###########################################################################
###########################################################################
##
##    PLOT PTRMS CONCENTRATIONS or FLUXES FROM UCDAVIS COW CHAMBERS 
##
###########################################################################
#############	created by Stephanie Shaw, May 2005 #########################


###Note - You need to have the following files in your '.data' directory.
###See 'ReadMe.doc' for more information:
PTR4inIM
PTR5inIM
PTR4ouIM
PTR5ouIM
PTR4flIM
PTR5flIM

PTR4inSC
PTR5inSC
PTR4ouSC
PTR5ouSC
PTR4flSC
PTR5flSC

PTR4flCM
PTR5flCM

###SIM MODE DATA###########################################################

###Inlet Concentrations###
# note - to plot 2004 data use 'PTR4inIM' below, for 2005 data use 'PTR5inIM'
par(mfrow=c(2,2))
par(mar=c(5,5,4,2))
masslab_c("m18","m21","m30","m31","m32","m33","m37","m41","m42","m43","m45","m47","m57",
	"m59","m61","m63","m69","m71","m73","m75","m77","m79","m81m137","m83","m87","m89",
	"m93","m95","m105","m107","m121","m28","m111","m113","m115","m123","m129","m139",
	"m151","m153","m154","m155","m159","m165","m171","m173","m85","m97","m99","m101")
rows_1:length(PTR4inIM[,1])
for (i in 6:length(PTR4inIM[1,])){
plot(PTR4inIM[rows,"toy"],PTR4inIM[rows,i], xlab="Day of Year", 
	ylab=paste(masslab[i-5],"umol/min"), pch=5, cex=1.3)
}

###Outlet Concentrations###
# note - to plot 2004 data use 'PTR4ouIM' below, for 2005 data use 'PTR5ouIM'
par(mfrow=c(2,2))
par(mar=c(5,5,4,2))
masslab_c("m18","m21","m30","m31","m32","m33","m37","m41","m42","m43","m45","m47","m57",
	"m59","m61","m63","m69","m71","m73","m75","m77","m79","m81m137","m83","m87","m89",
	"m93","m95","m105","m107","m121","m28","m111","m113","m115","m123","m129","m139",
	"m151","m153","m154","m155","m159","m165","m171","m173","m85","m97","m99","m101")
rows_1:length(PTR4ouIM[,1])
for (i in 6:length(PTR4ouIM[1,])){
plot(PTR4ouIM[rows,"toy"],PTR4ouIM[rows,i], xlab="Day of Year", 
	ylab=paste(masslab[i-5],"umol/min"), pch=5, cex=1.3)
}

###Fluxes###
# note - to plot 2004 data use 'PTR4flIM' below, for 2005 data use 'PTR5flIM'
par(mfrow=c(2,2))
par(mar=c(5,5,4,2))
masslab_c("m18","m21","m30","m31","m32","m33","m37","m41","m42","m43","m45","m47","m57",
	"m59","m61","m63","m69","m71","m73","m75","m77","m79","m81m137","m83","m87","m89",
	"m93","m95","m105","m107","m121","m28","m111","m113","m115","m123","m129","m139",
	"m151","m153","m154","m155","m159","m165","m171","m173","m85","m97","m99","m101")
rows_1:length(PTR4flIM[,1])
for (i in 6:length(PTR4flIM[1,])){
plot(PTR4flIM[rows,"toy"],PTR4flIM[rows,i], xlab="Day of Year", 
	ylab=paste(masslab[i-5],"umol/min"), pch=5, cex=1.3)
}


###SCAN MODE DATA##########################################################
###Inlet Concentrations###
# note - to plot 2004 data use 'PTR4inSC' below, for 2005 data use 'PTR5inSC'
par(mfrow=c(2,2))
par(mar=c(5,5,4,2))
masslab_c("m20","m21","m22","m23","m24","m25","m26","m27","m28","m29","m30",
	"m31","m32","m33","m34","m35","m36","m37","m38","m39","m40","m41","m42",
	"m43","m44","m45","m46","m47","m48","m49","m50","m51","m52","m53","m54",
	"m55","m56","m57","m58","m59","m60","m61","m62","m63","m64","m65","m66",
	"m67","m68","m69","m70","m71","m72","m73","m74","m75","m76","m77","m78",
	"m79","m80","m81m137","m82","m83","m84","m85","m86","m87","m88","m89",
	"m90","m91","m92","m93","m94","m95","m96","m97","m98","m99","m100","m101",
	"m102","m103","m104","m105","m106","m107","m108","m109","m110","m111","m112",
	"m113","m114","m115","m116","m117","m118","m119","m120","m121","m122","m123",
	"m124","m125","m126","m127","m128","m129","m130","m131","m132","m133","m134",
	"m135","m136","m138","m139","m140","m141","m142","m143","m144","m145","m146",
	"m147","m148","m149","m150","m151","m152","m153","m154","m155","m156","m157",
	"m158","m159","m160","m161","m162","m163","m164","m165","m166","m167","m168",
	"m169","m170","m171","m172","m173","m174","m175")
rows_1:length(PTR4inSC[,1])
for (i in 6:length(PTR4inSC[1,])){
plot(PTR4inSC[rows,"toy"],PTR4inSC[rows,i], xlab="Day of Year", 
	ylab=paste(masslab[i-5],"umol/min"), pch=5, cex=1.3)
}

