big commit with license (fixes PecanProject#926)

.bzrignore

@@ -24,7 +24,7 @@ data/FIA/tmp/
 web/STATUS
 
 # files generated by updatedescription.sh
-DESCRIPTION-e
+DESCRIPTION.bak
 
 # files generated by autobuild.sh
 autobuild

all/DESCRIPTION

@@ -3,7 +3,7 @@ Type: Package
 Title: PEcAn functions used for ecological forecasts and
     reanalysis
 Version: 1.2
-Date: 2012-06-13
+Date: 2012-07-15
 Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang,
     Mike Dietze, Carl Davidson, Rob Kooper, Shawn Serbin
 Maintainer: David LeBauer <[email protected]>

all/inst/tests/test.bety.depreciation.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 
 ## test for feature 896 
 test_that("all references to BETY have been removed from source code",{

all/inst/tests/test.workflow.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 context("tests of overall workflow")
 
 settings <<- read.settings("test.settings.xml")

common/DESCRIPTION

@@ -3,7 +3,7 @@ Type: Package
 Title: PEcAn functions used for ecological forecasts and
     reanalysis
 Version: 1.2
-Date: 2012-06-01
+Date: 2012-07-15
 Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang,
     Mike Dietze, Carl Davidson, Rob Kooper, Shawn Serbin
 Maintainer: David LeBauer <[email protected]>

common/inst/tests/test.read.settings.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 ## require(XML)
 
 ## context("tests for read.settings and related functions")

common/tests/run.all.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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(testthat)
 library(PEcAn.common)
 

db/DESCRIPTION

@@ -2,7 +2,7 @@ Package: PEcAn.DB
 Type: Package
 Title: PEcAn functions used for ecological forecasts and reanalysis
 Version: 1.2
-Date: 2012-06-01
+Date: 2012-07-15
 Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang, Mike Dietze, Carl
     Davidson, Rob Kooper, Shawn Serbin
 Maintainer: David LeBauer <[email protected]>

db/R/get.trait.data.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 ##--------------------------------------------------------------------------------------------------#
 ##' 
 ##' @name get.trait.data

db/R/query.allom.data.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 ## Module to grab allometric information from the raw data table
 ## Will grab both original field data and tallied equations
 ##

db/R/query.base.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 #---------------- Base database query function. ---------------------------------------------------#
 ##' Generic function to query trait database
 ##'

db/R/query.pft.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 #--------------------------------------------------------------------------------------------------#
 ##'  select plant id's associated with pft
 ##'

db/R/query.prior.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 #--------------------------------------------------------------------------------------------------#
 ##' Query priors associated with a string of traits and plant functional type
 ##'

db/R/query.trait.data.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 ##--------------------------------------------------------------------------------------------------#
 ##' Queries data from the trait database and transforms statistics to SE
 ##'

db/R/query.traits.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 #--------------------------------------------------------------------------------------------------#
 ##' Query available trait data associated with a given pft and a list of traits
 ##' 

db/inst/tests/derive.traits.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 test_that("take.samples works";{
   expect_equal(take.samples(summary = data.frame(mean = 1, stat = NA)), 1)
   set.seed(0)

db/inst/tests/test.query.base.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 ## This won't work for me remotely.  We need to figure out how to connect remotely for this test.
 #test_that("query.base does not keep opening connections without closing them", {
 #  newcon <- function() dbConnect("MySQL", group = "ebi_analysis", dbname = "ebi_analysis", password = "b742xsAu", username = "ebi_analys_user", host = 'ebi-forecast.igb.uiuc.edu', port=3306)

db/tests/run.all.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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(testthat)
 library(PEcAn.DB)
 

db/working/query.trait.data.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 #--------------------------------------------------------------------------------------------------#
 ##' Queries data from BETY and transforms statistics to SE
 ##'

db/working/query.trait.data.new.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 #--------------------------------------------------------------------------------------------------#
 ##' 
 ##'

db/working/test.query.bety.trait.data.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 dvr <-  dbDriver("MySQL")
 newcon <- function() dbConnect(dvr, group = "bety", dbname = "bety", password = "3Magic", username = "dlebauer")
 lapply(dbListConnections(drv = drv), dbDisconnect)

db/working/transform.trait.data.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 #--------------------------------------------------------------------------------------------------#
 ##'
 ##' Transforms statistics to SE for data queried from the database and scales relevant traits to a common temperature

depreciated/DESCRIPTION

@@ -2,7 +2,7 @@ Package: PEcAn
 Type: Package
 Title: PEcAn functions used for ecological forecasts and reanalysis
 Version: 1.2
-Date: 2012-05-25
+Date: 2012-07-15
 Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang, Mike Dietze, Carl
     Davidson, Rob Kooper
 Maintainer: David LeBauer <[email protected]>
@@ -27,7 +27,7 @@ Suggests:
     time
 SystemRequirements: JAGS2.2.0, bash, ED2, kepler
 OS_type: unix
-License: University of Illinois/NCSA Open Source License
+License: FreeBSD + file LICENSE
 Copyright: Energy Biosciences Institute, Authors
 LazyLoad: yes
 Collate:

depreciated/R/dtheta.q.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 dtheta.q <- function(x, tr, q) {
   ## find the quantile of the mean
   q.mean <- mean(mean(x) >= x)

depreciated/R/pecan.arrange.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 vp.layout <- function(x, y) viewport(layout.pos.row=x, layout.pos.col=y)
 arrange <- function(..., nrow=NULL, ncol=NULL, as.table=FALSE) {
   dots <- list(...)

depreciated/R/pecan.dtheta.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 pecan.dtheta <- function(samps, q){
   ##calculate values of:
   ## dtheta_0.35, dtheta_0.5, dtheta_0.65 

depreciated/R/pecan.samps.R

@@ -1,3 +1,11 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 pecan.samps <- function(trait.mcmc, priors) {
   trait.mat <- lapply(trait.mcmc, as.matrix)
   trait.nrows <- lapply(trait.mat, function(x) nrow(x))

depreciated/bash/allom.sh

@@ -1,4 +1,12 @@
 #!/bin/bash
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 echo "start allometry analysis"
 env PECANSETTINGS=$1 R --vanilla < ./rscripts/AllomAve.R
 wait

depreciated/bash/batch.jobs.lowp.sh

@@ -1,4 +1,12 @@
 #!/bin/bash
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 for f in ED2INc*[0-9n]; do
   LOG="$f-`date +%Y.%m.%d-%H.%M`.log" #name with date tag for log files, one per ED2IN file 
   if which qsub > /dev/null; then

depreciated/bash/batch.jobs.sh

@@ -1,4 +1,12 @@
 #!/bin/bash
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 for f in ED2INc2*[0-9n]; do
   LOG="$f-`date +%Y.%m.%d-%H.%M`.log" #name with date tag for log files, one per ED2IN file 
   if which qsub > /dev/null; then

depreciated/bash/clean.nodes.sh

@@ -1,4 +1,12 @@
 #!/bin/bash
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 for i in {1..24}
 do 
   ssh compute-0-$i "rm -rf /scratch/*"

depreciated/bash/cleanvm.sh

@@ -1,4 +1,12 @@
 #!/bin/bash
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 
 # run this as:
 # history -c && ./cleanvm.sh

depreciated/bash/create.db.subset.sh

@@ -1,4 +1,12 @@
 #!/bin/bash
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
 
 # to be run after dump.db.subset.sh