dateTime=1;

darkRefIntTime=2;

darkRef690=3;

darkRef590=4;

measureRefIntTime=5;

measureRef690=6;

measureRef590=7;

luminIntTime=8;

lumin690=9;

lumin590=10;

fluorIntTime=11;

fluor690=12;

fluor590=13;

phosIntTime=14;

phos690=15;

phos590=16;

fluorP61Data=Drop[Import["/Volumes/PBC/SES/Pulse\ 61/dep-2012.11.17-01-Pulse-61/fluorometer.csv"],1];

fluorP61Data[[1;;10]]

DateListPlot[fluorP61Data[[All,{dateTime,fluor690}]],{PlotRange->All,Joined->True,PlotLabel->"SES 690 nm Fluorescence on Pulse 61",FrameLabel->{"Date","Fluorescence (counts)"}}]

DateListPlot[fluorP61Data[[All,{dateTime,fluor590}]],{PlotRange->All,Joined->True,PlotLabel->"SES 590 nm Fluorescence on Pulse 61",FrameLabel->{"Date","Fluorescence (counts)"}}]

DateListPlot[{fluorP61Data[[All,{dateTime,measureRef690}]],fluorP61Data[[All,{dateTime,measureRef590}]]},{PlotRange->All,Joined->True,PlotLabel->"SES Fluorescence References on Pulse 61",FrameLabel->{"Date","Fluorescence (counts)"}}]

DateListPlot[{fluorP61Data[[All,{dateTime,fluor690}]],fluorP61Data[[All,{dateTime,fluor590}]]},{PlotRange->All,Joined->True,PlotLabel->"SES Fluorescence on Pulse 61",FrameLabel->{"Date","Fluorescence (counts)"}}]

f690p61=fluorP61Data[[All,{fluor690}]]-fluorP61Data[[All,{measureRef690}]];

f690p61date=Partition[Flatten[Riffle[fluorP61Data[[All,{dateTime}]],f690p61]],2];

f690p61date[[1;;10]]

pl690p61=DateListPlot[f690p61date,{PlotRange->All,Joined->True,PlotLabel->"SES 690 nm Fluorescence on Pulse 61",FrameLabel->{"Date","Fluorescence (counts)"},PlotStyle->Red}]

f590p61=fluorP61Data[[All,{fluor590}]]-fluorP61Data[[All,{measureRef590}]];

f590p61date=Partition[Flatten[Riffle[fluorP61Data[[All,{dateTime}]],f590p61]],2];

pl590p61=DateListPlot[f590p61date,{PlotRange->All,Joined->True,PlotLabel->"SES 590 nm Fluorescence on Pulse 61",FrameLabel->{"Date","Fluorescence (counts)"},PlotStyle->Orange}]

Show[pl690p61,pl590p61]

<<PlotLegends`

DateListPlot[{f590p61date,f690p61date},{PlotRange->All,Joined->True,BaseStyle->{FontWeight->"Bold",FontSize->14},PlotLabel->"SES Fluorescence on Pulse 61",FrameLabel->{"Date (2012-2013)","Fluorescence (PM counts)"},PlotStyle->{{Thick,Orange},{Thick,Red}},PlotLegend->{"590 nm","690 nm"},LegendShadow->None,LegendPosition->{-0.2,0.1},LegendSize->{0.3,0.2}}]

DateListPlot[{f690p61date,f590p61date},{PlotRange->All,Joined->True,BaseStyle->{FontWeight->"Bold",FontSize->14},PlotLabel->"SES Fluorescence on Pulse 61",FrameLabel->{"Date (2012-2013)","Fluorescence (PM counts)"},PlotStyle->{{Thick,Red},{Thick,Orange}},PlotLegend->{"690 nm","590 nm"},LegendShadow->None,LegendPosition->{-0.2,0.1},LegendSize->{0.3,0.2}}]

fluorP60Data=Drop[Import["/Volumes/PBC/SES/Pulse\ 60/dep-2012.06.10-02-SES-STATION_M-1/fluorometer.csv"],1];

fluorP60Data[[1;;10]]

fluorP6061Data=Join[fluorP60Data,fluorP61Data];

Length[fluorP6061Data]

DateListPlot[{fluorP6061Data[[All,{dateTime,fluor690}]],fluorP6061Data[[All,{dateTime,fluor590}]]},{PlotRange->All,Joined->True,PlotLabel->"SES Fluorescence on Pulse 60 and 61",FrameLabel->{"Date","Fluorescence (counts)"}}]

f690p6061=fluorP6061Data[[All,{fluor690}]]-fluorP6061Data[[All,{measureRef690}]];

f690p6061date=Partition[Flatten[Riffle[fluorP6061Data[[All,{dateTime}]],f690p6061]],2];

f590p6061=fluorP6061Data[[All,{fluor590}]]-fluorP6061Data[[All,{measureRef590}]];

f590p6061date=Partition[Flatten[Riffle[fluorP6061Data[[All,{dateTime}]],f590p6061]],2];

DateListPlot[{f590p6061date,f690p6061date},{PlotRange->All,Joined->True,BaseStyle->{FontWeight->"Bold",FontSize->14},PlotLabel->"SES Fluorescence on Pulse 60 and 61",FrameLabel->{"Date (2012-2013)","Fluorescence (PM counts)"},PlotStyle->{{Thick,Orange},{Thick,Red}},PlotLegend->{"590 nm","690 nm"},LegendShadow->None,LegendPosition->{-0.2,0.1},LegendSize->{0.3,0.2}}]

This works but there is a line joining the two separate data plot. To get rid of the line I’ll have to overlay two plots.

f690p60=fluorP60Data[[All,{fluor690}]]-fluorP60Data[[All,{measureRef690}]];

f690p60date=Partition[Flatten[Riffle[fluorP60Data[[All,{dateTime}]],f690p60]],2];

f590p60=fluorP60Data[[All,{fluor590}]]-fluorP60Data[[All,{measureRef590}]];

f590p60date=Partition[Flatten[Riffle[fluorP60Data[[All,{dateTime}]],f590p60]],2];

First[f690p60date]

Last[f690p61date]

plot1=DateListPlot[{f590p60date,f690p60date},ImagePadding->60,BaseStyle->{FontWeight->"Normal",FontSize->14},Frame->{True,True,True,False},FrameLabel->{{"Fluorescence (PM counts)",""},{"Time (month in 2012-2013)",Text[Style["SES Fluorescence on Pulse 60 and 61",18]]}},Joined->True,PlotStyle->{Orange,Red},PlotLegend->{"590 nm","690 nm"},LegendShadow->None,LegendPosition->{-0.2,0.1},LegendSize->{0.3,0.2},PlotRange->{{{2012,6,4,12,10},{2013,4,23,23,18}},{-30,830}},ImageSize->Large]

plot2=DateListPlot[{f590p61date,f690p61date},ImagePadding->60,BaseStyle->{FontWeight->"Normal",FontSize->14},Axes->False,Frame->{False,False,False,True},FrameTicks->{None,None,None,Automatic},FrameLabel->{{"",""},{"",""}},Joined->True,PlotStyle->{Orange,Red},PlotLegend->{"590 nm","690 nm"},LegendShadow->None,LegendPosition->{-0.2,0.1},LegendSize->{0.3,0.2},PlotRange->{{{2012,6,4,12,10},{2013,4,23,23,18}},{-30,830}},ImageSize->Large]

P6061Fluor=Overlay[{plot2,plot1}]

Export["P6061Fluor.pdf",P6061Fluor]