Merge branch 'master' of https://github.com/jingxia/pecan

models/biocro/vignettes/workflow.Rmd

@@ -0,0 +1,44 @@
+BioCro PEcAn workflow
+======================
+
+```{r, echo=FALSE,warning=FALSE}
+require(PEcAn.all)
+```
+### Load PEcAn settings file.
+
+Open and read in settings file for PEcAn run.
+
+
+```{r, echo=FALSE,warning=FALSE}
+settings <- read.settings(system.file("pecan.biocro.xml",
+                                      package = "PEcAn.BIOCRO"))
+model <- settings$model$name
+
+
+```
+### Run PEcAn workflow
+
+```{r, echo=FALSE,warning=FALSE,cache=TRUE}
+settings$pfts$pft$name <- "ebifarm.pavi"
+get.trait.data()        	# Query the trait database for data and priors
+
+run.meta.analysis()     	# Run the PEcAn meta.analysis
+```
+
+```{r, echo=FALSE,warning=FALSE,cache=TRUE}
+run.write.configs(model)        # Calls model specific write.configs e.g. write.config.ed.R
+## load met data
+start.model.runs(model)         # Start ecosystem model runs
+
+get.model.output(model)         # 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. 
+                                # OPTIONAL: run.ensemble.analysis(plot.timeseries=TRUE) to get an esemble 
+                                # time-series output for the target variables set in the PEcAn.xml file
+
+### PEcAn workflow run complete
+print("---------- PEcAn Workflow Complete ----------")
+#--------------------------------------------------------------------------------------------------#
+```

qaqc/DESCRIPTION

@@ -5,9 +5,12 @@ Version: 1.0
 Date: 2013-02-21
 Author: David LeBauer
 Maintainer: David LeBauer <[email protected]>
-Description: PEcAn integration and model skill testing 
-Depends: plotrix
+Description: PEcAn integration and model skill testing
+Depends:
+    plotrix
 License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
-LazyData: FALSE
+LazyData: FALSE
+Collate:
+    ''

qaqc/NAMESPACE

@@ -1 +0,0 @@
-exportPattern("^[[:alpha:]]+")

qaqc/R/compare ED2.R

@@ -0,0 +1,8 @@
+library(ncdf4)
+library(PEcAn.utils)
+ed2.2008 <- nc_open ('../output/PEcAn_9/out/9/2004.nc');
+xx <- nc_open ('../output/PEcAn_1/out/1/2004.nc')
+read.output(run.id=1, outdir='../output/PEcAn_1/out/1',
+            start.year=2004, end.year=2009,
+            variables="GPP",
+            model="SIPNET")

qaqc/R/taylor.plot.R

@@ -0,0 +1,35 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
+
+##' plot taylor diagram for benchmark sites
+##' @title Taylor Diagram
+##' @param runid a numeric vector with the id(s) of one or more runs (folder in runs) to plot
+<<<<<<< HEAD
+new.taylor <- function(dataset,runid,siteid){
+  attach(dataset)
+  for(run in runid){
+    for (si in siteid){
+      if (run==runid[1]&&si==siteid[1]){
+        taylor.diagram(obs[site %in% si],get(paste("model",run,sep=""))[site %in% si],pos.cor=FALSE)
+        R <- cor(obs[site %in% si],get(paste("model",run,sep=""))[site %in% si],use="pairwise")
+        sd.f <- sd(get(paste("model",run,sep=""))[site %in% si])
+        lab=paste(paste("model",run,sep=""), paste("site",si,sep=""))
+        text(sd.f * R, sd.f * sin(acos(R)), labels=lab,pos=3)
+      }
+      else {
+        taylor.diagram(obs[site %in% si],get(paste("model",run,sep=""))[site %in% si],pos.cor=FALSE,add=TRUE)
+        R <- cor(obs[site %in% si],get(paste("model",run,sep=""))[site %in% si],use="pairwise")
+        sd.f <- sd(get(paste("model",run,sep=""))[site %in% si])
+        lab=paste(paste("model",run,sep=""), paste("site",si,sep=""))
+        text(sd.f * R, sd.f * sin(acos(R)), labels=lab,pos=3)
+      }
+    }
+    }
+
+}

