require(PresenceAbsence)
## Loading required package: PresenceAbsence
alces.csv <- read.csv('/Users/milin/Library/Containers/com.tencent.xinWeChat/Data/Library/Application\ Support/com.tencent.xinWeChat/2.0b4.0.9/53566e35a70cea7efea3dd23a98b7c78/Message/MessageTemp/53de4b4fde8c4840c56f91eb1513f179/File/物种分布数据/Alces\ alces.csv')
bio2 <- read.csv('/Users/milin/Library/Containers/com.tencent.xinWeChat/Data/Library/Application\ Support/com.tencent.xinWeChat/2.0b4.0.9/53566e35a70cea7efea3dd23a98b7c78/Message/MessageTemp/53de4b4fde8c4840c56f91eb1513f179/File/物种分布数据/Camelus\ bactrianus.csv')
bio3 <- read.csv('/Users/milin/Library/Containers/com.tencent.xinWeChat/Data/Library/Application\ Support/com.tencent.xinWeChat/2.0b4.0.9/53566e35a70cea7efea3dd23a98b7c78/Message/MessageTemp/53de4b4fde8c4840c56f91eb1513f179/File/物种分布数据/Cervus\ elaphus.csv')
bio4 <- read.csv('/Users/milin/Library/Containers/com.tencent.xinWeChat/Data/Library/Application\ Support/com.tencent.xinWeChat/2.0b4.0.9/53566e35a70cea7efea3dd23a98b7c78/Message/MessageTemp/53de4b4fde8c4840c56f91eb1513f179/File/物种分布数据/Equus\ ferus\ przewalskii.csv')
bio5 <- read.csv('/Users/milin/Library/Containers/com.tencent.xinWeChat/Data/Library/Application\ Support/com.tencent.xinWeChat/2.0b4.0.9/53566e35a70cea7efea3dd23a98b7c78/Message/MessageTemp/53de4b4fde8c4840c56f91eb1513f179/File/物种分布数据/Equus\ hemionus.csv')
bio6 <- read.csv('/Users/milin/Library/Containers/com.tencent.xinWeChat/Data/Library/Application\ Support/com.tencent.xinWeChat/2.0b4.0.9/53566e35a70cea7efea3dd23a98b7c78/Message/MessageTemp/53de4b4fde8c4840c56f91eb1513f179/File/物种分布数据/Gazella\ subgutturosa.csv')
bio7 <- read.csv('/Users/milin/Library/Containers/com.tencent.xinWeChat/Data/Library/Application\ Support/com.tencent.xinWeChat/2.0b4.0.9/53566e35a70cea7efea3dd23a98b7c78/Message/MessageTemp/53de4b4fde8c4840c56f91eb1513f179/File/物种分布数据/Ovis\ ammon.csv')
bio8 <- read.csv('/Users/milin/Library/Containers/com.tencent.xinWeChat/Data/Library/Application\ Support/com.tencent.xinWeChat/2.0b4.0.9/53566e35a70cea7efea3dd23a98b7c78/Message/MessageTemp/53de4b4fde8c4840c56f91eb1513f179/File/物种分布数据/Saiga\ tatarica.csv')
names(bio2) <- names(alces.csv)
names(bio3) <- names(alces.csv)
names(bio4) <- names(alces.csv)
names(bio5) <- names(alces.csv)
names(bio6) <- names(alces.csv)
names(bio7) <- names(alces.csv)
names(bio8) <- names(alces.csv)
bio2$Alces.alces <- 0
bio3$Alces.alces <- 2
bio4$Alces.alces <- 3
bio5$Alces.alces <- 4
bio6$Alces.alces <- 5
bio7$Alces.alces <- 6
bio8$Alces.alces <- 7
library(tidyverse)
## ─ Attaching packages ─────────────────────── tidyverse 1.2.1 ─
## ✔ ggplot2 3.0.0.9000 ✔ purrr 0.2.5
## ✔ tibble 1.4.2 ✔ dplyr 0.7.8
## ✔ tidyr 0.8.2 ✔ stringr 1.3.1
## ✔ readr 1.1.1 ✔ forcats 0.3.0
## Warning: package 'tidyr' was built under R version 3.4.4
## Warning: package 'purrr' was built under R version 3.4.4
## Warning: package 'dplyr' was built under R version 3.4.4
## Warning: package 'stringr' was built under R version 3.4.4
## ─ Conflicts ───────────────────────── tidyverse_conflicts() ─
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()
alces.csv <- alces.csv %>% rbind(bio2) %>% rbind(bio3) %>% rbind(bio4) %>% rbind(bio5)%>% rbind(bio6) %>% rbind(bio7) %>% rbind(bio8)
# install.packages('biomod2')
# install.packages('rgdal')
# install.packages('mopa')
library(rgdal)
## Warning: package 'rgdal' was built under R version 3.4.4
## Loading required package: sp
## rgdal: version: 1.3-6, (SVN revision 773)
## Geospatial Data Abstraction Library extensions to R successfully loaded
## Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
## Path to GDAL shared files: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rgdal/gdal
## GDAL binary built with GEOS: FALSE
## Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
## Path to PROJ.4 shared files: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rgdal/proj
## Linking to sp version: 1.3-1
library(biomod2)
