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ebimodeling / biocro_regional

Enabling BioCro to run regionally, starting with midwest miscanthus
University of Illinois/NCSA Open Source License
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Compare Miscanthus parameters to defaults #9

Closed dlebauer closed 9 years ago

dlebauer commented 9 years ago
dlebauer commented 9 years ago

As discussed in ebimodeling/Miscanthus_water_use_manuscript#18:

Fernando's paper (Miguez et al 2009) used Vmax = 39 and ...

image

UrsulaRuiz commented 9 years ago

Hi Dave, In the figure I showed in the last meeting I used 39 for Vmax.

On Wed, Jul 1, 2015 at 12:30 PM, David LeBauer notifications@github.com wrote:

As discussed in ebimodeling/Miscanthus_water_use_manuscript#18 https://github.com/ebimodeling/Miscanthus_water_use_manuscript/issues/18 :

Fernando's paper (Miguez et al 2009 http://onlinelibrary.wiley.com/doi/10.1111/j.1757-1707.2009.01019.x/epdf) used Vmax = 39 and ...

[image: image] https://cloud.githubusercontent.com/assets/464871/8460747/d9317cbc-1fec-11e5-9a5b-cecffc8b70d9.png

— Reply to this email directly or view it on GitHub https://github.com/ebimodeling/biocro_regional/issues/9#issuecomment-117758762 .

Dr. Ursula Ruiz-Vera Postdoctoral Research Associate

Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign

1206 W. Gregory Drive, Room 1400 Urbana, Illinois 61801 ruizver1@illinois.edu +407-694-6405

dlebauer commented 9 years ago

@UrsulaRuiz are you otherwise using defaults?

UrsulaRuiz commented 9 years ago

Yes, I am using defaults. The values I entered before the run are: the type of soil, the day of emerge, day for the peak of yield, the initial rhizome .

I still need to change the Tp1 tp2 in phenology.

On Thu, Jul 2, 2015 at 9:27 AM, David LeBauer notifications@github.com wrote:

@UrsulaRuiz https://github.com/UrsulaRuiz are you otherwise using defaults?

— Reply to this email directly or view it on GitHub https://github.com/ebimodeling/biocro_regional/issues/9#issuecomment-118049943 .

Dr. Ursula Ruiz-Vera Postdoctoral Research Associate

Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign

1206 W. Gregory Drive, Room 1400 Urbana, Illinois 61801 ruizver1@illinois.edu +407-694-6405

dlebauer commented 9 years ago

What values are you using for

?

On Thu, Jul 2, 2015 at 9:36 AM, UrsulaRuiz notifications@github.com wrote:

Yes, I am using defaults. The values I entered before the run are: the type of soil, the day of emerge, day for the peak of yield, the initial rhizome .

I still need to change the Tp1 tp2 in phenology.

On Thu, Jul 2, 2015 at 9:27 AM, David LeBauer notifications@github.com wrote:

@UrsulaRuiz https://github.com/UrsulaRuiz are you otherwise using defaults?

— Reply to this email directly or view it on GitHub < https://github.com/ebimodeling/biocro_regional/issues/9#issuecomment-118049943

.

Dr. Ursula Ruiz-Vera Postdoctoral Research Associate

Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign

1206 W. Gregory Drive, Room 1400 Urbana, Illinois 61801 ruizver1@illinois.edu +407-694-6405

— Reply to this email directly or view it on GitHub https://github.com/ebimodeling/biocro_regional/issues/9#issuecomment-118052065 .

UrsulaRuiz commented 9 years ago

They are specified in the Miscanthus_Manuscript.RMd file in the inst folder which is inside the Miscanthus_water_use

The values are from the energy farm data

On Thu, Jul 2, 2015 at 9:43 AM, David LeBauer notifications@github.com wrote:

What values are you using for

  • day of emergence
  • day for the peak of yield (and what parameter is this?)
  • initial rhizome .
  • Tp1, tp2,

?

On Thu, Jul 2, 2015 at 9:36 AM, UrsulaRuiz notifications@github.com wrote:

Yes, I am using defaults. The values I entered before the run are: the type of soil, the day of emerge, day for the peak of yield, the initial rhizome .

I still need to change the Tp1 tp2 in phenology.