qaqc/inst/extdata/data.csv

@@ -0,0 +1,7 @@
+"","site","date","obs","model1","model2"
+"1",1,2001,8.75751883891639,14.4636635852943,14.8594772436841
+"2",1,2001,5.570600225645,13.7817039636525,12.831613781413
+"3",1,2002,12.2498618362862,14.7569321148247,12.532613479884
+"4",2,2003,9.91013278196954,14.3464089021932,8.58774284830218
+"5",2,2004,9.96761947380211,12.2236949500956,11.5655498346741
+"6",3,2005,11.8876724213706,6.03194491240988,14.2538246805991

qaqc/inst/extdata/extdata.R

@@ -0,0 +1,26 @@
+#-------------------------------------------------------------------------------
+# 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
+#-------------------------------------------------------------------------------
+
+#--------------------------------------------------------------------------------------------------#
+##' 
+##' generate benchmarking inputs table
+##' @title Generate benchmarking inputs
+##' @param runid the id of the run (folder in runs) to execute
+set.seed(1)
+<<<<<<< HEAD:qaqc/inst/extdata/extdata.R
+testdata=data.frame(site=c(1,1,1,2,2,3),time=c(2001,2001,2002,2003,2004,2005),obs=rnorm(6,10,2),model1=rnorm(6,10,3)+2,model2=rnorm(6,11,3)+2)
+write.csv(testdata, file="/home/carya/pecan/qaqc/inst/extdata/testdata.csv")
+
+read.csv(system.file("extdata/testdata.csv", package = "PEcAn.qaqc")）
+=======
+data=data.frame(site=c(1,1,1,2,2,3),date=c(2001,2001,2002,2003,2004,2005),obs=rnorm(6,10,2),model1=rnorm(6,10,3)+2,model2=rnorm(6,11,3)+2)
+write.csv(data, file="/home/carya/pecan/qaqc/inst/extdata/data.csv")
+
+read.csv(system.file("extdata/data.csv", package = "PEcAn.qaqc")）
+>>>>>>> 2e67e66597e65e855e75f651c1f13bae015c21af:qaqc/inst/extdata/extdata.R

qaqc/inst/test/test.taylor.plot.R

@@ -0,0 +1,25 @@
+#-------------------------------------------------------------------------------
+# 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("plotrix")
+<<<<<<< HEAD
+set.seed(5)
+testdata <- data.frame(site=c(1,1,1,2,2,3),
+                   date=c(2001,2001,2002,2003,2004,2005),
+                   obs=rnorm(6,10,2),model1=rnorm(6,10,3),model2=rnorm(6,10,3))
+=======
+set.seed(1)
+testdata <- data.frame(site=c(1,1,1,2,2,3),
+                   date=c(2001,2001,2002,2003,2004,2005),
+                   obs=rnorm(6,10,2),model1=rnorm(6,10,3)+2,model2=rnorm(6,11,3)+2)
+>>>>>>> 2e67e66597e65e855e75f651c1f13bae015c21af
+
+taylor.diagram(testdata$obs,testdata$model1,pos.cor=FALSE)
+taylor.diagram(testdata$obs,model=testdata$model2,add=TRUE,col="blue")

qaqc/vignettes/compare ED2.Rmd

@@ -0,0 +1,21 @@
+Title
+============
+
+looking at how read.output works
+------
+
+```{r, echo=FALSE, message=FALSE}
+library(ncdf4)
+library(PEcAn.utils)
+ed2.2008 <- nc_open ('../output/PEcAn_9/out/9/2004.nc');
+xx <- nc_open ('../output/PEcAn_13/out/13/2004.nc')
+read.output(run.id=1, outdir='../output/PEcAn_1/out/1',
+            start.year=2004, end.year=2009,
+            variables="GPP",
+            model="SIPNET")
+```
+
+
+```{r fig.width=7, fig.height=6}
+
+```