## Loading required package: raster
##
## Attaching package: 'raster'
## The following object is masked from 'package:dplyr':
##
## select
## The following object is masked from 'package:tidyr':
##
## extract
## Loading required package: parallel
## Loading required package: reshape
## Warning: package 'reshape' was built under R version 3.4.4
##
## Attaching package: 'reshape'
## The following object is masked from 'package:dplyr':
##
## rename
## The following objects are masked from 'package:tidyr':
##
## expand, smiths
## biomod2 3.3-7 loaded.
##
## Type browseVignettes(package='biomod2') to access directly biomod2 vignettes.
library(raster)
library(sp)
library(spatstat)
## Warning: package 'spatstat' was built under R version 3.4.4
## Loading required package: spatstat.data
## Warning: package 'spatstat.data' was built under R version 3.4.4
## Loading required package: nlme
##
## Attaching package: 'nlme'
## The following object is masked from 'package:raster':
##
## getData
## The following object is masked from 'package:dplyr':
##
## collapse
## Loading required package: rpart
##
## spatstat 1.57-1 (nickname: 'Cartoon Physics')
## For an introduction to spatstat, type 'beginner'
##
## Note: R version 3.4.3 (2017-11-30) is more than 9 months old; we strongly recommend upgrading to the latest version
##
## Attaching package: 'spatstat'
## The following objects are masked from 'package:raster':
##
## area, rotate, shift
## The following object is masked from 'package:PresenceAbsence':
##
## auc
library(mopa)
# Data<-readGDAL('/Users/milin/Downloads/bio1-bio5/bio1.tif')
myExpl = stack('/Users/milin/Downloads/bio1-bio5/bio1.tif',
'/Users/milin/Downloads/bio1-bio5/bio2.tif',
'/Users/milin/Downloads/bio1-bio5/bio3.tif',
'/Users/milin/Downloads/bio1-bio5/bio4.tif',
'/Users/milin/Downloads/bio1-bio5/bio5.tif')
# myExpl <- raster(Data)
myResp <- as.numeric(alces.csv[,'Alces.alces'])
myRespXY <- alces.csv[,c("lon","lat")]
myRespName <- 'Alces.alces'
myBiomodData <- BIOMOD_FormatingData(resp.var = myResp,
expl.var = myExpl,
resp.xy = myRespXY,
resp.name = myRespName)
##
## -=-=-=-=-=-=-=-=-=-=-=-= Alces.alces Data Formating -=-=-=-=-=-=-=-=-=-=-=-=
##
## > No pseudo absences selection !
## ! No data has been set aside for modeling evaluation
## ! Some NAs have been automaticly removed from your data
## -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Done -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
plot(myBiomodData)
myBiomodOption <- BIOMOD_ModelingOptions()
myBiomodModelOut <- BIOMOD_Modeling(
myBiomodData,
models = c('GLM','GBM','GAM','CTA','ANN',
'SRE','FDA','MARS','RF','MAXENT.Phillips',
"MAXENT.Tsuruoka"),
models.options = myBiomodOption,
NbRunEval=3,
DataSplit=80,
Prevalence=0.5,
VarImport=3,
models.eval.meth = c('KAPPA','TSS','ROC'),
SaveObj = TRUE,
rescal.all.models = TRUE,
do.full.models = FALSE,
modeling.id = paste(myRespName,"FirstModeling",sep=""))
