Accessing BIOMOD2 model output is possible, but a bit convoluted.
Here's a whole chunk of code that creates a reproducible example; the
most important part is at the end.
I hope this is enough to let you get going.
Sarah
### First use a slightly modified version of the example from the help file
# species occurrences
DataSpecies <-
read.csv(system.file("external/species/mammals_table.csv",
package="biomod2"))
# the name of studied species
myRespName <- 'GuloGulo'
# the presence/absences data for our species
myResp <- as.numeric(DataSpecies[,myRespName])
# the XY coordinates of species data
myRespXY <- DataSpecies[,c("X_WGS84","Y_WGS84")]
# Environmental variables extracted from BIOCLIM (bio_3, bio_4,
bio_7, bio_11 & bio_12)
myExpl = stack( system.file( "external/bioclim/current/bio3.grd",
package="biomod2"),
system.file( "external/bioclim/current/bio4.grd",
package="biomod2"),
system.file( "external/bioclim/current/bio7.grd",
package="biomod2"),
system.file(
"external/bioclim/current/bio11.grd", package="biomod2"),
system.file(
"external/bioclim/current/bio12.grd", package="biomod2"))
# 1. Formatting Data
myBiomodData <- BIOMOD_FormatingData(resp.var = myResp,
expl.var = myExpl,
resp.xy = myRespXY,
resp.name = myRespName)
# 2. Defining Models Options using default options.
myBiomodOption <- BIOMOD_ModelingOptions()
# 3. Doing Modelisation
myBiomodModelOut <- BIOMOD_Modeling( myBiomodData,
models = c('SRE','RF', 'GAM'),
models.options = myBiomodOption,
NbRunEval=2,
DataSplit=80,
VarImport=0,
models.eval.meth = c('ROC'),
do.full.models=FALSE,
modeling.id="test")
### assume we quit without saving the workspace, since everything is
on disk anyway
### q("no") ## commented out for your protection
### here's the access code
### come back later
### everything is stored in GuloGulo, and all thing are R objects
R
> library(biomod2)
# R objects can be imported with load()
R> load("GuloGulo/models/test/GuloGulo_AllData_RUN1_GAM")
R> ls()
[1] "GuloGulo_AllData_RUN1_GAM"
R> GuloGulo_AllData_RUN1_GAM
# various outputs deleted
## here's how to get the GAM itself
R> get_formal_model(GuloGulo_AllData_RUN1_GAM)
Family: binomial
Link function: logit
Formula:
GuloGulo ~ 1 + s(bio3, k = -1) + s(bio4, k = -1) + s(bio7, k = -1) +
s(bio11, k = -1) + s(bio12, k = -1)
<environment: 0x9a5e918>
Estimated degrees of freedom:
3.04 6.51 6.07 5.78 5.08 total = 27.47
UBRE score: -0.6562
## and it can be summarized
R> summary(get_formal_model(GuloGulo_AllData_RUN1_GAM))
Family: binomial
Link function: logit
Formula:
GuloGulo ~ 1 + s(bio3, k = -1) + s(bio4, k = -1) + s(bio7, k = -1) +
s(bio11, k = -1) + s(bio12, k = -1)
<environment: 0x9a5e918>
Parametric coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -11.14 4.23 -2.63 0.0085
Approximate significance of smooth terms:
edf Ref.df Chi.sq p-value
s(bio3) 3.04 3.74 15.9 0.0027
s(bio4) 6.51 6.98 151.1 < 2e-16
s(bio7) 6.07 6.77 107.6 < 2e-16
s(bio11) 5.78 6.46 130.5 < 2e-16
s(bio12) 5.08 6.06 59.2 7.3e-11
R-sq.(adj) = 0.738 Deviance explained = 72.2%
UBRE score = -0.65625 Scale est. = 1 n = 2488
On Wed, Feb 12, 2014 at 12:22 PM, Matthew Bayly <matt.j.ba...@gmail.com> wrote:
> 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
>>
>>
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