loading maxent into biomod2

[Hisham Ali]

Hi all, 

I am really stuck trying to run maxent in biomod2. I have tried a couple things which I outlined below. Would really appreciate help,Please see an outline of script below.

many thanks,

Hisham 

I added maxent to working directory: 

I ran this script and got the error below it: 

myBiomodOption <- BIOMOD_ModelingOptions() 

myBiomodModelOut2 <- BIOMOD_Modeling(

+ myBiomodData,                              #formatted biomod data

+ models = c('MAXENT'),#algorithms used 

+ models.options = myBiomodOption,           #algorithms' parameters

+ NbRunEval=1,                              #No. of evaluation runs

+ DataSplit=75,                              # % used to train, rest for test

+ Prevalence=0.5,                            #                          

+ VarImport=3,                               # 

+ models.eval.meth = c('ROC'),         #evaluation metics

+ SaveObj = TRUE,                            #keep results/output on hard drive

+ rescal.all.models = TRUE,                  #

+ do.full.models = FALSE,                    #

+ modeling.id = paste(myRespName,"FirstModeling",sep="")

+    )

Error: Unable to access jarfile /Users/hishamali/Documents/MPhil

 Getting predictions...Error in file(file, "rt") : cannot open the connection

In addition: Warning messages:

1: In system(command = maxent.cmd, wait = TRUE, intern = TRUE, ignore.stdout = FALSE,  :

  running command 'java -mx512m -jar /Users/hishamali/Documents/MPhil data/HPC files/maxent.jar environmentallayers="PA/models/PAFirstModeling/m_13581801/Back_swd.csv" samplesfile="PA/models/PAFirstModeling/m_13581801/Sp_swd.csv" projectionlayers="PA/models/PAFirstModeling/m_13581801/Predictions/Pred_swd.csv" outputdirectory="PA/models/PAFirstModeling/PA_AllData_RUN1_MAXENT.Phillips_outputs" outputformat=logistic  redoifexists visible=FALSE linear=TRUE quadratic=TRUE product=TRUE threshold=TRUE hinge=TRUE lq2lqptthreshold=80 l2lqthreshold=10 hingethreshold=15 beta_threshold=-1 beta_categorical=-1 beta_lqp=-1 beta_hinge=-1 betamultiplier=1 defaultprevalence=0.5 autorun nowarnings notooltips noaddsamplestobackground' had status 1

2: In file(file, "rt") :

  cannot open file 'PA/models/PAFirstModeling/PA_AllData_RUN1_MAXENT.Phillips_outputs/PA_AllData_RUN1_Pred_swd.csv': No such file or directory

Removing Maxent Temp Data..

*** inherits(g.pred,'try-error')

   ! Note :  PA_AllData_RUN1_MAXENT.Phillips failed!

Error in (function (cl, name, valueClass)  : 

  assignment of an object of class “NULL” is not valid for @‘val’ in an object of class “BIOMOD.stored.array”; is(value, "array") is not TRUE

I tried this line, which successfully loaded Maxent I think into R:

mxtPh<- BIOMOD_ModelingOptions (MAXENT = list(. path_to_maxent.jar = "/Users/hishamali/Documents/MPhil data/HPC files"))

which gave:

$path_to_maxent.jar

[1] "/Users/hishamali/Documents/MPhil data/HPC files"

This time, running the same model gave a different error:

Checking Models arguments...

Error in .Models.check.args(data, models, models.options, NbRunEval, DataSplit,  : 

  models.options argument must be a 'BIOMOD.Model.Options.object' (obtained by running ... ) 

The output of calling mxtPh and myBiomodOption are below.

head(  mxtPh)

1 function (GLM = NULL, GBM = NULL, GAM = NULL, CTA = NULL, ANN = NULL,       

2     SRE = NULL, FDA = NULL, MARS = NULL, RF = NULL, MAXENT.Phillips = NULL, 

3     MAXENT.Tsuruoka = NULL)                                                 

4 {                                                                           

5     opt <- new("BIOMOD.Model.Options")                                      

6     if (!is.null(GLM)) {  

myBiomodOption

GLM = list( type = 'quadratic',

            interaction.level = 0,

            myFormula = NULL,

            test = 'AIC',

            family = binomial(link = 'logit'),

            mustart = 0.5,

            control = glm.control(epsilon = 1e-08, maxit = 50, trace = FALSE

) ),

...................

MAXENT.Phillips = list( path_to_maxent.jar = '/Users/hishamali/Documents/MPhil data/HPC files',

               memory_allocated = 512,

               background_data_dir = 'default',

               maximumbackground = 'default',

               maximumiterations = 200,

               visible = FALSE,

               linear = TRUE,

               quadratic = TRUE,

               product = TRUE,

               threshold = TRUE,

               hinge = TRUE,

               lq2lqptthreshold = 80,

               l2lqthreshold = 10,

               hingethreshold = 15,

               beta_threshold = -1,

               beta_categorical = -1,

               beta_lqp = -1,

               beta_hinge = -1,

               betamultiplier = 1,

               defaultprevalence = 0.5),