Reputation: 1
I'm running into warning messages when I include several model methods into my 'sdmData' function. Here's the code:
d <- sdmData(formula = sp~.,train=PO, predictors=env_raster, bg=background)
#PO = SpatialPointsDataFrame
#sp = presence-only data
#env_raster = raster stack of 5 layers
#background = dataframe with coordinates and values for each of the 5 environmental layers
m1 <- sdm(sp~.,data=d,methods=c('mars', 'maxlike', 'glm', 'rf', 'gam', 'brt'), replication = c('cv'), cv.folds=5)
Here are the warning messages from each individual package: 'rf' - Warning: The response has five or fewer unique values. Are you sure you want to do regression? 'mars' - Warning: glm.fit: algorithm did not converge Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred Warning: the glm algorithm did not converge for response "sp"
Additionally, my 'gam' model has zero successful model runs.
I've been following the 'sdm' package tutorial. Here is a partial view of the 'sdmdata' file being input into the 'sdm' function:
str(d)
Formal class 'sdmdata' [package "sdm"] with 9 slots
..@ species.names: chr "sp"
..@ species :List of 1
.. ..$ sp:Formal class '.species.data' [package "sdm"] with 8 slots
.. .. .. ..@ name : chr "sp"
.. .. .. ..@ type : chr "Presence-Background"
.. .. .. ..@ presence : num [1:128] 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. ..@ absence : NULL
.. .. .. ..@ background : num [1:9991] 129 130 131 132 133 134 135 136 137 138 ...
.. .. .. ..@ abundance : NULL
.. .. .. ..@ numerical : NULL
.. .. .. ..@ Multinomial: NULL
I have tried to convert the presence values in 'd' to factors, but this creates 128 level.
Here are previews of my inputs:
head(PO)
sp
1 1
2 1
3 1
4 1
5 1
6 1
head(background)
x y mean_NDVI soil_moisture fish insulation soil_nutrient
1 1233499 474434.2 0.6909310 1.2899151 1.281423 0.1708845 0.2821959
2 1208509 479954.2 0.2846706 1.5684123 1.210001 0.2893450 -1.0284775
3 1213729 461984.2 -0.4229073 1.2899151 1.262468 0.2301146 -1.0284775
4 1206619 470384.2 0.6999793 1.5684123 1.257669 0.1708845 -1.0284775
5 1223149 468404.2 -1.3116429 1.8469099 1.252390 0.2301146 -1.0284775
6 1244779 450044.2 0.7546983 0.1759251 1.137140 0.3485751 0.9375325
Does anyone have any solutions?
Upvotes: 0
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