##
##
## Loading required library...
##
## Checking Models arguments...
## Warning 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.Phillips was switched off
##
## Creating suitable Workdir...
##
## > Automatic weights creation to rise a 0.5 prevalence
##
##
## -=-=-=-=-=-=-=-=-=-=-= Alces.alces Modeling Summary -=-=-=-=-=-=-=-=-=-=-=
##
## 5 environmental variables ( bio1 bio2 bio3 bio4 bio5 )
## Number of evaluation repetitions : 3
## Models selected : GLM GBM GAM CTA ANN SRE FDA MARS RF MAXENT.Tsuruoka
##
## Total number of model runs : 30
##
## -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
##
##
## -=-=-=- Run : Alces.alces_AllData
##
##
## -=-=-=--=-=-=- Alces.alces_AllData_RUN1
##
## Model=GLM ( quadratic with no interaction )
## Stepwise procedure using AIC criteria
## selected formula : Alces.alces ~ bio2 + I(bio5^2) + I(bio4^2) + bio4 + I(bio1^2) +
## bio5 + bio1 + I(bio3^2) + I(bio2^2)
## <environment: 0x7fc7a1119318>
##
## Model scaling...
## Evaluating Model stuff...
## Evaluating Predictor Contributions...
##
## Model=Generalised Boosting Regression
## 2500 maximum different trees and 3 Fold Cross-Validation
## Model scaling...
## Evaluating Model stuff...
## Evaluating Predictor Contributions...
##
## Model=GAM
## GAM_mgcv algorithm chosen
## Automatic formula generation...
## > GAM (mgcv) modelling...
## Warning in newton(lsp = lsp, X = G$X, y = G$y, Eb = G$Eb, UrS = G$UrS, L =
## G$L, : Iteration limit reached without full convergence - check carefully
##
## Model scaling...
## Evaluating Model stuff...
## Evaluating Predictor Contributions...
##
## Model=Classification tree
## 5 Fold Cross-Validation
## Model scaling...
## Evaluating Model stuff...
## Evaluating Predictor Contributions...
##
## Model=Artificial Neural Network
## 5 Fold Cross Validation + 3 Repetitions
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
##
## Model scaling...
## Evaluating Model stuff...
## Evaluating Predictor Contributions...
##
## Model=Surface Range Envelop
## Evaluating Model stuff...
## Evaluating Predictor Contributions...
##
## Model=Flexible Discriminant Analysis
## Model scaling...
## Warning: glm.fit: algorithm did not converge
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
##
## Evaluating Model stuff...
## Evaluating Predictor Contributions...
##
## Model=Multiple Adaptive Regression Splines ( simple with no interaction )
## Warning: glm.fit: algorithm did not converge
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
## earth glm Alces.alces: did not converge after 25 iterations
##
## Model scaling...
## Evaluating Model stuff...
## Evaluating Predictor Contributions...
##
## Model=Breiman and Cutler's random forests for classification and regression
## Model scaling...
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
##
## Evaluating Model stuff...
## Evaluating Predictor Contributions...
## Warning in newton(lsp = lsp, X = G$X, y = G$y, Eb = G$Eb, UrS = G$UrS, L =
## G$L, : Iteration limit reached without full convergence - check carefully
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
## Warning: glm.fit: algorithm did not converge
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
## Warning in newton(lsp = lsp, X = G$X, y = G$y, Eb = G$Eb, UrS = G$UrS, L =
## G$L, : Iteration limit reached without full convergence - check carefully
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning in roc.default(Target[Samp$evaluation], predict(nn,
## Input[Samp$evaluation, : Deprecated use a matrix as predictor. Unexpected
## results may be produced, please pass a numeric vector.
## Warning: glm.fit: algorithm did not converge
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
## Warning: glm.fit: algorithm did not converge
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
myBiomodModelOut
##
## -=-=-=-=-=-=-=-=-=-=-=-=-=-= BIOMOD.models.out -=-=-=-=-=-=-=-=-=-=-=-=-=-=
##
## Modeling id : Alces.alcesFirstModeling
##
## Species modeled : Alces.alces
##
## Considered variables : bio1 bio2 bio3 bio4 bio5
##
##
## Computed Models : Alces.alces_AllData_RUN1_GLM
## Alces.alces_AllData_RUN1_GBM Alces.alces_AllData_RUN1_GAM
## Alces.alces_AllData_RUN1_CTA Alces.alces_AllData_RUN1_ANN
## Alces.alces_AllData_RUN1_SRE Alces.alces_AllData_RUN1_FDA
## Alces.alces_AllData_RUN1_MARS Alces.alces_AllData_RUN1_RF
## Alces.alces_AllData_RUN1_MAXENT.Tsuruoka Alces.alces_AllData_RUN2_GLM
## Alces.alces_AllData_RUN2_GBM Alces.alces_AllData_RUN2_GAM
## Alces.alces_AllData_RUN2_CTA Alces.alces_AllData_RUN2_ANN
## Alces.alces_AllData_RUN2_SRE Alces.alces_AllData_RUN2_FDA
## Alces.alces_AllData_RUN2_MARS Alces.alces_AllData_RUN2_RF
## Alces.alces_AllData_RUN2_MAXENT.Tsuruoka Alces.alces_AllData_RUN3_GLM
## Alces.alces_AllData_RUN3_GBM Alces.alces_AllData_RUN3_GAM
## Alces.alces_AllData_RUN3_CTA Alces.alces_AllData_RUN3_ANN
## Alces.alces_AllData_RUN3_SRE Alces.alces_AllData_RUN3_FDA
## Alces.alces_AllData_RUN3_MARS Alces.alces_AllData_RUN3_RF
## Alces.alces_AllData_RUN3_MAXENT.Tsuruoka
##
##
## Failed Models : none
##
## -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
myBiomodModelEval <- get_evaluations(myBiomodModelOut)
get_variables_importance(myBiomodModelOut)
## , , RUN1, AllData
##
## GLM GBM GAM CTA ANN SRE FDA MARS RF MAXENT.Tsuruoka
## bio1 0.123 0.086 0.262 0.191 0.367 0.209 0.198 0.273 0.269 0.241
## bio2 0.866 0.668 0.792 0.947 1.000 0.189 0.923 1.000 0.586 1.000
## bio3 0.063 0.099 0.108 0.375 0.153 0.155 0.010 0.000 0.382 0.213
## bio4 0.788 0.297 0.668 0.322 0.960 0.294 0.464 0.096 0.410 0.535
## bio5 0.229 0.043 0.288 0.267 0.511 0.162 0.041 0.321 0.272 0.033
##
## , , RUN2, AllData
##
## GLM GBM GAM CTA ANN SRE FDA MARS RF MAXENT.Tsuruoka
## bio1 0.209 0.066 0.183 0.000 0.544 0.208 0.252 0.080 0.208 0.375
## bio2 0.167 0.718 0.681 0.189 1.000 0.189 0.950 0.055 0.368 1.000
## bio3 0.495 0.032 0.348 0.362 0.249 0.155 0.000 0.548 0.442 0.214
## bio4 0.900 0.305 0.819 0.960 0.411 0.294 0.538 0.933 0.336 0.530
## bio5 0.533 0.022 0.411 0.096 0.855 0.162 0.063 0.000 0.203 0.375
##
## , , RUN3, AllData
##
## GLM GBM GAM CTA ANN SRE FDA MARS RF MAXENT.Tsuruoka
## bio1 0.118 0.075 0.385 0.105 0.297 0.205 0.206 0.231 0.245 0.197
## bio2 0.302 0.539 0.734 0.930 1.000 0.187 0.705 0.470 0.372 1.000
## bio3 0.191 0.133 0.387 0.431 0.081 0.152 0.024 0.163 0.425 0.209
## bio4 0.999 0.371 0.709 0.336 0.886 0.308 0.420 0.941 0.344 0.518
## bio5 0.225 0.020 0.451 0.273 0.568 0.159 0.159 0.196 0.367 0.000
myBiomodEM <- BIOMOD_EnsembleModeling( modeling.output = myBiomodModelOut,
chosen.models = 'all',
em.by = 'PA_dataset+repet',
eval.metric = c('TSS'),
eval.metric.quality.threshold = c(0.7),
models.eval.meth = c('TSS','ROC'),
prob.mean = TRUE,
prob.cv = FALSE,
prob.ci = FALSE,
prob.ci.alpha = 0.05,
prob.median = FALSE,
committee.averaging = FALSE,
prob.mean.weight = TRUE,
prob.mean.weight.decay = 'proportional' )
