Issue with write.config.MODEL w/ PFT w/ only a single prior / param

[serbinsh]

Running a model with a single prior / param seems to result in a improperly formated trait.samples() object to write.config.MODEL.

2016-04-04 16:46:05 INFO   [run.write.configs] :
   Selected Quantiles: '0.159','0.5','0.841'
2016-04-04 16:46:05 INFO   [run.write.configs] :
   ----- Writing model run config files ----

Run directory:
/data/sserbin/Modeling/maat/maat_test//run/SA-median

Run scripts directory:
/data/software/maat/dev_ngeet//run_scripts

Source directory:
/data/software/maat/dev_ngeet//src

mkdir: cannot create directory `/data/sserbin/Modeling/maat/maat_test//run/SA-median': File exists
mkdir: cannot create directory `/data/sserbin/Modeling/maat/maat_test//run/SA-median/logs': File exists
[1] 73.6921
NULL
NULL

Run directory:
/data/sserbin/Modeling/maat/maat_test//run/SA-maat.all.plants-Vcmax-0.159

Run scripts directory:
/data/software/maat/dev_ngeet//run_scripts

Source directory:
/data/software/maat/dev_ngeet//src

mkdir: cannot create directory `/data/sserbin/Modeling/maat/maat_test//run/SA-maat.all.plants-Vcmax-0.159': File exists
mkdir: cannot create directory `/data/sserbin/Modeling/maat/maat_test//run/SA-maat.all.plants-Vcmax-0.159/logs': File exists
            Vcmax
73.69210 72.33965
NULL
NULL

Run directory:
/data/sserbin/Modeling/maat/maat_test//run/SA-maat.all.plants-Vcmax-0.841

Run scripts directory:
/data/software/maat/dev_ngeet//run_scripts

Source directory:
/data/software/maat/dev_ngeet//src

mkdir: cannot create directory `/data/sserbin/Modeling/maat/maat_test//run/SA-maat.all.plants-Vcmax-0.841': File exists
mkdir: cannot create directory `/data/sserbin/Modeling/maat/maat_test//run/SA-maat.all.plants-Vcmax-0.841/logs': File exists
            Vcmax
73.69210 75.04328
NULL
NULL

Run directory:
/data/sserbin/Modeling/maat/maat_test//run/ENS-00001

Run scripts directory:
/data/software/maat/dev_ngeet//run_scripts

Source directory:
/data/software/maat/dev_ngeet//src

mkdir: cannot create directory `/data/sserbin/Modeling/maat/maat_test//run/ENS-00001': File exists
mkdir: cannot create directory `/data/sserbin/Modeling/maat/maat_test//run/ENS-00001/logs': File exists
[1] 73.6921
NULL
NULL
2016-04-04 16:46:05 INFO   [run.write.configs] :
   ###### Finished writing model run config files #####

Note that despite only running with Vcmax the object expects two params resulting in a blank value or the median being copied together with the quantile value. If I then add, say, SLA to the pft then the expected behavior is the result

2016-04-04 16:52:54 INFO   [run.write.configs] :
   Selected Quantiles: '0.159','0.5','0.841'
2016-04-04 16:52:54 INFO   [run.write.configs] :
   ----- Writing model run config files ----

Run directory:
/data/sserbin/Modeling/maat/maat_test//run/SA-median

Run scripts directory:
/data/software/maat/dev_ngeet//run_scripts

Source directory:
/data/software/maat/dev_ngeet//src

mkdir: cannot create directory `/data/sserbin/Modeling/maat/maat_test//run/SA-median': File exists
mkdir: cannot create directory `/data/sserbin/Modeling/maat/maat_test//run/SA-median/logs': File exists
List of 2
 $ maat.all.plants:'data.frame':    1 obs. of  2 variables:
  ..$ SLA  : num 16.9
  ..$ Vcmax: num 73.7
 $ env            :'data.frame':    1 obs. of  0 variables
        SLA   Vcmax
50 16.94213 73.6921
[1] "SLA"   "Vcmax"
[1] "SLA"   "Vcmax"

Run directory:
/data/sserbin/Modeling/maat/maat_test//run/SA-maat.all.plants-SLA-0.159

Run scripts directory:
/data/software/maat/dev_ngeet//run_scripts

Source directory:
/data/software/maat/dev_ngeet//src

mkdir: cannot create directory `/data/sserbin/Modeling/maat/maat_test//run/SA-maat.all.plants-SLA-0.159': File exists
List of 2
 $ maat.all.plants:'data.frame':    1 obs. of  2 variables:
  ..$ SLA  : num 16.8
  ..$ Vcmax: num 73.7
 $ env            :'data.frame':    1 obs. of  0 variables
        SLA   Vcmax
50 16.82486 73.6921
[1] "SLA"   "Vcmax"
[1] "SLA"   "Vcmax"

Run directory:
/data/sserbin/Modeling/maat/maat_test//run/SA-maat.all.plants-SLA-0.841

