Forum: help

RE: Generating binary projections [ Reply ] By: Maya Guéguen on 2023-02-17 08:39	[forum:49598]
Hello Waléria, This forum is no longer maintained. All biomod2 package is now on github, as well as issues so it is easier for us to manage and keep track. Please repost your message with as many details of your error as possible on this page : https://github.com/biomodhub/biomod2/issues Thanks in advance, Maya

RE: Generating binary projections [ Reply ]
By: Waléria Monteiro on 2023-02-16 19:54

[forum:49597]

Hi!! Guys, im the same problem in "BIOMOD_Modeling"

my TSSbin file is not generated for the model Current.

I'm using this command:

myBiomodModelOut <- BIOMOD_Modeling (bm.format = myBiomodData_fev,
models = c("GLM", "GBM", "GAM", "CTA", "ANN",
"SRE", "FDA", "MARS", "RF",
"MAXENT.Phillips.2"),
bm.options = myBiomodOption,
nb.rep = 10,
data.split.perc = 80,
weights = NULL,
var.import = 5,
metric.eval= c('TSS', 'ROC'),
save.output = T,
scale.models = T,
do.full.models = F,
modeling.id = paste(myRespName_fev, sep = ""))

myBiomodProj_fev <- BIOMOD_Projection (bm.mod = myBiomodModelOut,
new.env = myExpl_crop_fev, #myExpl_crop
proj.name = 'atual',
xy.new.env = NULL,
selected.models = 'all',
binary.meth = 'TSS',
compress = F,
build.clamping.mask = F,
do.stack = F,
output.format = '.grd')

RE: Generating binary projections [ Reply ] By: Nick Crowe on 2021-10-27 17:15	[forum:49184]
Hi Damien, Yes, for each future scenario I defined a different proj.name in the BIOMOD_Projection step following the examples provided. For example proj.name = "Future_2050". The individual model projections show up in this folder with the binary projection, but the final ensemble never appears as binary, only probability scale. Best,

RE: Generating binary projections [ Reply ] By: damien georges on 2021-10-15 08:31	[forum:49151]
Hi Nick, Did you defined a different proj.name argument for your current and future projections? Best, Damien

RE: Generating binary projections [ Reply ] By: Nick Crowe on 2021-10-14 14:18	[forum:49150]
Hi Damien, That is the issue- there are no TSSbin.img being generated. For current projection I get the bin.img projections with no problem. I am able to load it just fine. For future projections it is not generating the bin.img files. Going into the proj_current/individual_projections/etc. file I find no binaries projections. Thank you for your help. Best, Nick

RE: Generating binary projections [ Reply ]
By: damien georges on 2021-10-14 08:35

[forum:49149]

Hi Nick,

You have to load the binary projections mannally. Did you do it?

Should be something like:

## load binary projections
ProLau_bin_proj_current <- stack(
c( ca = "Protea.laurifolia/proj_current/individual_projections/Protea.laurifolia_EMcaByTSS_mergedAlgo_mergedRun_mergedData_TSSbin.img",
wm = "Protea.laurifolia/proj_current/individual_projections/Protea.laurifolia_EMwmeanByTSS_mergedAlgo_mergedRun_mergedData_TSSbin.img") )

Please have a look to the first example of HSDM book part 6 which code can be found here:

https://github.com/vdicolab/hsdm/blob/master/Part_6.Rmd

The part of interest for you is from l370.

HTH,
Damien

RE: Generating binary projections [ Reply ] By: Nick Crowe on 2021-10-13 18:07	[forum:49148]
Hi Damien, Thank you for your reply. I have been using binary_meth = 'ROC' (have also tried TSS). For the current projections I am able to generate binary projections. However, for the future projections I do not get binary projections, even using the same binary_meth = 'ROC'. Does this have to do with a lower predicted habitat suitability for future projections? Thanks in advance, Nick

RE: Generating binary projections [ Reply ]
By: damien georges on 2021-10-13 09:33

[forum:49147]

Hi Nick,

You are right you need to work with binary projections in order to compute the species range change.
In BIOMOD_Projection and BIOMOD_EnsembleForecasting you can use binary.meth arg to produce binary transformed projections (in additionof the continuous ones). Then You should load this binary projections and use them to feed BIOMOD_RangeSize function. Please have a look to the example of BIOMOD_RangeSize in the help file for further information.

Hope that helps,
Damien

Generating binary projections [ Reply ]
By: Nick Crowe on 2021-10-07 14:58

[forum:49139]

Hello,

I am unable to generate binary projections for some of my datasets, while some do generate binary projections. The scale for predicted habitat suitability is up to 880 (or lower) and does not reach 1000 for those without binary projections. I am trying to calculate changes in species ranges over time, so I do need to generate binaries. Any ideas on what is going wrong or work arounds to generate binaries independently? I appreciate any help or advice.