Hello, I would like to know whether there are some criteria to judge the relative importance of sensitivity analysis results. that is, if the value of the analysis results is greater than a certain value, it can be judged that the parameter is a sensitivity parameter. For example, if the analysis result is more than 10%, it can be determined that the parameter is sensitive, and the next step of parameter optimization process is needed. Thank you.

Description

calibMuso() and related functions do not work if any of the parameters changed, when paramSweep function is used previously.

How to reproduce the problem?

Run a paramSweep() function without arguments in the directory of the hhs example files (You can download these with the copyMusoExampleTo() function), after that run musoSensi() function in a same way.

RBBGCMuso version:

> 6.0

Possible reason of the failure

CalibMuso uses previous tmp.ini-s so It works on only reduced parameter set, it can be a problem, if you want to use more than one output.

Workaround:

Delete all temporary ini files manually!

Described in the title.

conduct_calc.c

/* Leaf conductance to sensible heat, per unit all-sided LAI */
gl_sh = gl_bl;

/* Canopy conductance to evaporated water vapor */
gc_e_wv = gl_e_wv * epv->proj_lai;

/* Canopy conductane to sensible heat */
gc_sh = gl_sh * epv->proj_lai;

setupMuso(calibrationPar =c(26,50),epcInput="dbf.epc")
compareMuso(
settings = NULL,
parameters=45,
variable = 3009,
calibrationPar = 26,
fileToChange = "epc",
skipSpinup = TRUE,
timeFrame = "day"
)

error:
Error in calibMuso(postProcString = postProcString, settings, calibrationPar = calibrationPar, :
Modell Failure

Hello，I'm sorry to bother you again. When will the detailed description of the GLUE based optimization method be released? How to get the package for sample R scripts that executes the GLUE-based parameter estimation?Thank you.

Hello Sir
How can I get the model simulations at regional scale using RBBGCMuso? I want to simulate the GPP for 10 years at regional scale.

I tried to use the muso4.1.exe with the package, but failed.

Error in (outIndex + 1):(outIndex + numVar) : NA/NaN argument
In addition: Warning messages:
1: In readLines(x, -1) :
incomplete final line found on 'D:\BIOME-BGC\muso4.1/s.ini'
2: In readLines(x, -1) :
incomplete final line found on 'D:\BIOME-BGC\muso4.1/n.ini'

The muso4.1.exe worked well with s.ini/n.ini out of Rstudio.
I am not sure the package (0.6.3.0) is just suitable for the newest version of muso.exe?

parameters.csv:
NAME,INDEX,MIN,MAX
CGP,227,0.3000,0.9000

command:
./musoRand.sh c3grass_apriori_MuSo5.epc EPC 10
c3grass_apriori_MuSo5.epc.zip

Result:
R version 3.3.3 (2017-03-06) -- "Another Canoe"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

RBBGCMuso::randEpc(sourceEpc = "c3grass_apriori_MuSo5.epc", iterations = 10, location = "EPC")
Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 0, 2
Calls: -> musoRand -> cbind -> cbind -> data.frame
In addition: Warning message:
no DISPLAY variable so Tk is not available
Execution halted

Hello, Thanks for your effort in The RBBGCMuso Package, I am planning to run based on the prepared data of the RBBGCMuso Package (https://github.com/hollorol/RBBGCMuso) and run the model step by step based on the manual. I found some errors after running aramSweep(), Please see the below, Could you please help me with how to handle this error?

Warning message:
tbl_df() was deprecated in dplyr 1.0.0.
i Please use tibble::as_tibble() instead.
i The deprecated feature was likely used in the RBBGCMuso
package.
Please report the issue to the authors.
This warning is displayed once every 8 hours.
Call lifecycle::last_lifecycle_warnings() to see where this
warning was generated.

paramSweep()
[1] codes names units descriptions
<0 rows> (or 0-length row.names)

processing file: cfa2b6b8eef9fcf938c7daaaae73308e-paramsweep.rmd
|........... | 20%
ordinary text without R code

|...................... | 40%
label: setup (with options)
List of 1
$ include: logi FALSE

|................................ | 60%
label: unnamed-chunk-1 (with options)
List of 1
$ echo: logi FALSE

|........................................... | 80%
label: unnamed-chunk-2 (with options)
List of 1
$ echo: logi FALSE

Quitting from lines 11-12 (cfa2b6b8eef9fcf938c7daaaae73308e-paramsweep.rmd)
Error in parse(text = x, srcfile = src) : :1:28: unexpected symbol
1: parameters <- read.csv("c("TRANSFERGROWTHP
^
In addition: Warning messages:
1: In paramSweep() :
There are more than one output variable in conection with 3009. The first possibility were choosen.
2: In rmdVec[11] <- paste0("parameters <- read.csv("", parameters, :
number of items to replace is not a multiple of replacement length
3: In do_once((if (is_R_CMD_check()) stop else warning)("The function xfun::isFALSE() will be deprecated in the future. Please ", :
The function xfun::isFALSE() will be deprecated in the future. Please consider using base::isFALSE(x) or identical(x, FALSE) instead.