Run scripts directory:
/data/software/maat/dev_ngeet//run_scripts

Source directory:
/data/software/maat/dev_ngeet//src

mkdir: cannot create directory `/data/sserbin/Modeling/maat/maat_test//run/SA-maat.all.plants-SLA-0.841': File exists
List of 2
 $ maat.all.plants:'data.frame':    1 obs. of  2 variables:
  ..$ SLA  : num 17.1
  ..$ Vcmax: num 73.7
 $ env            :'data.frame':    1 obs. of  0 variables
        SLA   Vcmax
50 17.05622 73.6921
[1] "SLA"   "Vcmax"
[1] "SLA"   "Vcmax"

Run directory:
/data/sserbin/Modeling/maat/maat_test//run/SA-maat.all.plants-Vcmax-0.159

Run scripts directory:
/data/software/maat/dev_ngeet//run_scripts

Source directory:
/data/software/maat/dev_ngeet//src

mkdir: cannot create directory `/data/sserbin/Modeling/maat/maat_test//run/SA-maat.all.plants-Vcmax-0.159': File exists
mkdir: cannot create directory `/data/sserbin/Modeling/maat/maat_test//run/SA-maat.all.plants-Vcmax-0.159/logs': File exists
List of 2
 $ maat.all.plants:'data.frame':    1 obs. of  2 variables:
  ..$ SLA  : num 16.9
  ..$ Vcmax: num 72.3
 $ env            :'data.frame':    1 obs. of  0 variables
        SLA    Vcmax
50 16.94213 72.33965
[1] "SLA"   "Vcmax"
[1] "SLA"   "Vcmax"

Run directory:
/data/sserbin/Modeling/maat/maat_test//run/SA-maat.all.plants-Vcmax-0.841

Run scripts directory:
/data/software/maat/dev_ngeet//run_scripts

Source directory:
/data/software/maat/dev_ngeet//src

mkdir: cannot create directory `/data/sserbin/Modeling/maat/maat_test//run/SA-maat.all.plants-Vcmax-0.841': File exists
mkdir: cannot create directory `/data/sserbin/Modeling/maat/maat_test//run/SA-maat.all.plants-Vcmax-0.841/logs': File exists
List of 2
 $ maat.all.plants:'data.frame':    1 obs. of  2 variables:
  ..$ SLA  : num 16.9
  ..$ Vcmax: num 75
 $ env            :'data.frame':    1 obs. of  0 variables
        SLA    Vcmax
50 16.94213 75.04328
[1] "SLA"   "Vcmax"
[1] "SLA"   "Vcmax"

Run directory:
/data/sserbin/Modeling/maat/maat_test//run/ENS-00001

Run scripts directory:
/data/software/maat/dev_ngeet//run_scripts

Source directory:
/data/software/maat/dev_ngeet//src

mkdir: cannot create directory `/data/sserbin/Modeling/maat/maat_test//run/ENS-00001': File exists
mkdir: cannot create directory `/data/sserbin/Modeling/maat/maat_test//run/ENS-00001/logs': File exists
List of 2
 $ maat.all.plants:'data.frame':    1 obs. of  2 variables:
  ..$ SLA  : num 16.9
  ..$ Vcmax: num 73.7
 $ env            :'data.frame':    1 obs. of  0 variables
        SLA   Vcmax
50 16.94213 73.6921
[1] "SLA"   "Vcmax"
[1] "SLA"   "Vcmax"
2016-04-04 16:52:55 INFO   [run.write.configs] :
   ###### Finished writing model run config files #####

There is no more NULL when trying to display print(trait.values[[settings$pfts$pft$name]]) ##HAACK OR traits <- convert.samples.MAAT(trait.samples = trait.values[[settings$pfts$pft$name]]) print(traits)

Which is this function:

convert.samples.MAAT <- function(trait.samples){

    if(is.list(trait.samples)) trait.samples <- as.data.frame(trait.samples)
    ## first rename variables
    trait.names <- colnames(trait.samples)
    print(trait.names)
}

[serbinsh]

@dlebauer when you were working up BIOCRO did you notice anything like this?

[dlebauer]

I've seen the 'cannot create directory' errors in the last few weeks but if I recall I 'solved' it by changing permissions to allow write access. I didn't realize it was a bigger problem. On Mon, Apr 4, 2016 at 4:01 PM Shawn P. Serbin notifications@github.com wrote:

@dlebauer https://github.com/dlebauer when you were working up BIOCRO did you notice anything like this?

— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub https://github.com/PecanProject/pecan/issues/776#issuecomment-205495066

[mdietze]

I suspect the code is balking to run a single parameter PFT because R is automatically changing the type of a data object somewhere from data.frame or matrix to vector.

[serbinsh]

@mdietze Yeah, I think you are correct. Will have to go back further in the code to see if we can suss this type change out. However, running with two priors works fine.

[tonygardella]

I'll be adding instructions in the "Adding an Ecosystem" page in gitbook to associate two priors with a pft for a given model before writing write.configs.

Also, leave this open for reference.

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