checkout MAXENT issue in modules issues

[goldingn]

Tim has an old issue here: https://github.com/zoonproject/modules/issues/9

may not still be a problem, but worth checking out.

For future I think we should continue using zoon issues for tracking modules issues, since they interact

[AugustT]

I can confirm that this still produces an error:

sdm <- workflow(SpOcc(species = 'Eresus sandaliatus', extent = c(-10, 45, 10, 65), databases = 'gbif'), 
                Bioclim(extent = c(-10, 45, 10, 65)), 
                OneHundredBackground, 
                BiomodModel(modelType = 'MAXENT'), 
                SurfaceMap
                )

Caught errors: Error in modOut[[i]][[j]][[k]]: subscript out of bounds

I'm looking into this now

[AugustT]

The warnings that arrived with the error above suggest I was missing a nessecary file:

In addition: Warning messages:
1: package ‘spocc’ was built under R version 3.2.2 
2: In .Models.check.args(data, models, models.options, NbRunEval, DataSplit,  :
  The maxent.jar file is missing. You need to download this file (http://www.cs.princeton.edu/~schapire/maxent) and put the maxent.jar file in your working directory -> MAXENT was switched off

When I downloaded this file into my working directory I no longer had the error, though a new error arrived:

Error in file(file, "rt") : cannot open the connection
In addition: Warning messages:
1: running command 'java' had status 1 
2: running command 'java -mx512m -jar W:/PYWELL_SHARED/Pywell Projects/BRC/Tom August/ZOON/zoon_package/maxent.jar environmentallayers="Species/models/1439988028/m_33731353/Back_swd.csv" samplesfile="Species/models/1439988028/m_33731353/Sp_swd.csv" projectionlayers="Species/models/1439988028/m_33731353/Predictions/Pred_swd.csv" outputdirectory="Species/models/1439988028/Species_AllData_Full_MAXENT_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 defaultprevalence=0.5 autorun nowarnings notooltips noaddsamplestobackground' had status 1 
3: In file(file, "rt") :
  cannot open file 'Species/models/1439988028/Species_AllData_Full_MAXENT_outputs/Species_AllData_Full_Pred_swd.csv': No such file or directory

This looks like a file is supposed to be written but isn't, and it looks to be during the predictions step. has anyone seen this before @timcdlucas ?

[timcdlucas]

I'm not really the right person to ask as I'm not sure I've ever actually run a maxent model...

Found this from google that is the same error. But there's quite a large number of potential fixes. https://groups.google.com/forum/#!topic/maxent/_MBiGp5eDGw

Definitely worth making sure biomod is working first, then dealing with biomod in zoon problems.

[AugustT]

I'm not getting anywhere with this. I followed @timcdlucas suggestion and can't even get it to work in biomod using the package example. I would be interesetd to know if this code works for anyone else? (remember you have to download the maxent.jar file first)

# species occurrences
DataSpecies <- read.csv(system.file("external/species/mammals_table.csv",
                                    package="biomod2"))
head(DataSpecies)

# 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('MAXENT','RF'), 
                                     models.options = myBiomodOption, 
                                     NbRunEval=2, 
                                     DataSplit=80, 
                                     VarImport=0, 
                                     models.eval.meth = c('TSS','ROC'),
                                     do.full.models=FALSE,
                                     modeling.id="test")

[goldingn]

Bombed out on my mac as I don't have JRE installed (nope, you can't make me). So ran it on an ubuntu machine and it ran just fine.

What error are you getting?

[timcdlucas]

It did not work for me until I used myBiomodOption <- BIOMOD_ModelingOptions( MAXENT = list( path_to_maxent.jar = getwd()) )

instead. With the jar file in the working directory. Also on Ubuntu.

[AugustT]

Thanks guys, I'll pick this up tomorrow

[AugustT]

Think I got to the bottom of this error. It is because of a space in the file path to the .jar file. This then breaks when it is used in a shell command call to java.

I moved the .jar file to a path without a space and it ran just fine using the code:

myBiomodOption <- BIOMOD_ModelingOptions(MAXENT = list(path_to_maxent.jar = 'C:/Users/tomaug/Documents/maxent.jar'))

I could then also get zoon to run without error by setting this as my working directory:

setwd('C:/Users/tomaug/Documents')

sdm <- workflow(SpOcc(species = 'Eresus sandaliatus', extent = c(-10, 45, 10, 65), databases = 'gbif'), 
                Bioclim(extent = c(-10, 45, 10, 65)), 
                OneHundredBackground, 
                BiomodModel(modelType = c('MAXENT')), 
                SurfaceMap)

This is really a bug with biomod2, I'll raise it with their maintainer

[AugustT]

This is not an issue with...

# _____________     ____________       ____________         ___________________
#  \  ______   \__ _\   ______  \     _\   ______  \       _\      ___  \______
#   \       /   \  \ \  \     \  \__ _\ \  \     \  \     _\ \  \/    \  \_____
#    \     /     \  \ \  \     \  \  \ \ \  \     \  \__ _\ \ \  \     \  \____
#     \   /______ \  \ \  \_____\  \  \ \ \  \_____\  \  \ \ \ \  \     \  \___
#      \___________\__\_\___________\__\_\_\___________\__\_\_\_\___________\__
#                      \____________\___\_\____________\___\_\_\____________\__
#                                        \____________\_____\_\____________\___
# SPECIES DISTRIBUTION MODELLING                             \____________\____

...it is an issue with Biomod, so I am closing it. The bug is known the the biomod dev team. Worth remembering though as it is an issue people are likely to come across.