musoQuickEffect(calibrationPar = 13, startVal = 0, endVal = 9, nSteps = 5, outVar = 3009, yearNum=3)
paramSweep()
[1] codes names units descriptions
<0 rows> (or 0-length row.names)

processing file: 164e1e5a1b2df8a7b2fb3302d7e2e019-paramsweep.rmd
|........... | 20%
ordinary text without R code

|...................... | 40%
label: setup (with options)
List of 1
$ include: logi FALSE

|................................ | 60%
label: unnamed-chunk-1 (with options)
List of 1
$ echo: logi FALSE

|........................................... | 80%
label: unnamed-chunk-2 (with options)
List of 1
$ echo: logi FALSE

Quitting from lines 11-12 (164e1e5a1b2df8a7b2fb3302d7e2e019-paramsweep.rmd)
Error in parse(text = x, srcfile = src) : :1:28: unexpected symbol
1: parameters <- read.csv("c("TRANSFERGROWTHP
^
In addition: Warning messages:
1: In paramSweep() :
There are more than one output variable in conection with 3009. The first possibility were choosen.
2: In rmdVec[11] <- paste0("parameters <- read.csv("", parameters, :
number of items to replace is not a multiple of replacement length

Solution is related to calibMuso call

Add datasource info into the header of the soil file created with the pacakge

musoSensi(parameters = parameters, monteCarloFile="./preservedEpc.csv")
Saving 6.52 x 3.57 in image
BASETEMP WPM CN_lv CN_li CN_root
NaN NaN NaN NaN NaN
CN_fruit CN_stem CLEC FLNR STOMA
NaN NaN NaN NaN NaN
ROOTDEPTH SWCGERMIN MAXLIFETIME NH4MOBILEPROP EMERGENCE
NaN NaN NaN NaN NaN
Warning messages:
1: Removed 15 rows containing missing values (position_stack).
2: Removed 15 rows containing missing values (position_stack).

In this context silhouette means an ensemble of simulations that sweeps the entire output variable space for a Monte-Carlo based experiment. The output can be a plethora of gray curves for e.g. LAI or GPP that shows all possible annual curves. The functionality can be used to highlight incorrect parameterization or improper parameter intervals. It can improve the quality of the optimization process by visual inspection.

Description

In quickeffect the parameter values are rounded to the second decimal places. In some cases 4 decimal places would be needed. For example if you provide 0.00-0.05 values for fraction of leaf N in PEP, the simulation is running only 6 times.

How to reproduce the bug

musoQuickEffect(calibrationPar = 62, startVal = 0, endVal = 0.05, nSteps = 10, outVar = 3009)

Hello,I used the sample data and my own data for sensitivity analysis according to the description of RBBGCMuso, but I don't know why there is such an error prompt,thank you.
library(RBBGCMuso)

setwd("D:/F8_BGC_R")
parameters <- read.csv("parameters.csv")
musoSensi(iterations = 10000, varIndex = 2)
[1] 1
Error in ans[npos] <- rep(no, length.out = len)[npos] :replacement has length zero
musoMonte(parameters=parameters,iterations=1000,varIndex=8)
[1] 1
Error in ans[npos] <- rep(no, length.out = len)[npos] : replacement has length zero

The package's GitHub page does not have a proper description.

I am a student who is very interested in ecology. I am very interested in your work. I am currently trying to test.
I have an immature question, paramSweep and musosensi，are there any differences between these two functions？and why should they be developed separately?
I understand that they are also used to obtain the parameters with the smallest error from the actual results. Otherwise, I can’t think of the difference.

I am trying to change some lines of the ini file and after that runs the BBGC-MuSo (I already know how to change the EPC file):
`library(RBBGCMuso)
setwd("E:/language/R_yuyan/muso_run/space_run/space_test")
settings = setupMuso(calibrationPar =c(4,31,39,42), # row indices of the variables in INI file that I wish to change
)
p = read.table("E:/language/R_yuyan/muso_run/space_run/space_test/TEST.txt",header=F)

change some lines of ini and then runs the BBGC-MuSo 10 times

for(i in 1:10){
results = calibMuso(settings,skipSpinup = TRUE,parameters=p[i,], timee="d", fileToChange="ini",
)

}
where TEST.txt is:cbs.met43 700 cbs.soi dbf.epc
dhs.met43 300 dhs.soi enf.epc`

I encounter the following error:
Biome-BGC simulation started 20902ERROR reading int value from enf.epc ERROR reading woody/non-woody flag, epc_init() ERROR in call to epc_init() from pointbgc.c... Exiting Error in value[[3L]](cond) : Cannot read binary output, please check if the output type is set 2 in the ini files! besides : Warning message: In file(binaryname, "rb") :
and I found that the INI file has not changed, while the EPC file has changed by the given row indices
So, if i want to change the parameters in INI file, especially the SOIL filename, what can I do ?

Dear professor,
When I start the sensitivity analysis by the function musoSensi, there was an unexpected problem as below:
musoSensi(iterations = 10000, varIndex = 1)
Error in depTableMaker(constMatrix, parameters) :
All group members of the group (6) have to be in parameters if sourceFile not(epc file)
I am confused in this problem. Sorry to bother you , and hope to get your respond early!