##
## -=-=-=-=-=-=-=-=-=-=-=-=-= Build Ensemble Models -=-=-=-=-=-=-=-=-=-=-=-=-=
##
## ! all models available will be included in ensemble.modeling
## > Evaluation & Weighting methods summary :
## TSS over 0.7
##
##
## > mergedAlgo_RUN1_AllData ensemble modeling
## > Mean of probabilities...
## Evaluating Model stuff...
## > Prababilities wegthing mean...
## original models scores = 0.848 0.868 0.838 0.838 0.839 0.811 0.836 0.884 0.806
## final models weights = 0.112 0.115 0.111 0.111 0.111 0.107 0.11 0.117 0.107
## Evaluating Model stuff...
##
## > mergedAlgo_RUN2_AllData ensemble modeling
## > Mean of probabilities...
## Evaluating Model stuff...
## > Prababilities wegthing mean...
## original models scores = 0.868 0.834 0.824 0.778 0.838 0.802 0.794 0.833 0.831
## final models weights = 0.117 0.113 0.111 0.105 0.113 0.108 0.107 0.113 0.112
## Evaluating Model stuff...
##
## > mergedAlgo_RUN3_AllData ensemble modeling
## > Mean of probabilities...
## Evaluating Model stuff...
## > Prababilities wegthing mean...
## original models scores = 0.856 0.874 0.778 0.819 0.907 0.832 0.769 0.812 0.833
## final models weights = 0.114 0.117 0.104 0.109 0.121 0.111 0.103 0.109 0.111
## Evaluating Model stuff...
## -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Done -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
# evaluate Biomod models with the Boyce index and MPA
myBiomodEM
##
## -=-=-=-=-=-=-=-=-=-=-= 'BIOMOD.EnsembleModeling.out' -=-=-=-=-=-=-=-=-=-=-=
##
## sp.name : Alces.alces
##
## expl.var.names : bio1 bio2 bio3 bio4 bio5
##
##
## models computed:
## Alces.alces_EMmeanByTSS_mergedAlgo_RUN1_AllData, Alces.alces_EMwmeanByTSS_mergedAlgo_RUN1_AllData, Alces.alces_EMmeanByTSS_mergedAlgo_RUN2_AllData, Alces.alces_EMwmeanByTSS_mergedAlgo_RUN2_AllData, Alces.alces_EMmeanByTSS_mergedAlgo_RUN3_AllData, Alces.alces_EMwmeanByTSS_mergedAlgo_RUN3_AllData
##
## -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
get_evaluations(myBiomodEM)
## $Alces.alces_EMmeanByTSS_mergedAlgo_RUN1_AllData
## Testing.data Cutoff Sensitivity Specificity
## TSS 0.861 585 95.469 90.625
## ROC 0.956 582 95.535 90.625
##
## $Alces.alces_EMwmeanByTSS_mergedAlgo_RUN1_AllData
## Testing.data Cutoff Sensitivity Specificity
## TSS 0.861 586 95.469 90.625
## ROC 0.956 583 95.535 90.625
##
## $Alces.alces_EMmeanByTSS_mergedAlgo_RUN2_AllData
## Testing.data Cutoff Sensitivity Specificity
## TSS 0.863 860.0 86.474 100
## ROC 0.980 856.5 86.540 100
##
## $Alces.alces_EMwmeanByTSS_mergedAlgo_RUN2_AllData
## Testing.data Cutoff Sensitivity Specificity
## TSS 0.863 859.0 86.408 100
## ROC 0.980 854.5 86.671 100
##
## $Alces.alces_EMmeanByTSS_mergedAlgo_RUN3_AllData
## Testing.data Cutoff Sensitivity Specificity
## TSS 0.878 664.0 94.091 93.75
## ROC 0.958 662.5 94.156 93.75
##
## $Alces.alces_EMwmeanByTSS_mergedAlgo_RUN3_AllData
## Testing.data Cutoff Sensitivity Specificity
## TSS 0.879 664.0 94.222 93.75
## ROC 0.958 658.5 94.353 93.75
pres.only.eval <- BIOMOD_presenceonly(myBiomodModelOut, myBiomodEM)
