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David LeBauer dlebauer

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dlebauer / error.sh
Created April 28, 2015 22:44
glibc error
> library(BioCro)
Loading required package: lattice
Loading required package: data.table
data.table 1.9.4 For help type: ?data.table
*** NB: by=.EACHI is now explicit. See README to restore previous behaviour.
Loading required package: coda
Loading required package: knitr
Loading required package: roxygen2
> data(weather05)
> soyGro(weather05)
@dlebauer
dlebauer / read.settings.R
Last active August 29, 2015 14:20
##-------------------------------------------------------------------------------
## Copyright (c) 2012 University of Illinois, NCSA.
## All rights reserved. This program and the accompanying materials
## are made available under the terms of the
## University of Illinois/NCSA Open Source License
## which accompanies this distribution, and is available at
## http://opensource.ncsa.illinois.edu/license.html
##-------------------------------------------------------------------------------
library(XML)
library(lubridate)
@dlebauer
dlebauer / output.csv
Created May 22, 2015 16:01
example ghgvc output
Location Biome S_CO2 S_CH4 S_N2O F_CO2 F_CH4 F_N2O GHGV_CO2 GHGV_CH4 GHGV_N2O swRFV latent crv GHGV
1 tropical_pasture 176.4 0.2 0.2 61.4 -73.5 -36.3 237.8 -73.3 -36.1 NA NA NA 128.4
1 BR_sugarcane 67 NA NA 12.1 1.3 -62.8 79.1 1.3 -62.8 -90.67 358.4 323 17.6
1 BR_soy 7.9 NA NA -15.6 2.5 -61.9 -7.7 2.5 -61.9 -30.12 110.86 -1.5 -67.1
@dlebauer
dlebauer / mxg_treatments.txt
Created June 10, 2015 22:33
Acaroglu 2005 The cultivation and ...
Fertilized (50 kg N ha-) : - Acaroglu 2005
1999-05-01 - planting (plants m-2) : 1.0
1998-05-01 - fertilizer_N : 50.0
- irrigation :
Fertilized (100 kg N ha-) : - Acaroglu 2005
1999-05-01 - planting (plants m-2) : 1.0
1999-05-01 - fertilizer_N : 100.0
- irrigation :
Fertilized (150 kg N ha-) : - Acaroglu 2005
@dlebauer
dlebauer / biocro_miscanthus_median.xml
Created June 11, 2015 04:18
Parameterization of Miscanthus based on priors, data, and tuning
<canopyControl>
<Sp>1.51097549604222</Sp>
<SpD>0</SpD>
<nlayers>10</nlayers>
<kd>0.468201279061426</kd>
<chi.l>1</chi.l>
<mResp>0.02,0.03</mResp>
<heightFactor>3</heightFactor>
<leafwidth>0.04</leafwidth>
<eteq>0</eteq>
@dlebauer
dlebauer / champaign_mxg_settings.xml
Created June 30, 2015 23:59
miscanthus regional settings file
<?xml version="1.0"?>
<pecan>
<outdir>/home/dlebauer/.pecan/biocrotest/</outdir>
<pfts>
<pft>
<name>Miscanthus_x_giganteus</name>
</pft>
</pfts>
<database>
<bety>
@dlebauer
dlebauer / rcp.csv
Created July 1, 2015 21:44
Historical and predicted atmospheric CO2 concentrations
YEAR RCP3_CO2 RCP45_CO2 RCP60_CO2 RCP85_CO2
1765 278.1 278.1 278.1 278.1
1766 278.1 278.1 278.1 278.1
1767 278.2 278.2 278.2 278.2
1768 278.3 278.3 278.3 278.3
1769 278.5 278.5 278.5 278.5
1770 278.6 278.6 278.6 278.6
1771 278.7 278.7 278.7 278.7
1772 278.9 278.9 278.9 278.9
1773 279 279 279 279
@dlebauer
dlebauer / config.xml
Created July 7, 2015 20:39
BioCro config file for pecan
<?xml version="1.0"?>
<config>
<run>
<start.date>1990-01-01 00:00:00</start.date>
<end.date>1995-12-31 23:59:59</end.date>
<met.file>/home/dlebauer/.pecan/dbfiles/met/narr/threehourly//champaign.nc</met.file>
<soil.file>/gpfs_scratch/haohu3//hwsd.nc</soil.file>
</run>
<location>
<latitude>40.1304186951347</latitude>
@dlebauer
dlebauer / alljobs.sh
Last active August 29, 2015 14:24
Batch jobs on roger
#!/bin/bash
# generate list of qsub -t commands for submitting arrays of jobs
# from http://stackoverflow.com/a/31388638/199217
count=20 # number of cores / node
off=0
dirs=({9348..9914})
echo "#!/bin/bash" > runs.sh
@dlebauer
dlebauer / info.xml
Last active September 4, 2015 02:10
<metadatadictionary>
<!-- a dictionary of key value pairs of all available meta data, related to this measurement with this sensor/camera-->
<!--fixed camera data-->
<entry key="camera type" value="vis rgb"/>
<entry key="camera model" value="allied vision GT 3300"/>
<entry key="camera serial number" value="12345678"/>
<entry key="image size width" value="3345"/>
<entry key="image size height" value="2566"/>
<emtry key="rgb bayer pattern" value = "RGGB"/>