###Outlet Concentrations###
# note - to plot 2004 data use 'PTR4ouSC' below, for 2005 data use 'PTR5ouSC'
par(mfrow=c(2,2))
par(mar=c(5,5,4,2))
masslab_c("m20","m21","m22","m23","m24","m25","m26","m27","m28","m29","m30",
	"m31","m32","m33","m34","m35","m36","m37","m38","m39","m40","m41","m42",
	"m43","m44","m45","m46","m47","m48","m49","m50","m51","m52","m53","m54",
	"m55","m56","m57","m58","m59","m60","m61","m62","m63","m64","m65","m66",
	"m67","m68","m69","m70","m71","m72","m73","m74","m75","m76","m77","m78",
	"m79","m80","m81m137","m82","m83","m84","m85","m86","m87","m88","m89",
	"m90","m91","m92","m93","m94","m95","m96","m97","m98","m99","m100","m101",
	"m102","m103","m104","m105","m106","m107","m108","m109","m110","m111","m112",
	"m113","m114","m115","m116","m117","m118","m119","m120","m121","m122","m123",
	"m124","m125","m126","m127","m128","m129","m130","m131","m132","m133","m134",
	"m135","m136","m138","m139","m140","m141","m142","m143","m144","m145","m146",
	"m147","m148","m149","m150","m151","m152","m153","m154","m155","m156","m157",
	"m158","m159","m160","m161","m162","m163","m164","m165","m166","m167","m168",
	"m169","m170","m171","m172","m173","m174","m175")
rows_1:length(PTR4ouSC[,1])
for (i in 6:length(PTR4ouSC[1,])){
plot(PTR4ouSC[rows,"toy"],PTR4ouSC[rows,i], xlab="Day of Year", 
	ylab=paste(masslab[i-5],"umol/min"), pch=5, cex=1.3)
}

###Fluxes###
# note - to plot 2004 data use 'PTR4flSC' below, for 2005 data use 'PTR5flSC'
par(mfrow=c(2,2))
par(mar=c(5,5,4,2))
masslab_c("m20","m21","m22","m23","m24","m25","m26","m27","m28","m29","m30",
	"m31","m32","m33","m34","m35","m36","m37","m38","m39","m40","m41","m42",
	"m43","m44","m45","m46","m47","m48","m49","m50","m51","m52","m53","m54",
	"m55","m56","m57","m58","m59","m60","m61","m62","m63","m64","m65","m66",
	"m67","m68","m69","m70","m71","m72","m73","m74","m75","m76","m77","m78",
	"m79","m80","m81m137","m82","m83","m84","m85","m86","m87","m88","m89",
	"m90","m91","m92","m93","m94","m95","m96","m97","m98","m99","m100","m101",
	"m102","m103","m104","m105","m106","m107","m108","m109","m110","m111","m112",
	"m113","m114","m115","m116","m117","m118","m119","m120","m121","m122","m123",
	"m124","m125","m126","m127","m128","m129","m130","m131","m132","m133","m134",
	"m135","m136","m138","m139","m140","m141","m142","m143","m144","m145","m146",
	"m147","m148","m149","m150","m151","m152","m153","m154","m155","m156","m157",
	"m158","m159","m160","m161","m162","m163","m164","m165","m166","m167","m168",
	"m169","m170","m171","m172","m173","m174","m175")
rows_1:length(PTR4flSC[,1])
for (i in 6:length(PTR4flSC[1,])){
plot(PTR4flSC[rows,"toy"],PTR4flSC[rows,i], xlab="Day of Year", 
	ylab=paste(masslab[i-5],"umol/min"), pch=5, cex=1.3)
}


###SCAN&SIM DATA FOR RELEVANT MASSES###################################
# note - to plot 2004 data use 'PTR4flCM' below, for 2005 data use 'PTR5flCM'
par(mfrow=c(2,2))
par(mar=c(5,5,4,2))
masslab_c("m21","m30","m31","m32","m33","m37","m41","m42","m43","m45","m47","m57",
	"m59","m61","m63","m69","m71","m73","m75","m77","m79","m81m137","m83","m87","m89",
	"m93","m95","m105","m107","m121","m28","m111","m113","m115","m123","m129","m139",
	"m151","m153","m154","m155","m159","m165","m171","m173","m85","m97","m99","m101")
rows_1:length(PTR4flCM[,1])
for (i in 7:length(PTR4flCM[1,])){
plot(PTR4flCM[rows,"toy"],PTR4flCM[rows,i], xlab="Day of Year", 
	ylab=paste(masslab[i-6],"umol/min"), pch=5, cex=1.3)
}