added files for energy farm calibration

inst/extdata/defaults/miscanthus_ebifarm2012.xml

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+<constants>
+  <type>
+    <photosynthesis>C4</photosynthesis>
+    <genus>Miscanthus</genus>
+  </type>
+  <canopyControl>
+    <Sp>1.7</Sp>
+    <SpD>0</SpD>
+    <nlayers>10</nlayers>
+    <kd>0.1</kd>
+    <chi.l>1</chi.l>
+    <mResp>0.02,0.03</mResp>
+    <heightFactor>3</heightFactor>
+    <leafwidth>0.04</leafwidth>
+    <eteq>0</eteq>
+  </canopyControl>
+  <iPlantControl>
+    <iRhizome>3</iRhizome>
+    <iStem>1</iStem>
+    <iLeaf>0</iLeaf>
+    <iRoot>1</iRoot>
+    <ifrRhizome>0.01</ifrRhizome>
+    <ifrStem>0.01</ifrStem> 
+  </iPlantControl>
+  <photoParms>
+    <vmax>39</vmax>
+    <alpha>0.04</alpha>
+    <kparm>0.7</kparm>
+    <theta>0.83</theta>
+    <beta>0.93</beta>
+    <Rd>0.8</Rd>
+    <Catm>400</Catm>
+    <b0>0.01</b0>
+    <b1>3</b1>
+    <ws>1</ws>
+    <UPPERTEMP>37.5</UPPERTEMP>
+    <LOWERTEMP>3</LOWERTEMP>
+  </photoParms>
+  <phenoControl>
+    <Tbase>0</Tbase>
+  </phenoControl>
+  <seneControl>
+    <senLeaf>3000</senLeaf>
+    <senStem>3500</senStem>
+    <senRoot>4000</senRoot>
+    <senRhizome>4000</senRhizome>
+  </seneControl>
+  <soilControl>
+    <FieldC>-1</FieldC>
+    <WiltP>-1</WiltP>
+    <phi1>0.01</phi1>
+    <phi2>10</phi2>
+    <soilDepth>1</soilDepth>
+    <iWatCont>0.32</iWatCont>
+    <soilType>6</soilType>
+    <soilLayers>1</soilLayers>
+    <soilDepths/>
+    <wsFun>0</wsFun>
+    <scsf>1</scsf>
+    <transpRes>5000000</transpRes>
+    <leafPotTh>-800</leafPotTh>
+    <hydrDist>0</hydrDist>
+    <rfl>0.2</rfl>
+    <rsec>0.2</rsec>
+    <rsdf>0.44</rsdf>
+  </soilControl>
+  <phenoParms>
+    <tp1>562</tp1>
+    <tp2>1312</tp2>
+    <tp3>2063</tp3>
+    <tp4>2676</tp4>
+    <tp5>3211</tp5>
+    <tp6>7000</tp6>
+    <kStem1>0.37</kStem1>
+    <kLeaf1>0.33</kLeaf1>
+    <kRoot1>0.3</kRoot1>
+    <kRhizome1>-0.0008</kRhizome1>
+    <kStem2>0.85</kStem2>
+    <kLeaf2>0.14</kLeaf2>
+    <kRoot2>0.01</kRoot2>
+    <kRhizome2>-0.0005</kRhizome2>
+    <kStem3>0.63</kStem3>
+    <kLeaf3>0.01</kLeaf3>
+    <kRoot3>0.01</kRoot3>
+    <kRhizome3>0.35</kRhizome3>
+    <kStem4>0.63</kStem4>
+    <kLeaf4>0.01</kLeaf4>
+    <kRoot4>0.01</kRoot4>
+    <kRhizome4>0.35</kRhizome4>
+    <kStem5>0.63</kStem5>
+    <kLeaf5>0.01</kLeaf5>
+    <kRoot5>0.01</kRoot5>
+    <kRhizome5>0.35</kRhizome5>
+    <kStem6>0.63</kStem6>
+    <kLeaf6>0.01</kLeaf6>
+    <kRoot6>0.01</kRoot6>
+    <kRhizome6>0.35</kRhizome6>
+    <kGrain6>0</kGrain6>
+  </phenoParms>
+</constants>

