raster package and predict for GBM models

Thu, Nov 4, 2010 12:26 PM

Robert, sorry. Yes, myData is my gbm object. 

Also, I figured out what I had done wrong. The raster stack I created specified a data set name that was lowercase and the the gbm model was specifying upper case for the same raster layer. Once I use the correct name, it worked.

Thank you for the response.
Mike

--- On Thu, 11/4/10, Robert J. Hijmans <r.hijmans at gmail.com> wrote:

From: Robert J. Hijmans <r.hijmans at gmail.com>
Subject: Re: [R-sig-Geo] raster package and predict for GBM models
To: "Michael ODonnell" <odonnems at yahoo.com>
Cc: r-sig-geo at stat.math.ethz.ch
Date: Thursday, November 4, 2010, 10:58 AM
Hi Mike,

I cannot know from what you send, but the second argument
should be
your gbm object, and from your name "myData" I am guessing
it is not
(unless it really is referring to youModel).
One of the two vignettes of the 'dismo' package is about
'gbm'
(boosted regression trees) and 'raster' . So in principle
it should
work.

Robert

On Thu, Nov 4, 2010 at 7:34 AM, Michael ODonnell <odonnems at yahoo.com>
wrote:

Hello,

I have little experience using the raster package and

I am currently trying to develop a predicted surface based
on a gradient boosted model (gbm package).

The basic steps I am using include the following:

# Creating a raster stack of independent variables
USHGT <- raster("ushgt.asc", package="raster")
... (other variables omitted for post)
ras_stk <- stack(USHGT, HYELB, T1TO5LE, URBD_D,

SG_UNIT, MINTEMP, ANNPCP, TC_B04, TC_B07)

# Create the prediction model
... I am using a separate script that creates the gbm

object and due to the length I will not include. The outcome
is a gbm object.

.. Now I use the following, which fails:
r <- predict(ras_stk, myData, filename=OutFile,

na.rm=TRUE, overwrite=TRUE, n.trees=myData$n.trees,
type="response", progress="window")

Error:
Error in

model.frame.default(terms(reformulate(object$var.names)),
newdata, ?:object is not a matrix

The raster package manual states that the predict

function will work on any model that a predict method has
been implemented.

Does anyone have experience with this or possibly an

idea on how I might solve the issue.

Thank you,
mike

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raster package and predict for GBM models

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