##
## -=-=-=-=-=-=-=-=-=-=-= Do Ensemble Models Projections -=-=-=-=-=-=-=-=-=-=-=
##
## > Projecting Alces.alces_AllData_RUN1_GLM ...
## > Projecting Alces.alces_AllData_RUN1_GBM ...
## > Projecting Alces.alces_AllData_RUN1_GAM ...
## > Projecting Alces.alces_AllData_RUN1_CTA ...
## > Projecting Alces.alces_AllData_RUN1_ANN ...
## > Projecting Alces.alces_AllData_RUN1_FDA ...
## > Projecting Alces.alces_AllData_RUN1_MARS ...
## > Projecting Alces.alces_AllData_RUN1_RF ...
pres.only.eval$eval
## Model.name Eval.metric
## 1 Alces.alces_AllData_RUN1_GLM KAPPA
## 2 Alces.alces_AllData_RUN1_GLM TSS
## 3 Alces.alces_AllData_RUN1_GLM ROC
## 4 Alces.alces_AllData_RUN1_GBM KAPPA
## 5 Alces.alces_AllData_RUN1_GBM TSS
## 6 Alces.alces_AllData_RUN1_GBM ROC
## 7 Alces.alces_AllData_RUN1_GAM KAPPA
## 8 Alces.alces_AllData_RUN1_GAM TSS
## 9 Alces.alces_AllData_RUN1_GAM ROC
## 10 Alces.alces_AllData_RUN1_CTA KAPPA
## 11 Alces.alces_AllData_RUN1_CTA TSS
## 12 Alces.alces_AllData_RUN1_CTA ROC
## 13 Alces.alces_AllData_RUN1_ANN KAPPA
## 14 Alces.alces_AllData_RUN1_ANN TSS
## 15 Alces.alces_AllData_RUN1_ANN ROC
## 16 Alces.alces_AllData_RUN1_SRE KAPPA
## 17 Alces.alces_AllData_RUN1_SRE TSS
## 18 Alces.alces_AllData_RUN1_SRE ROC
## 19 Alces.alces_AllData_RUN1_FDA KAPPA
## 20 Alces.alces_AllData_RUN1_FDA TSS
## 21 Alces.alces_AllData_RUN1_FDA ROC
## 22 Alces.alces_AllData_RUN1_MARS KAPPA
## 23 Alces.alces_AllData_RUN1_MARS TSS
## 24 Alces.alces_AllData_RUN1_MARS ROC
## 25 Alces.alces_AllData_RUN1_RF KAPPA
## 26 Alces.alces_AllData_RUN1_RF TSS
## 27 Alces.alces_AllData_RUN1_RF ROC
## 28 Alces.alces_AllData_RUN1_MAXENT.Tsuruoka KAPPA
## 29 Alces.alces_AllData_RUN1_MAXENT.Tsuruoka TSS
## 30 Alces.alces_AllData_RUN1_MAXENT.Tsuruoka ROC
## 31 Alces.alces_AllData_RUN2_GLM KAPPA
## 32 Alces.alces_AllData_RUN2_GLM TSS
## 33 Alces.alces_AllData_RUN2_GLM ROC
## 34 Alces.alces_AllData_RUN2_GBM KAPPA
## 35 Alces.alces_AllData_RUN2_GBM TSS
## 36 Alces.alces_AllData_RUN2_GBM ROC
## 37 Alces.alces_AllData_RUN2_GAM KAPPA
## 38 Alces.alces_AllData_RUN2_GAM TSS
## 39 Alces.alces_AllData_RUN2_GAM ROC
## 40 Alces.alces_AllData_RUN2_CTA KAPPA
## 41 Alces.alces_AllData_RUN2_CTA TSS
## 42 Alces.alces_AllData_RUN2_CTA ROC
## 43 Alces.alces_AllData_RUN2_ANN KAPPA
## 44 Alces.alces_AllData_RUN2_ANN TSS
## 45 Alces.alces_AllData_RUN2_ANN ROC
## 46 Alces.alces_AllData_RUN2_SRE KAPPA
## 47 Alces.alces_AllData_RUN2_SRE TSS
## 48 Alces.alces_AllData_RUN2_SRE ROC
## 49 Alces.alces_AllData_RUN2_FDA KAPPA
## 50 Alces.alces_AllData_RUN2_FDA TSS
## 51 Alces.alces_AllData_RUN2_FDA ROC
## 52 Alces.alces_AllData_RUN2_MARS KAPPA
## 53 Alces.alces_AllData_RUN2_MARS TSS
## 54 Alces.alces_AllData_RUN2_MARS ROC
## 55 Alces.alces_AllData_RUN2_RF KAPPA
## 56 Alces.alces_AllData_RUN2_RF TSS
## 57 Alces.alces_AllData_RUN2_RF ROC
## 58 Alces.alces_AllData_RUN2_MAXENT.Tsuruoka KAPPA
## 59 Alces.alces_AllData_RUN2_MAXENT.Tsuruoka TSS
## 60 Alces.alces_AllData_RUN2_MAXENT.Tsuruoka ROC
## 61 Alces.alces_AllData_RUN3_GLM KAPPA
## 62 Alces.alces_AllData_RUN3_GLM TSS
## 63 Alces.alces_AllData_RUN3_GLM ROC
## 64 Alces.alces_AllData_RUN3_GBM KAPPA
## 65 Alces.alces_AllData_RUN3_GBM TSS
## 66 Alces.alces_AllData_RUN3_GBM ROC
## 67 Alces.alces_AllData_RUN3_GAM KAPPA
## 68 Alces.alces_AllData_RUN3_GAM TSS
## 69 Alces.alces_AllData_RUN3_GAM ROC
## 70 Alces.alces_AllData_RUN3_CTA KAPPA
## 71 