SLA-test.R

library(PEcAn.all)
download.file(url = "http://goo.gl/kPlJ47", 
    destfile = "foo.xml", method = 'wget', extra = '--no-check-certificate')
settings <- read.settings("foo.xml")
settings$pfts <- get.trait.data(pfts = settings$pfts, 
                                  modeltype = "BIOCRO", dbfiles = settings$run$dbfiles, 
                                  database = settings$database$bety, forceupdate = TRUE) 
run.meta.analysis(pfts = settings$pfts, 
                    iterations = settings$meta.analysis$iter, 
                    dbfiles = settings$run$dbfiles, 
                    database = settings$database$bety)
load(file.path(settings$pfts$outdir, "trait.mcmc.Rdata"))
SLA <- as.matrix(trait.mcmc$SLA)

tully.salix.xml

<?xml version="1.0"?>
<pecan>
  <outdir>/home/dlebauer/out/salix/</outdir>
  <pfts>
    <pft>
      <name>salix</name>
       <constants><file>/home/dlebauer/dev/willow_da/vignettes/salix.xml</file></constants>
    </pft>
  </pfts>
  <database>
    <bety>
      <user>bety</user>
      <password>bety</password>
      <dbname>ebi_production</dbname>
      <host>ebi-forecast.igb.illinois.edu</host>
      <dbfiles>$HOME/.pecan/dbfiles</dbfiles>
      <write>FALSE</write>
    </bety>
  </database>
  <meta.analysis>
    <iter>2000</iter>
    <random.effects>TRUE</random.effects>
    <update>TRUE</update>
  </meta.analysis>
  <ensemble>
    <size>500</size>
    <variable>TVeg</variable>
    <variable>StemBiom</variable>
 </ensemble>
  <sensitivity.analysis>
    <quantiles>
      <sigma>-3</sigma>
      <sigma>-2</sigma>
      <sigma>-1</sigma>
      <sigma>1</sigma>
      <sigma>2</sigma>
      <sigma>3</sigma>
    </quantiles>
    <variable>TVeg</variable>
    <variable>StemBiom</variable>
  </sensitivity.analysis>
  <model>
    <type>BIOCRO</type>
    <id>7</id>
    <binary>/home/dlebauer/dev/willow_da/inst/biocro.Rscript</binary>
  </model>
  <run>
    <site>
      <id>154</id>
    </site>
    <inputs><met>/home/dlebauer/dev/willow_da/inst/extdata/tully_met.csv</met></inputs>
    <start.date>2013-03-26 19:00:00</start.date>
    <end.date>2013-10-15 22:00:00</end.date>
    <host> 
      <name>localhost</name>
    </host>
  </run>
</pecan>