Description Usage Details Value Author(s) Examples
This function print the default parameters used to build each model.
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This function is useful to parameterize the selected models. It gives a formated list of all parameters the user can modify. You can copy this function output, modify all parameters you want in a text editor and paste the modified string as argument to (BIOMOD_ModelingOptions) function.
Nothing returned.
Wilfried Thuiller, Damien Georges
1 2 | # print default models options
Print_Default_ModelingOptions()
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Loading required package: sp
Loading required package: raster
Loading required package: parallel
Loading required package: reshape
Loading required package: ggplot2
biomod2 3.3-7 loaded.
Type browseVignettes(package='biomod2') to access directly biomod2 vignettes.
Defaut modeling options. copy, change what you want paste it as arg to BIOMOD_ModelingOptions
-=-=-=-=-=-=-=-=-=-=-=-=-=-= 'BIOMOD.Model.Options' -=-=-=-=-=-=-=-=-=-=-=-=-=-=
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
) ),
GBM = list( distribution = 'bernoulli',
n.trees = 2500,
interaction.depth = 7,
n.minobsinnode = 5,
shrinkage = 0.001,
bag.fraction = 0.5,
train.fraction = 1,
cv.folds = 3,
keep.data = FALSE,
verbose = FALSE,
perf.method = 'cv'),
GAM = list( algo = 'GAM_mgcv',
type = 's_smoother',
k = -1,
interaction.level = 0,
myFormula = NULL,
family = binomial(link = 'logit'),
method = 'GCV.Cp',
optimizer = c('outer','newton'),
select = FALSE,
knots = NULL,
paraPen = NULL,
control = list(nthreads = 1, irls.reg = 0, epsilon = 1e-07
, maxit = 200, trace = FALSE, mgcv.tol = 1e-07, mgcv.half = 15
, rank.tol = 1.49011611938477e-08
, nlm = list(ndigit=7, gradtol=1e-06, stepmax=2, steptol=1e-04, iterlim=200, check.analyticals=0)
, optim = list(factr=1e+07)
, newton = list(conv.tol=1e-06, maxNstep=5, maxSstep=2, maxHalf=30, use.svd=0)
, outerPIsteps = 0, idLinksBases = TRUE, scalePenalty = TRUE, keepData = FALSE
, scale.est = fletcher, edge.correct = FALSE) ),
CTA = list( method = 'class',
parms = 'default',
cost = NULL,
control = list(xval = 5, minbucket = 5, minsplit = 5, cp = 0.001
, maxdepth = 25) ),
ANN = list( NbCV = 5,
size = NULL,
decay = NULL,
rang = 0.1,
maxit = 200),
SRE = list( quant = 0.025),
FDA = list( method = 'mars',
add_args = NULL),
MARS = list( type = 'simple',
interaction.level = 0,
myFormula = NULL,
nk = NULL,
penalty = 2,
thresh = 0.001,
nprune = NULL,
pmethod = 'backward'),
RF = list( do.classif = TRUE,
ntree = 500,
mtry = 'default',
nodesize = 5,
maxnodes = NULL),
MAXENT.Phillips = list( path_to_maxent.jar = '/work/tmp',
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),
MAXENT.Tsuruoka = list( l1_regularizer = 0,
l2_regularizer = 0,
use_sgd = FALSE,
set_heldout = 0,
verbose = FALSE)
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