Alces.alces_AllData_RUN3_CTA TSS
## 72 Alces.alces_AllData_RUN3_CTA ROC
## 73 Alces.alces_AllData_RUN3_ANN KAPPA
## 74 Alces.alces_AllData_RUN3_ANN TSS
## 75 Alces.alces_AllData_RUN3_ANN ROC
## 76 Alces.alces_AllData_RUN3_SRE KAPPA
## 77 Alces.alces_AllData_RUN3_SRE TSS
## 78 Alces.alces_AllData_RUN3_SRE ROC
## 79 Alces.alces_AllData_RUN3_FDA KAPPA
## 80 Alces.alces_AllData_RUN3_FDA TSS
## 81 Alces.alces_AllData_RUN3_FDA ROC
## 82 Alces.alces_AllData_RUN3_MARS KAPPA
## 83 Alces.alces_AllData_RUN3_MARS TSS
## 84 Alces.alces_AllData_RUN3_MARS ROC
## 85 Alces.alces_AllData_RUN3_RF KAPPA
## 86 Alces.alces_AllData_RUN3_RF TSS
## 87 Alces.alces_AllData_RUN3_RF ROC
## 88 Alces.alces_AllData_RUN3_MAXENT.Tsuruoka KAPPA
## 89 Alces.alces_AllData_RUN3_MAXENT.Tsuruoka TSS
## 90 Alces.alces_AllData_RUN3_MAXENT.Tsuruoka ROC
## 91 Alces.alces_EMmeanByTSS_mergedAlgo_RUN1_AllData TSS
## 92 Alces.alces_EMmeanByTSS_mergedAlgo_RUN1_AllData ROC
## 93 Alces.alces_EMwmeanByTSS_mergedAlgo_RUN1_AllData TSS
## 94 Alces.alces_EMwmeanByTSS_mergedAlgo_RUN1_AllData ROC
## 95 Alces.alces_EMmeanByTSS_mergedAlgo_RUN2_AllData TSS
## 96 Alces.alces_EMmeanByTSS_mergedAlgo_RUN2_AllData ROC
## 97 Alces.alces_EMwmeanByTSS_mergedAlgo_RUN2_AllData TSS
## 98 Alces.alces_EMwmeanByTSS_mergedAlgo_RUN2_AllData ROC
## 99 Alces.alces_EMmeanByTSS_mergedAlgo_RUN3_AllData TSS
## 100 Alces.alces_EMmeanByTSS_mergedAlgo_RUN3_AllData ROC
## 101 Alces.alces_EMwmeanByTSS_mergedAlgo_RUN3_AllData TSS
## 102 Alces.alces_EMwmeanByTSS_mergedAlgo_RUN3_AllData ROC
## 110 Alces.alces_AllData_RUN1_GLM boyce
## 410 Alces.alces_AllData_RUN1_GBM boyce
## 710 Alces.alces_AllData_RUN1_GAM boyce
## 103 Alces.alces_AllData_RUN1_CTA boyce
## 131 Alces.alces_AllData_RUN1_ANN boyce
## 161 Alces.alces_AllData_RUN1_SRE boyce
## 191 Alces.alces_AllData_RUN1_FDA boyce
## 221 Alces.alces_AllData_RUN1_MARS boyce
## 251 Alces.alces_AllData_RUN1_RF boyce
## 281 Alces.alces_AllData_RUN1_MAXENT.Tsuruoka boyce
## 311 Alces.alces_AllData_RUN2_GLM boyce
## 341 Alces.alces_AllData_RUN2_GBM boyce
## 371 Alces.alces_AllData_RUN2_GAM boyce
## 401 Alces.alces_AllData_RUN2_CTA boyce
## 431 Alces.alces_AllData_RUN2_ANN boyce
## 461 Alces.alces_AllData_RUN2_SRE boyce
## 491 Alces.alces_AllData_RUN2_FDA boyce
## 521 Alces.alces_AllData_RUN2_MARS boyce
## 551 Alces.alces_AllData_RUN2_RF boyce
## 581 Alces.alces_AllData_RUN2_MAXENT.Tsuruoka boyce
## 611 Alces.alces_AllData_RUN3_GLM boyce
## 641 Alces.alces_AllData_RUN3_GBM boyce
## 671 Alces.alces_AllData_RUN3_GAM boyce
## 701 Alces.alces_AllData_RUN3_CTA boyce
## 731 Alces.alces_AllData_RUN3_ANN boyce
## 761 Alces.alces_AllData_RUN3_SRE boyce
## 791 Alces.alces_AllData_RUN3_FDA boyce
## 821 Alces.alces_AllData_RUN3_MARS boyce
## 851 Alces.alces_AllData_RUN3_RF boyce
## 881 Alces.alces_AllData_RUN3_MAXENT.Tsuruoka boyce
## 911 Alces.alces_EMmeanByTSS_mergedAlgo_RUN1_AllData boyce
## 931 Alces.alces_EMwmeanByTSS_mergedAlgo_RUN1_AllData boyce
## 951 Alces.alces_EMmeanByTSS_mergedAlgo_RUN2_AllData boyce
## 971 Alces.alces_EMwmeanByTSS_mergedAlgo_RUN2_AllData boyce
## 991 Alces.alces_EMmeanByTSS_mergedAlgo_RUN3_AllData boyce
## 1011 Alces.alces_EMwmeanByTSS_mergedAlgo_RUN3_AllData boyce
## 111 Alces.alces_AllData_RUN1_GLM mpa
## 411 Alces.alces_AllData_RUN1_GBM mpa
## 711 Alces.alces_AllData_RUN1_GAM mpa
## 104 Alces.alces_AllData_RUN1_CTA mpa
## 132 Alces.alces_AllData_RUN1_ANN mpa
## 