revdep/checks.noindex/SSDM/old/SSDM.Rcheck/SSDM-Ex.R

In gbm-developers/gbm: Generalized Boosted Regression Models

pkgname <- "SSDM"
source(file.path(R.home("share"), "R", "examples-header.R"))
options(warn = 1)
library('SSDM')

base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
cleanEx()
nameEx("ensemble")
### * ensemble

flush(stderr()); flush(stdout())

### Name: ensemble
### Title: Methods to assemble multiple algorithms in an ensemble SDM
### Aliases: ensemble ensemble,Algorithm.SDM-method
###   sum,Algorithm.SDM-method

### ** Examples

## Not run: 
##D # Loading data
##D data(Env)
##D data(Occurrences)
##D Occurrences <- subset(Occurrences, Occurrences$SPECIES == 'elliptica')
##D 
##D # ensemble SDM building
##D CTA <- modelling('CTA', Occurrences, Env, Xcol = 'LONGITUDE', Ycol = 'LATITUDE')
##D SVM <- modelling('SVM', Occurrences, Env, Xcol = 'LONGITUDE', Ycol = 'LATITUDE')
##D ESDM <- ensemble(CTA, SVM, ensemble.thresh = c(0.6))
##D 
##D # Results plotting
##D plot(ESDM)
## End(Not run)




cleanEx()
nameEx("ensemble_modelling")
### * ensemble_modelling

flush(stderr()); flush(stdout())

### Name: ensemble_modelling
### Title: Build an ensemble SDM that assembles multiple algorithms
### Aliases: ensemble_modelling

### ** Examples

## Not run: 
##D # Loading data
##D data(Env)
##D data(Occurrences)
##D Occurrences <- subset(Occurrences, Occurrences$SPECIES == 'elliptica')
##D 
##D # ensemble SDM building
##D ESDM <- ensemble_modelling(c('CTA', 'MARS'), Occurrences, Env, rep = 1,
##D                           Xcol = 'LONGITUDE', Ycol = 'LATITUDE',
##D                           ensemble.thresh = c(0.6))
##D 
##D # Results plotting
##D plot(ESDM)
## End(Not run)




cleanEx()
nameEx("evaluate")
### * evaluate

flush(stderr()); flush(stdout())

### Name: evaluate
### Title: Evaluate
### Aliases: evaluate evaluate,Algorithm.SDM-method
###   evaluate,MAXENT.SDM-method evaluate,Stacked.SDM-method

### ** Examples


## Not run: 
##D # Loading data
##D data(Env)
##D data(Occurrences)
##D # SSDM building
##D SSDM <- stack_modelling(c('CTA', 'SVM'), Occurrences, Env, rep = 1,
##D                        Xcol = 'LONGITUDE', Ycol = 'LATITUDE',
##D                        Spcol = 'SPECIES')
##D 
##D # Evaluation
##D evaluate(SSDM)
##D 
## End(Not run)




cleanEx()
nameEx("gui")
### * gui

flush(stderr()); flush(stdout())

### Name: gui
### Title: SSDM package Graphic User Interface
### Aliases: gui

### ** Examples

## Not run: 
##D gui()
## End(Not run)




cleanEx()
nameEx("load_occ")
### * load_occ

flush(stderr()); flush(stdout())

### Name: load_occ
### Title: Load occurrence data
### Aliases: load_occ

### ** Examples


## Not run: 
##D load_occ(path = system.file('extdata',  package = 'SSDM'), Env,
##D          Xcol = 'LONGITUDE', Ycol = 'LATITUDE',
##D          file = 'Occurrences.csv', sep = ',')
## End(Not run)




cleanEx()
nameEx("load_var")
### * load_var

flush(stderr()); flush(stdout())

### Name: load_var
### Title: Load environmental variables
### Aliases: load_var

### ** Examples

## Not run: 
##D load_var(system.file('extdata',  package = 'SSDM'))
## End(Not run)




cleanEx()
nameEx("mapDiversity")
### * mapDiversity

flush(stderr()); flush(stdout())

