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Jenny Williams

2013-Aug-15 08:32 UTC

[R] Biomod model access

I am still trying to get my head around biomod2. I have run through the tutorial
a few times, which works really well in a linear format.

But, I want to see the models and assess them at every part of the process. So,
I need to:

1: be able to re-access all the files from /.BIOMOD_DATA/ once R is closed and
all the file links are lost.
e.g myBiomodModelOut

2: call the summary parameters for the models e.g GLM, I can see the files but
not sure how to access them.
e.g>myGLMs <- BIOMOD_LoadModels(myBiomodModelOut, models='GLM')
#just produces a list>summary(myGLMs[1])   Length     Class      Mode
   1 character character
#summary(GLM) doesn't work, but is the output that I am looking to find.

3. find the split datasets used for each of the iterations BIOMOD_Modeling
options; NbRunEval for DataSplit

Any help or pointers in the right direction would be greatly appreciated.
FYI the vignette does not seem to work:
http://127.0.0.1:15505/library/biomod2/doc/index.html


******************
Jenny Williams
Spatial Information Scientist, GIS Unit
Herbarium, Library, Art & Archives Directorate
Royal Botanic Gardens, Kew
Richmond, TW9 3AB, UK

Tel: +44 (0)208 332 5277
email: jenny.williams@kew.org<mailto:jenny.williams@kew.org>
******************

Film: The Forgotten Home of Coffee - Beyond the
Gardens<http://www.youtube.com/watch?v=-uDtytKMKpA&sns=tw>
Stories: Coffee Expedition -
Ethiopia<http://storify.com/KewGIS/coffee-expedition-ethiopia>
             Kew in Harapan Rainforest
Sumatra<http://storify.com/KewGIS/kew-in-harapan-rainforest>
Articles: Seeing the wood for the
trees<http://www.kew.org/ucm/groups/public/documents/document/kppcont_060602.pdf>
How Kew's GIS team and South East Asia botanists are working to help
conserve and restore a rainforest in Sumatra. Download a pdf of this article
here.<http://www.kew.org/ucm/groups/public/documents/document/kppcont_060602.pdf>


________________________________
The Royal Botanic Gardens, Kew is a non-departmental public body with exempt
charitable status, whose principal place of business is at Royal Botanic
Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom.

The information contained in this email and any attachments is intended solely
for the addressee(s) and may contain confidential or legally privileged
information. If you have received this message in error, please return it
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information contained in this email or in any attachment.

Any views expressed in this email do not necessarily reflect the opinions of RBG
Kew.

Any files attached to this email have been inspected with virus detection
software by RBG Kew before transmission, however you should carry out your own
virus checks before opening any attachments. RBG Kew accepts no liability for
any loss or damage which may be caused by software viruses.

	[[alternative HTML version deleted]]

Matthew Bayly

2014-Feb-12 17:22 UTC

head link

[R] Biomod model access

I have been struggling with this same problem. I always have to re-run. 
PLEASE HELP!!

I have however figured out the whole data-format issue & am now able to 
save grid files for use in other GIS programs after they are re-exported.

On Thursday, August 15, 2013 1:32:31 AM UTC-7, Jenny Williams
wrote:>
> I am still trying to get my head around biomod2. I have run through the 
> tutorial a few times, which works really well in a linear format. 
>
> But, I want to see the models and assess them at every part of the 
> process. So, I need to: 
>
> 1: be able to re-access all the files from /.BIOMOD_DATA/ once R is closed 
> and all the file links are lost. 
> e.g myBiomodModelOut 
>
> 2: call the summary parameters for the models e.g GLM, I can see the files 
> but not sure how to access them. 
> e.g 
> >myGLMs <- BIOMOD_LoadModels(myBiomodModelOut, models='GLM') 
> #just produces a list 
> >summary(myGLMs[1]) 
>    Length     Class      Mode 
>    1 character character 
> #summary(GLM) doesn't work, but is the output that I am looking to
find.
>
> 3. find the split datasets used for each of the iterations BIOMOD_Modeling 
> options; NbRunEval for DataSplit 
>
> Any help or pointers in the right direction would be greatly appreciated. 
> FYI the vignette does not seem to work: 
> http://127.0.0.1:15505/library/biomod2/doc/index.html 
>
>
> ****************** 
> Jenny Williams 
> Spatial Information Scientist, GIS Unit 
> Herbarium, Library, Art & Archives Directorate 
> Royal Botanic Gardens, Kew 
> Richmond, TW9 3AB, UK 
>
> Tel: +44 (0)208 332 5277 
> email: jenny.w... at kew.org <javascript:><mailto:jenny.williams
at kew.org<javascript:>>
>
> ****************** 
>
> Film: The Forgotten Home of Coffee - Beyond the Gardens<
> http://www.youtube.com/watch?v=-uDtytKMKpA&sns=tw> 
> Stories: Coffee Expedition - Ethiopia<
> http://storify.com/KewGIS/coffee-expedition-ethiopia> 
>              Kew in Harapan Rainforest Sumatra<
> http://storify.com/KewGIS/kew-in-harapan-rainforest> 
> Articles: Seeing the wood for the trees<
>
http://www.kew.org/ucm/groups/public/documents/document/kppcont_060602.pdf>
>
> How Kew's GIS team and South East Asia botanists are working to help 
> conserve and restore a rainforest in Sumatra. Download a pdf of this 
> article here.<
>
http://www.kew.org/ucm/groups/public/documents/document/kppcont_060602.pdf>
>
>
>
> ________________________________ 
> The Royal Botanic Gardens, Kew is a non-departmental public body with 
> exempt charitable status, whose principal place of business is at Royal 
> Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom. 
>
> The information contained in this email and any attachments is intended 
> solely for the addressee(s) and may contain confidential or legally 
> privileged information. If you have received this message in error, please 
> return it immediately and permanently delete it. Do not use, copy or 
> disclose the information contained in this email or in any attachment. 
>
> Any views expressed in this email do not necessarily reflect the opinions 
> of RBG Kew. 
>
> Any files attached to this email have been inspected with virus detection 
> software by RBG Kew before transmission, however you should carry out your 
> own virus checks before opening any attachments. RBG Kew accepts no 
> liability for any loss or damage which may be caused by software viruses. 
>
>         [[alternative HTML version deleted]] 
>
> ______________________________________________ 
> R-h... at r-project.org <javascript:> mailing list 
> https://stat.ethz.ch/mailman/listinfo/r-help 
> PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html 
> and provide commented, minimal, self-contained, reproducible code. 
>

Matthew Bayly

2014-Feb-14 00:03 UTC

head link

[R] Biomod model access

Hi great that was easy I feel like a bit of a fool for not figuring this 
out.


TO LOAD ALL SAVED MODELS AT ONCE:

library(biomod2)
# change directory to where you stored you?re original models (my documents 
is default if you did not specify). Go into the file models

*# TO LOAD ALL SAVED MODELS FROM PREVIOUS RUN*

rm(list=ls()) #will remove ALL objects currently stored in R

# open old models with the load command load()
list.files() # check to see if all your files appeared correctly

f <- as.list(list.files()) # get ready to load

for(i in f) {

  load(i)

}

R help - Aug 2013 - Biomod model access

[R] Biomod model access

[R] Biomod model access

[R] Biomod model access