162 Alces.alces_AllData_RUN1_SRE mpa
## 192 Alces.alces_AllData_RUN1_FDA mpa
## 222 Alces.alces_AllData_RUN1_MARS mpa
## 252 Alces.alces_AllData_RUN1_RF mpa
## 282 Alces.alces_AllData_RUN1_MAXENT.Tsuruoka mpa
## 312 Alces.alces_AllData_RUN2_GLM mpa
## 342 Alces.alces_AllData_RUN2_GBM mpa
## 372 Alces.alces_AllData_RUN2_GAM mpa
## 402 Alces.alces_AllData_RUN2_CTA mpa
## 432 Alces.alces_AllData_RUN2_ANN mpa
## 462 Alces.alces_AllData_RUN2_SRE mpa
## 492 Alces.alces_AllData_RUN2_FDA mpa
## 522 Alces.alces_AllData_RUN2_MARS mpa
## 552 Alces.alces_AllData_RUN2_RF mpa
## 582 Alces.alces_AllData_RUN2_MAXENT.Tsuruoka mpa
## 612 Alces.alces_AllData_RUN3_GLM mpa
## 642 Alces.alces_AllData_RUN3_GBM mpa
## 672 Alces.alces_AllData_RUN3_GAM mpa
## 702 Alces.alces_AllData_RUN3_CTA mpa
## 732 Alces.alces_AllData_RUN3_ANN mpa
## 762 Alces.alces_AllData_RUN3_SRE mpa
## 792 Alces.alces_AllData_RUN3_FDA mpa
## 822 Alces.alces_AllData_RUN3_MARS mpa
## 852 Alces.alces_AllData_RUN3_RF mpa
## 882 Alces.alces_AllData_RUN3_MAXENT.Tsuruoka mpa
## 912 Alces.alces_EMmeanByTSS_mergedAlgo_RUN1_AllData mpa
## 932 Alces.alces_EMwmeanByTSS_mergedAlgo_RUN1_AllData mpa
## 952 Alces.alces_EMmeanByTSS_mergedAlgo_RUN2_AllData mpa
## 972 Alces.alces_EMwmeanByTSS_mergedAlgo_RUN2_AllData mpa
## 992 Alces.alces_EMmeanByTSS_mergedAlgo_RUN3_AllData mpa
## 1012 Alces.alces_EMwmeanByTSS_mergedAlgo_RUN3_AllData mpa
## Testing.data Evaluating.data Cutoff Sensitivity Specificity
## 1 0.789 NA 35.5 99.8 71.9
## 2 0.848 NA 555.0 91.1 93.8
## 3 0.963 NA 551.0 91.1 93.8
## 4 0.762 NA 16.0 99.7 71.9
## 5 0.868 NA 501.0 96.2 90.6
## 6 0.971 NA 504.5 96.2 90.6
## 7 0.706 NA 13.0 100.0 0.0
## 8 0.838 NA 772.0 93.2 90.6
## 9 0.951 NA 764.5 93.4 90.6
## 10 0.569 NA 46.0 97.8 84.4
## 11 0.838 NA 70.0 96.3 87.5
## 12 0.916 NA 63.5 97.1 87.5
## 13 0.716 NA 15.0 100.0 0.0
## 14 0.839 NA 671.0 96.4 87.5
## 15 0.937 NA 666.0 96.5 87.5
## 16 0.090 NA 495.0 90.0 37.5
## 17 0.275 NA 495.0 90.0 37.5
## 18 0.637 NA 500.0 90.0 37.5
## 19 0.775 NA 151.0 99.7 71.9
## 20 0.811 NA 764.0 93.6 87.5
## 21 0.885 NA 758.5 95.0 87.5
## 22 0.323 NA 507.0 93.0 90.6
## 23 0.836 NA 507.0 93.0 90.6
## 24 0.918 NA 511.5 93.0 90.6
## 25 0.830 NA 5.0 99.8 78.1
## 26 0.884 NA 918.0 97.8 90.6
## 27 0.961 NA 917.5 97.8 90.6
## 28 0.660 NA 71.0 99.3 65.6
## 29 0.806 NA 792.0 90.4 87.5
## 30 0.940 NA 792.5 90.0 90.6
## 31 0.558 NA 33.0 99.3 46.9
## 32 0.868 NA 779.0 86.9 100.0
## 33 0.974 NA 775.0 86.9 100.0
## 34 0.733 NA 27.0 99.4 75.0
## 35 0.834 NA 948.0 89.6 93.8
## 36 0.977 NA 942.0 90.0 93.8
## 37 0.696 NA 12.0 100.0 0.0
## 38 0.824 NA 577.0 94.9 84.4
## 39 0.937 NA 581.5 94.9 87.5
## 40 0.533 NA 37.5 97.9 75.0
## 41 0.778 NA 122.0 96.6 81.2
## 42 0.843 NA 124.0 96.6 81.2
## 43 0.613 NA 30.0 98.8 71.9
## 44 0.838 NA 887.0 90.1 93.8
## 45 0.962 NA 881.5 90.3 93.8
## 46 0.050 NA 495.0 88.4 28.1
## 47 0.166 NA 495.0 88.4 28.1
## 48 0.583 NA 500.0 88.4 28.1
## 49 0.701 NA 124.5 99.3 71.9
## 50 0.802 NA 682.0 95.8 84.4
## 51 0.892 NA 684.0 95.8 84.4
## 52 0.381 NA 492.0 95.0 84.4
## 53 0.794 NA 492.0 95.0 84.4
## 54 0.897 NA 496.5 95.0 84.4
## 55 0.803 NA 63.0 99.7 78.1
## 56 0.833 NA 744.0 98.9 84.4
## 57 0.958 NA 962.5 90.9 93.8
## 58 0.541 NA 246.5 98.8 59.4
## 59 0.831 NA 794.0 89.5 90.6
## 60 0.969 NA 804.5 86.3 96.9
## 61 0.824 NA 33.0 99.9 75.0
## 62 0.856 NA 431.0 91.9 93.8
## 63 0.962 NA 429.0 91.9 93.8