On Thu, Jul 2, 2015 at 9:27 AM, David LeBauer notifications@github.com wrote:

@UrsulaRuiz https://github.com/UrsulaRuiz are you otherwise using defaults?

— Reply to this email directly or view it on GitHub <

https://github.com/ebimodeling/biocro_regional/issues/9#issuecomment-118049943

.

Dr. Ursula Ruiz-Vera Postdoctoral Research Associate

Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign

1206 W. Gregory Drive, Room 1400 Urbana, Illinois 61801 ruizver1@illinois.edu +407-694-6405

— Reply to this email directly or view it on GitHub < https://github.com/ebimodeling/biocro_regional/issues/9#issuecomment-118052065

.

— Reply to this email directly or view it on GitHub https://github.com/ebimodeling/biocro_regional/issues/9#issuecomment-118054930 .

Dr. Ursula Ruiz-Vera Postdoctoral Research Associate

Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign

1206 W. Gregory Drive, Room 1400 Urbana, Illinois 61801 ruizver1@illinois.edu +407-694-6405

dlebauer commented 9 years ago

both the definition of newphenoParms and its use are commented out ... are you planning to use these values?

#newphenoParms <- phenoParms(tp1=525, tp2=1226, tp3=1927, tp4=3500, tp5=3600, tp6=4000, kRhizome1=-0.1, kRhizome2=-0.08)
...
res09 <- BioGro(WetDat=weather09, iRhizome=iRhizome, day1=day1, dayn=dayn, photoControl=newphotoparameters, soilControl = soilparameters_565B)#, phenoControl=newphenoParms)
UrsulaRuiz commented 9 years ago

I need to change tp1 and tp2 in each year.

On Thu, Jul 2, 2015 at 11:52 AM, David LeBauer notifications@github.com wrote:

both the definition of newphenoParms and its use are commented out ... are you planning to use these values?

newphenoParms <- phenoParms(tp1=525, tp2=1226, tp3=1927, tp4=3500, tp5=3600, tp6=4000, kRhizome1=-0.1, kRhizome2=-0.08)...res09 <- BioGro(WetDat=weather09, iRhizome=iRhizome, day1=day1, dayn=dayn, photoControl=newphotoparameters, soilControl = soilparameters_565B)#, phenoControl=newphenoParms)

— Reply to this email directly or view it on GitHub https://github.com/ebimodeling/biocro_regional/issues/9#issuecomment-118091461 .

Dr. Ursula Ruiz-Vera Postdoctoral Research Associate

Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign

1206 W. Gregory Drive, Room 1400 Urbana, Illinois 61801 ruizver1@illinois.edu +407-694-6405

dlebauer commented 9 years ago

How do you determine tp1 and tp2?

On Friday, July 3, 2015, UrsulaRuiz notifications@github.com wrote:

I need to change tp1 and tp2 in each year.

On Thu, Jul 2, 2015 at 11:52 AM, David LeBauer <notifications@github.com javascript:_e(%7B%7D,'cvml','notifications@github.com');> wrote:

both the definition of newphenoParms and its use are commented out ... are you planning to use these values?

newphenoParms <- phenoParms(tp1=525, tp2=1226, tp3=1927, tp4=3500,

tp5=3600, tp6=4000, kRhizome1=-0.1, kRhizome2=-0.08)...res09 <- BioGro(WetDat=weather09, iRhizome=iRhizome, day1=day1, dayn=dayn, photoControl=newphotoparameters, soilControl = soilparameters_565B)#, phenoControl=newphenoParms)

— Reply to this email directly or view it on GitHub < https://github.com/ebimodeling/biocro_regional/issues/9#issuecomment-118091461

.

Dr. Ursula Ruiz-Vera Postdoctoral Research Associate

Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign

1206 W. Gregory Drive, Room 1400 Urbana, Illinois 61801 ruizver1@illinois.edu javascript:_e(%7B%7D,'cvml','ruizver1@illinois.edu'); +407-694-6405

— Reply to this email directly or view it on GitHub https://github.com/ebimodeling/biocro_regional/issues/9#issuecomment-118397637 .

djaiswal commented 9 years ago

@dlebauer We are adjusting them empirically to match observations of LAI growth observed at the Efarm. Even if we do not change tp1 and tp2, final yields estimates are still acceptable. we plan to change them only to match pattern of LAI growth. There should not be any need to change them if you are, at this moment, interested in final yield.