qaqc/vignettes/compare ED2.html

@@ -0,0 +1,167 @@
+<!DOCTYPE html>
+<!-- saved from url=(0014)about:internet -->
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
+
+<title></title>
+
+<style type="text/css">
+body, td {
+   font-family: sans-serif;
+   background-color: white;
+   font-size: 12px;
+   margin: 8px;
+}
+
+tt, code, pre {
+   font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Monaco, monospace;
+}
+
+h1 { 
+   font-size:2.2em; 
+}
+
+h2 { 
+   font-size:1.8em; 
+}
+
+h3 { 
+   font-size:1.4em; 
+}
+
+h4 { 
+   font-size:1.0em; 
+}
+
+h5 { 
+   font-size:0.9em; 
+}
+
+h6 { 
+   font-size:0.8em; 
+}
+
+a:visited {
+   color: rgb(50%, 0%, 50%);
+}
+
+pre {	
+   margin-top: 0;
+   max-width: 95%;
+   border: 1px solid #ccc;
+   white-space: pre-wrap;
+}
+
+pre code {
+   display: block; padding: 0.5em;
+}
+
+code.r, code.cpp {
+   background-color: #F8F8F8;
+}
+
+table, td, th {
+  border: none;
+}
+
+blockquote {
+   color:#666666;
+   margin:0;
+   padding-left: 1em;
+   border-left: 0.5em #EEE solid;
+}
+
+hr {
+   height: 0px;
+   border-bottom: none;
+   border-top-width: thin;
+   border-top-style: dotted;
+   border-top-color: #999999;
+}
+
+@media print {
+   * { 
+      background: transparent !important; 
+      color: black !important; 
+      filter:none !important; 
+      -ms-filter: none !important; 
+   }
+
+   body { 
+      font-size:12pt; 
+      max-width:100%; 
+   }
+
+   a, a:visited { 
+      text-decoration: underline; 
+   }
+
+   hr { 
+      visibility: hidden;
+      page-break-before: always;
+   }
+
+   pre, blockquote { 
+      padding-right: 1em; 
+      page-break-inside: avoid; 
+   }
+
+   tr, img { 
+      page-break-inside: avoid; 
+   }
+
+   img { 
+      max-width: 100% !important; 
+   }
+
+   @page :left { 
+      margin: 15mm 20mm 15mm 10mm; 
+   }
+
+   @page :right { 
+      margin: 15mm 10mm 15mm 20mm; 
+   }
+
+   p, h2, h3 { 
+      orphans: 3; widows: 3; 
+   }
+
+   h2, h3 { 
+      page-break-after: avoid; 
+   }
+}
+
+</style>
+
+
+
+
+
+</head>
+
+<body>
+<pre><code>## Error in R_nc4_open: No such file or directory
+</code></pre>
+
+<pre><code>## Error: Error in nc_open trying to open file
+## ../output/PEcAn_9/out/9/2004.nc
+</code></pre>
+
+<pre><code>## Error in R_nc4_open: No such file or directory
+</code></pre>
+
+<pre><code>## Error: Error in nc_open trying to open file
+## ../output/PEcAn_1/out/1/2004.nc
+</code></pre>
+
+<pre><code>## 2013-03-07 15:24:53 WARN  [&lt;text&gt;#5: read.output(run.id = 1, outdir = &quot;../output/PEcAn_1/out/1&quot;, ] : File conversion function model2netcdf does not exist for SIPNET
+</code></pre>
+
+<pre><code>## [1] NA
+</code></pre>
+
+</body>
+
+</html>
+

qaqc/vignettes/compare ED2.md

@@ -0,0 +1,28 @@
+
+
+```
+## Error in R_nc4_open: No such file or directory
+```
+
+```
+## Error: Error in nc_open trying to open file
+## ../output/PEcAn_9/out/9/2004.nc
+```
+
+```
+## Error in R_nc4_open: No such file or directory
+```
+
+```
+## Error: Error in nc_open trying to open file
+## ../output/PEcAn_1/out/1/2004.nc
+```
+
+```
+## 2013-03-07 15:24:53 WARN  [<text>#5: read.output(run.id = 1, outdir = "../output/PEcAn_1/out/1", ] : File conversion function model2netcdf does not exist for SIPNET
+```
+
+```
+## [1] NA
+```
+