## 64 0.816 NA 30.0 99.7 78.1
## 65 0.874 NA 926.0 90.6 96.9
## 66 0.968 NA 918.0 90.7 96.9
## 67 0.770 NA 23.0 99.7 75.0
## 68 0.778 NA 954.0 90.3 87.5
## 69 0.935 NA 959.5 90.2 90.6
## 70 0.550 NA 34.0 100.0 0.0
## 71 0.819 NA 34.0 100.0 0.0
## 72 0.909 NA 34.5 97.6 84.4
## 73 0.580 NA 379.0 97.6 90.6
## 74 0.907 NA 574.0 97.0 93.8
## 75 0.975 NA 571.0 97.1 93.8
## 76 0.087 NA 495.0 87.7 43.8
## 77 0.314 NA 495.0 87.7 43.8
## 78 0.657 NA 500.0 87.7 43.8
## 79 0.783 NA 86.0 99.7 75.0
## 80 0.832 NA 436.0 98.8 84.4
## 81 0.928 NA 437.5 98.8 84.4
## 82 0.225 NA 528.0 89.4 87.5
## 83 0.769 NA 528.0 89.4 87.5
## 84 0.884 NA 532.5 89.4 87.5
## 85 0.879 NA 0.0 100.0 0.0
## 86 0.812 NA 0.0 100.0 0.0
## 87 0.944 NA 962.5 91.6 90.6
## 88 0.660 NA 71.0 99.3 65.6
## 89 0.833 NA 795.0 89.7 93.8
## 90 0.952 NA 789.5 90.7 93.8
## 91 0.861 NA 585.0 95.5 90.6
## 92 0.956 NA 582.0 95.5 90.6
## 93 0.861 NA 586.0 95.5 90.6
## 94 0.956 NA 583.0 95.5 90.6
## 95 0.863 NA 860.0 86.5 100.0
## 96 0.980 NA 856.5 86.5 100.0
## 97 0.863 NA 859.0 86.4 100.0
## 98 0.980 NA 854.5 86.7 100.0
## 99 0.878 NA 664.0 94.1 93.8
## 100 0.958 NA 662.5 94.2 93.8
## 101 0.879 NA 664.0 94.2 93.8
## 102 0.958 NA 658.5 94.4 93.8
## 110 0.426 NA 918.0 86.8 96.9
## 410 0.555 NA 929.0 90.3 90.6
## 710 0.271 NA 807.0 93.0 90.6
## 103 0.690 NA 104.0 95.7 87.5
## 131 -0.260 NA 690.0 96.3 87.5
## 161 NA NA 50.0 90.0 37.5
## 191 -0.033 NA 745.0 95.4 78.1
## 221 NA NA 112.0 93.0 90.6
## 251 -0.117 NA 910.0 97.8 84.4
## 281 0.166 NA 769.0 93.0 81.2
## 311 0.345 NA 813.0 86.4 100.0
## 341 0.307 NA 920.0 91.1 90.6
## 371 0.337 NA 919.0 91.9 87.5
## 401 0.631 NA 154.0 94.9 81.2
## 431 -0.649 NA 909.0 89.3 93.8
## 461 NA NA 50.0 88.4 28.1
## 491 0.103 NA 719.0 95.4 84.4
## 521 NA NA 99.0 95.0 84.4
## 551 -0.246 NA 768.0 98.8 84.4
## 581 0.336 NA 771.0 92.2 84.4
## 611 0.332 NA 842.0 86.7 96.9
## 641 -0.390 NA 918.0 90.7 96.9
## 671 0.003 NA 908.0 92.1 78.1
## 701 0.035 NA 81.0 96.7 84.4
## 731 0.566 NA 772.0 84.0 96.9
## 761 NA NA 50.0 87.7 43.8
## 791 0.440 NA 751.0 94.5 84.4
## 821 NA NA 142.0 89.4 87.5
## 851 -0.111 NA 906.0 98.4 81.2
## 881 0.454 NA 764.0 93.1 84.4
## 911 0.703 NA 885.0 86.5 93.8
## 931 0.713 NA 886.0 86.5 93.8
## 951 0.493 NA 881.0 85.8 100.0
## 971 0.494 NA 880.0 85.8 100.0
## 991 0.419 NA 690.0 92.1 93.8
## 1011 0.471 NA 690.0 92.3 93.8
## 111 NA NA 630.4 80.0 96.9
## 411 NA NA 946.0 0.0 100.0
## 711 NA NA 965.2 0.0 100.0
## 104 NA NA 956.0 10.0 96.9
## 132 NA NA 738.0 47.3 93.8
## 162 NA NA 200.0 100.0 0.0
## 192 NA NA 784.0 3.5 93.8
## 222 NA NA 955.0 0.0 100.0
## 252 NA NA 967.0 91.5 93.8
## 282 NA NA 793.0 47.1 96.9
## 312 NA NA 569.6 7.2 100.0
## 342 NA NA 940.2 1.0 100.0
## 372 NA NA 970.0 0.0 100.0
## 402 NA NA 956.0 12.0 87.5
## 432 NA NA 888.0 5.3 100.0
## 462 NA NA 0.0 0.0 100.0
## 492 NA NA 802.0 29.7 93.8
## 522 NA NA 938.0 0.0 100.0
## 552 NA NA 963.0 0.0 100.0
## 582 NA NA 790.0 20.7 100.0
## 612 NA NA 583.0 82.7 96.9
## 642 NA NA 943.0 0.0 100.0
## 672 NA NA 962.0 0.0 100.0
## 702 NA NA 969.0 0.0 100.0
## 732 NA NA 711.0 0.0 100.0
## 762 NA NA 0.0 0.0 100.0
## 792 NA NA 792.0 47.9 93.8
## 822 NA NA 99.0 0.0 100.0
## 852 NA NA 963.0 0.0 100.0
## 882 NA NA 792.2 25.9 96.9
## 912 NA NA 801.6 5.6 96.9
## 932 NA NA 803.6 23.9 96.9
## 952 NA NA 818.4 19.0 100.0
## 972 NA NA 817.0 2.7 100.0
## 992 NA NA 751.2 54.8 96.9
## 1012 NA NA 753.0 65.2 96.9