From 714698856414e245187dac9075c191f15fc5581a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Zolt=C3=A1n=20BARCZA?= Date: Tue, 22 Jan 2019 15:57:53 +0100 Subject: [PATCH] Update README.org almost ready --- README.org | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/README.org b/README.org index 7da9d33..0be6728 100644 --- a/README.org +++ b/README.org @@ -141,15 +141,23 @@ Assume that we would like to dig a bit deeper with the model and understand the musoQuickEffect(calibrationPar = 25, startVal = 0,endVal = 9,nSteps = 5,outVar = 3009) #+END_SRC +This command selects the 25th line in the ecophysiological constants (EPC) file (this is base temperature), then it starts to replace the original value from 0 to 9 in 5 consecutive steps. In this example GPP is selected (variable number 3009, which is the 27th variable), so the effect of varying base temperature on GPP is calculated using 9 simulations. The result is a spectacular plot where color coding is used distinguish the parameter values. -*** Study the effect of ecophysiological parameters using parameterSweep +*** Study the effect of ecophysiological parameters using paramSweep -The parameterSweep function is the extension of the musoQuickEffect. It can test the effect of the selected parameters on the model results in once. The result of the parameterSweep function is a single HTML file with embedded images. +The paramSweep function is the extension of the musoQuickEffect. It can test the effect of the selected parameters on the model results in once. The result of the paramSweep function is a single HTML file with embedded images. paramSweep needs a csv file called parameters.csv which defines the parameters of interest and the corresponding parameter intervals. In case of the hhs sample dataset there is an example parameters/csv file (please open it and check). Note that there is a tricky part in the parameters.csv as the parameter selection is not straightforward in case of multiple columns (see the end of the EPC file). The logic is that real numbers are used to select the appropriate parameter from multiple columns. In the provided example "keles,170.61,0,1000" means that in the 170th line of the EPC file there are 7 columns (numbering starts from 0, so it is 6), and we would like to adjust the 2nd column (marked by 1), which ends up with 170.61. 0,1000 means that sweep starts at 0 and ends with 1000. Invoke the paramSweep with simply issuing this command: + +#+BEGIN_SRC R :eval no +paramSweep() +#+END_SRC + +*IMPORTANT NOTE: After the execution of thos command a pop-up window will be opened to select the appropriate parameters.csv file. Due to some R related issues at present the dialog window will appear BEHIND THE MAIN R WINDOW, so it might be hidden from the user. Please check the Windows taskbar and find the dialog window, then select the parameters.csv.* +In advanced mode there is possibility to select the parameters.csv file using the parameters of paramSweep. *** Sensitivity analysis [[http://agromo.agrar.mta.hu/files/musoSensi_usage_v6_FINAL.pdf][See this link for details about the sensitivity analysis.]] -Note that parameters.csv is provided in the hhs example dataset, so you don't have to create it manually. +Note that parameters.csv is provided in the hhs example dataset, so you don't have to create it manually. *** Contact