### Name: mapDiversity
### Title: Map Diversity
### Aliases: mapDiversity mapDiversity,Stacked.SDM-method

### ** Examples


## Not run: 
##D # Loading data
##D data(Env)
##D data(Occurrences)
##D # SSDM building
##D SSDM <- stack_modelling(c('CTA', 'SVM'), Occurrences, Env, rep = 1,
##D                        Xcol = 'LONGITUDE', Ycol = 'LATITUDE',
##D                        Spcol = 'SPECIES')
##D 
##D # Diversity mapping
##D mapDiversity(SSDM, mathod = 'pSSDM')
##D 
## End(Not run)




cleanEx()
nameEx("modelling")
### * modelling

flush(stderr()); flush(stdout())

### Name: modelling
### Title: Build an SDM using a single algorithm
### Aliases: modelling

### ** Examples

# Loading data
data(Env)
data(Occurrences)
Occurrences <- subset(Occurrences, Occurrences$SPECIES == 'elliptica')

# SDM building
SDM <- modelling('GLM', Occurrences, Env, Xcol = 'LONGITUDE', Ycol = 'LATITUDE')

# Results plotting
## Not run: 
##D plot(SDM)
## End(Not run)





cleanEx()
nameEx("stack_modelling")
### * stack_modelling

flush(stderr()); flush(stdout())

### Name: stack_modelling
### Title: Build an SSDM that assembles multiple algorithms and species.
### Aliases: stack_modelling

### ** Examples

## Not run: 
##D # Loading data
##D data(Env)
##D data(Occurrences)
##D 
##D # SSDM building
##D SSDM <- stack_modelling(c('CTA', 'SVM'), Occurrences, Env, rep = 1,
##D                        Xcol = 'LONGITUDE', Ycol = 'LATITUDE',
##D                        Spcol = 'SPECIES')
##D 
##D # Results plotting
##D plot(SSDM)
## End(Not run)




cleanEx()
nameEx("stacking")
### * stacking

flush(stderr()); flush(stdout())

### Name: stacking
### Title: Stack different ensemble SDMs in an SSDM
### Aliases: stacking stacking,Ensemble.SDM-method

### ** Examples

## Not run: 
##D # Loading data
##D data(Env)
##D data(Occurrences)
##D Occ1 <- subset(Occurrences, Occurrences$SPECIES == 'elliptica')
##D Occ2 <- subset(Occurrences, Occurrences$SPECIES == 'gracilis')
##D 
##D # SSDM building
##D ESDM1 <- ensemble_modelling(c('CTA', 'SVM'), Occ1, Env, rep = 1,
##D                            Xcol = 'LONGITUDE', Ycol = 'LATITUDE',
##D                            name = 'elliptica', ensemble.thresh = c(0.6))
##D ESDM2 <- ensemble_modelling(c('CTA', 'SVM'), Occ2, Env, rep = 1,
##D                            Xcol = 'LONGITUDE', Ycol = 'LATITUDE',
##D                            name = 'gracilis', ensemble.thresh = c(0.6))
##D SSDM <- stacking(ESDM1, ESDM2)
##D 
##D # Results plotting
##D plot(SSDM)
## End(Not run)




cleanEx()
nameEx("update-Stacked.SDM-method")
### * update-Stacked.SDM-method

flush(stderr()); flush(stdout())

### Name: update,Stacked.SDM-method
### Title: Update a previous SSDM
### Aliases: update,Stacked.SDM-method

### ** Examples

## Not run: 
##D update(stack, Occurrences, Env, Spname = 'NewSpecie')
## End(Not run)




### * <FOOTER>
###
cleanEx()
options(digits = 7L)
base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
grDevices::dev.off()
###
### Local variables: ***
### mode: outline-minor ***
### outline-regexp: "\\(> \\)?### [*]+" ***
### End: ***
quit('no')