'Re: [R-sig-Geo] [R-sig-eco] raster::predict example doesn't work?'

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List:       r-sig-geo
Subject:    Re: [R-sig-Geo] [R-sig-eco] raster::predict example doesn't work?
From:       "Gonzalez-Mirelis, Genoveva via R-sig-Geo" <r-sig-geo () r-project ! org>
Date:       2018-12-05 9:06:29
Message-ID: e6f6bae646a84cc2afdc91c9ed522bbb () hi ! no
[Download RAW message or body]

Thank you Ákos, your solution does work. One caveat, though: the 'predict' function \
from 'stats' returns a matrix, whereas that from the 'raster' package returns a \
raster object of identical extent and resolution as the supplied predictor stack, \
which is very handy. If no other solutions arise I will just convert that matrix to a \
raster as follows:

r <- raster(ncol=ncol(logo), nrow=nrow(logo))
extent(r) <- extent(logo)
values(r) <- pc

-----Original Message-----
From: R-sig-ecology <r-sig-ecology-bounces@r-project.org> On Behalf Of Bede-Fazekas \
                Ákos
Sent: 4. desember 2018 16:50
To: r-sig-ecology@r-project.org; R-sig-geo <r-sig-geo@r-project.org>
Subject: Re: [R-sig-eco] raster::predict example doesn't work?

Dear Genoveva,

All the examples in the help file of package 'party' 
(https://cran.r-project.org/web/packages/party/party.pdf) use the function predict() \
from package 'stats' instead of package 'raster'. But converting the RasterStack to \
data.frame, changing the column 'red'  from numeric to factor, using \
stats::predict(..., newdata), and create a new layer of the RasterStack can solve the \
problem. logo_df <- as.data.frame(logo)
logo_df$red <- factor(logo_df$red, levels = levels(v$red)) pc <- stats::predict(m, \
OOB = TRUE, newdata = logo_df) logo$pc <- pc

HTH,
Ákos Bede-Fazekas
Hungarian Academy of Sciences

2018.12.04. 15:52 keltezéssel, Gonzalez-Mirelis, Genoveva írta:
> Dear list,
> 
> I posted this question recently on another list so I apologize for any \
> cross-posting. Still no solution. 
> 
> I would like to use the 'predict' function in the 'raster' package in an \
> implementation of species distribution modelling with a couple of factor variables. \
> Furthermore, I would like to set this up exactly as the cforest example listed in \
> the help file. Unfortunately, I cannot get the example to work! 
> 
> 
> # create a RasterStack or RasterBrick with with a set of predictor 
> layers
> 
> 
> 
> logo <- brick(system.file("external/rlogo.grd", package="raster"))
> 
> names(logo)
> 
> 
> 
> # known presence and absence points
> 
> p <- matrix(c(48, 48, 48, 53, 50, 46, 54, 70, 84, 85, 74, 84, 95, 85,
> 
> 66, 42, 26, 4, 19, 17, 7, 14, 26, 29, 39, 45, 51, 56, 
> 46, 38, 31,
> 
> 22, 34, 60, 70, 73, 63, 46, 43, 28), ncol=2)
> 
> 
> 
> a <- matrix(c(22, 33, 64, 85, 92, 94, 59, 27, 30, 64, 60, 33, 31, 9,
> 
> 99, 67, 15, 5, 4, 30, 8, 37, 42, 27, 19, 69, 60, 73, 3, 
> 5, 21,
> 
> 37, 52, 70, 74, 9, 13, 4, 17, 47), ncol=2)
> 
> 
> 
> # extract values for points
> 
> xy <- rbind(cbind(1, p), cbind(0, a))
> 
> v <- data.frame(cbind(pa=xy[,1], extract(logo, xy[,2:3])))
> 
> 
> 
> # cforest (other Random Forest implementation) example with factors 
> argument
> 
> 
> 
> v$red <- as.factor(round(v$red/100))
> 
> logo$red <- round(logo[[1]]/100)
> 
> 
> 
> library(party)
> 
> m <- cforest(pa~., control=cforest_unbiased(mtry=3), data=v) f <- 
> list(levels(v$red))
> 
> names(f) <- 'red'
> 
> pc <- predict(logo, m, OOB=TRUE, factors=f)
> 
> 
> 
> # Error in v[cells, ] <- predv :
> 
> # number of items to replace is not a multiple of replacement length
> 
> 
> 
> # If you change the order of the first two arguments (I read this somewhere) then \
> the error changes, like this: 
> 
> 
> pc <- predict(m, logo, OOB=TRUE, factors=f)
> 
> 
> 
> # Error in RET@prediction_weights(newdata = newdata, mincriterion = mincriterion,  \
> : 
> # unused argument (factors = f)
> 
> 
> 
> # Lastly, if I run the line without the 'factors' argument
> 
> pc <- predict(m, logo, OOB=TRUE)
> 
> 
> 
> # Then I get no errors, but I don't understand the result. It's a 
> vector of 40 values (predictions?)
> 
> 
> 
> I am using Package 'raster' version 2.6-7 in RStudio 1.1.453, running off a server. \
> I have tried the on several other computers, though, and the error persisted. 
> 
> 
> Many thanks for any help,
> 
> 
> 
> Genoveva
> 
> Genoveva Gonzalez Mirelis, Scientist
> Institute of Marine Research
> Nordnesgaten 50
> 5005 Bergen, Norway
> Phone number +47 55238510
> 
> 
> Genoveva Gonzalez Mirelis, Scientist
> Institute of Marine Research
> Nordnesgaten 50
> 5005 Bergen, Norway
> Phone number +47 55238510
> 
> 
> 	[[alternative HTML version deleted]]
> 
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> R-sig-ecology mailing list
> R-sig-ecology@r-project.org
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> 

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