inst/extdata/remote_sensing_da.xml

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+<?xml version="1.0"?>
+<pecan>
+  <outdir>/home/dlebauer/pecan_remote/remote_sensing_da</outdir>
+  <constants>
+    <file>/home/dlebauer/dev/biocro_regional/inst/extdata/defaults/miscanthus_ebifarm2012.xml</file>
+  </constants>
+  <pfts>
+    <pft>
+      <name>Miscanthus_x_giganteus</name>
+    </pft>
+  </pfts>
+  <meta.analysis>
+    <iter>3000</iter>
+    <random.effects>FALSE</random.effects>
+  </meta.analysis>
+  <ensemble>
+    <size>500</size>
+    <variable>StemBiom</variable>
+    <variable>LAI</variable>
+    <variable>TotLivBiom</variable>
+    <variable>Yield</variable>
+    <variable>Evap</variable>
+    <variable>TVeg</variable>
+  </ensemble>
+  <sensitivity.analysis>
+    <variable>StemBiom</variable>
+    <variable>LAI</variable>
+    <variable>TotLivBiom</variable>
+    <variable>Yield</variable>
+    <variable>Evap</variable>
+    <variable>TVeg</variable>
+    <start.year>2012</start.year>
+    <end.year>2012</end.year>
+  </sensitivity.analysis>
+  <model>
+    <type>BIOCRO</type>
+    <id>12</id>
+  </model>
+  <run>
+    <site>
+      <id>368</id>
+      <name>SoyFACE</name>	
+      <lat>40.0415</lat>
+      <lon>-88.2373</lon>
+    </site>
+      <inputs>
+       <met>
+        <id>305</id><!--305 is SoyFACE; 306 is EBI Farm-->
+       </met>
+       <soil>
+        <id>303</id>
+       </soil>
+   </inputs>
+    <start.date>2012-01-01 00:00:00</start.date>
+    <end.date>2012-12-31 00:00:00</end.date>
+    <host>
+     <name>roger-login.ncsa.illinois.edu</name>
+     <qsub>qsub -l walltime=05:00:00,nodes=5:ppn=10 -N @NAME@ -o @STDOUT@ -e @STDERR@</qsub>
+     <qsub.jobid>lionxo_test ([0-9]+) .*</qsub.jobid>
+     <qstat>qstat -j @JOBID@ 2&gt;1 &gt;/dev/null || echo DONE</qstat>
+     <modellauncher>
+       <binary>/home/dlebauer/dev/pecan/utils/modellauncher/modellauncher</binary>
+       <qsub.extra>-l ncpus=10</qsub.extra>
+     </modellauncher>
+   <rundir>/home/dlebauer/pecan_remote/remote_sensing_da/run</rundir>
+   <outdir>/home/dlebauer/pecan_remote/remote_sensing_da/out</outdir>
+  </host>
+  </run>
+  <database>
+    <bety>
+      <driver>PostgreSQL</driver>
+      <user>bety</user>
+      <password>bety</password>
+      <host>ebi-forecast.igb.illinois.edu</host>
+      <dbname>ebi_production</dbname>
+    </bety>
+  </database>
+  <bety>
+    <write>TRUE</write>
+  </bety>
+</pecan>

vignettes/remote_sensing_da.Rmd

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+
+## Prepare met data
+
+```{r eval = FALSE}
+library(PEcAn.all)
+format <- list(orig = c("TIMESTAMP",
+                        "PAR_APOGE_Avg", "AirTC_Avg", "RH1_Avg", 
+                        "RAIN_Tot", "WindSpd_Avg"
+                        ),
+               units = c("ymd_hms",
+                         "J m-2 s-1", "celsius", "%", 
+                         "mm", "m s-1"
+                        ),
+               bety = c("datetime", 
+                       "solar_radiation",  "airT", "relative_humidity",
+                        "precipitation_flux", "Wspd"
+                       ),
+               skip = 1, unit.row = TRUE, na.strings = NA)
+met2CF.csv(in.path = "~/Downloads/", in.file = "WeatherSE_Avg15 2012.csv", 
+           outfolder = "data/", lat = 40.04, lon = -88.24, format = format)
+```
+
+## PEcAn workflow
+
+
+Note - This was run on ebi-forecast. To run on your VM, you will need to change the location of the settings files. 
+
+
+```{r}
+library(PEcAn.all)
+logger.setQuitOnSevere(FALSE)
+setwd("/home/a-m/dlebauer/dev/")
+settings <- read.settings("biocro_regional/inst/extdata/remote_sensing_da.xml")
+
+
+# Query the trait database for data and priors
+settings$pfts <- get.trait.data(pft = settings$pfts, modeltype = settings$model$type, 
+                                dbfiles = settings$run$dbfiles, 
+                                database = settings$database$bety, forceupdate = TRUE)
+
+# Run the PEcAn meta.analysis
+run.meta.analysis(pfts = settings$pfts, iterations = settings$meta.analysis$iter, 
+                  threshold = settings$meta.analysis$threshold, 
+                  dbfiles = settings$run$dbfiles, database = settings$database$bety)
+
+settings$model$binary <- gsub("regional", "point", settings$model$binary)
+
+run.write.configs(settings = settings, write = TRUE) # Calls model specific write.configs e.g. write.config.ed.R
+## load met data
+
+start.model.runs(settings = settings, write = TRUE)    # Start ecosystem model runs
+
+get.results(settings)         # Get results of model runs
+
+run.sensitivity.analysis()      # Run sensitivity analysis and variance decomposition on model output
+
+run.ensemble.analysis()		      # Run ensemble analysis on model output. 
+```