.uV, typ='b', col='red') points(indy,Origin.Y.2.uV, typ='b', col='green') points(indy,Origin.Y.3.uV, typ='b', col='blue') points(indy,AvgOrigin.YuV, typ='b', col='black', lwd=2) plot(c(1,ll),c(MinZ,MaxZ), typ='n', main=paste(filnam,"Z: 1st=red, 2nd=blue, 3rd=green, Avg=black")) points(indy,Origin.Z.1.uV, typ='b', col='red') points(indy,Origin.Z.2.uV, typ='b', col='green') points(indy,Origin.Z.3.uV, typ='b', col='blue') points(indy,AvgOrigin.ZuV, typ='b', col='black', lwd=2) plot(c(1,ll),c(MinMed,MaxMed), typ='n', main="Medians: x-red, y-green, z-blue") points(indy,xmed, typ='b', col='red') points(indy,ymed, typ='b', col='green') points(indy,zmed, typ='b', col='blue') detach(XX)