CHOLMOD and GetClass error when running errorsarlmfrom spdep package with method = Matrix or SparseM

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Hi,

I'm working on Windows with 2GB RAM.

I'm trying to run the errorsarlm with 28 predictor variables and 16,854
records. The listw object is created by the dnearneigh function with upper
limit of distance as 2500m. Following are the sequence of codes.
Quote:

CHOLMOD error: out of memory

seems quite clear. How dense is your weights matrix - just say:

print(wts2500)

If it is such that some observations have many neighbours, the matrix will 
still be large. Users have run with n > 30,000, so 16,000 is feasible, but 
your case may be special - distance is not an ideal criterion.

Roger
## Read polygon shape file
adrbaseshp<-readShapePoly("tricounty_2005_12JAN_WORKING.shp", IDvar="ID",
verbose=TRUE)

### creating neighbor list
coords<-coordinates(adrbaseshp)
rn<-sapply(slot(adrbaseshp, "polygons"), function(x) slot(x, "ID"))
nb2500<-dnearneigh(coords, 0, 2500, row.names=rn)

## neighbor to weigth matrix
wts2500<-nb2listw(nb2500, zero.policy=TRUE)

## lagrange diagnostics
adr_rd_ols.lagrange<-lm.LMtests(adr_rd_ols.lm, wts2500, test="all",
zero.policy=TRUE)

# Spatial error model package spdep
##  To work around the memory problem I used method="Matrix" (suggested by
Roger Bivand)

adr_rd.saerror<-errorsarlm(LN_PRICE~., data=adr_rd_ols, wts2500,
zero.policy=TRUE, method="Matrix")

## It gave me the following error which I can't understand
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
CHOLMOD error: out of memory
Error in asMethod(object) : no function to return from, jumping to top level
In addition: Warning messages:
1: NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
2: NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
3: NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
CHOLMOD error: out of memory
Error in switch(.Generic, "+" = , "-" = .Call(Tsparse_to_Csparse,
new("dgTMatrix",  :
       no function to return from, jumping to top level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
CHOLMOD error: out of memory
Error in switch(.Generic, "+" = , "-" = .Call(Tsparse_to_Csparse,
new("dgTMatrix",  :
       no function to return from, jumping to top level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
CHOLMOD error: out of memory
Error in switch(.Generic, "+" = , "-" = .Call(Tsparse_to_Csparse,
new("dgTMatrix",  :
       no function to return from, jumping to top level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
CHOLMOD error: out of memory
Error in switch(.Generic, "+" = , "-" = .Call(Tsparse_to_Csparse,
new("dgTMatrix",  :
       no function to return from, jumping to top level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
CHOLMOD error: out of memory
Error in switch(.Generic, "+" = , "-" = .Call(Tsparse_to_Csparse,
new("dgTMatrix",  :
       no function to return from, jumping to top level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
CHOLMOD error: out of memory
Error in switch(.Generic, "+" = , "-" = .Call(Tsparse_to_Csparse,
new("dgTMatrix",  :
       no function to return from, jumping to top level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
CHOLMOD error: out of memory
Error in switch(.Generic, "+" = , "-" = .Call(Tsparse_to_Csparse,
new("dgTMatrix",  :
       no function to return from, jumping to top level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
CHOLMOD error: out of memory
Error in switch(.Generic, "+" = , "-" = .Call(Tsparse_to_Csparse,
new("dgTMatrix",  :
       no function to return from, jumping to top level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
CHOLMOD error: out of memory
Error in switch(.Generic, "+" = , "-" = .Call(Tsparse_to_Csparse,
new("dgTMatrix",  :
       no function to return from, jumping to top level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
CHOLMOD error: out of memory
Error in switch(.Generic, "+" = , "-" = .Call(Tsparse_to_Csparse,
new("dgTMatrix",  :
       no function to return from, jumping to top level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in initialize(value, ...) : no function to return from, jumping to top
level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in initialize(value, ...) : no function to return from, jumping to top
level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in initialize(value, ...) : no function to return from, jumping to top
level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in initialize(value, ...) : no function to return from, jumping to top
level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in initialize(value, ...) : no function to return from, jumping to top
level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in initialize(value, ...) : no function to return from, jumping to top
level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in initialize(value, ...) : no function to return from, jumping to top
level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in initialize(value, ...) : no function to return from, jumping to top
level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in initialize(value, ...) : no function to return from, jumping to top
level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in initialize(value, ...) : no function to return from, jumping to top
level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in initialize(value, ...) : no function to return from, jumping to top
level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in initialize(value, ...) : no function to return from, jumping to top
level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in initialize(value, ...) : no function to return from, jumping to top
level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in initialize(value, ...) : no function to return from, jumping to top
level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in initialize(value, ...) : no function to return from, jumping to top
level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in initialize(value, ...) : no function to return from, jumping to top
level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in initialize(value, ...) : no function to return from, jumping to top
level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in initialize(value, ...) : no function to return from, jumping to top
level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in initialize(value, ...) : no function to return from, jumping to top
level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in initialize(value, ...) : no function to return from, jumping to top
level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in `slot<-`(.Object, slotName, check = FALSE, slotVal) :
       no function to return from, jumping to top level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in `slot<-`(.Object, slotName, check = FALSE, slotVal) :
       no function to return from, jumping to top level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in `slot<-`(.Object, slotName, check = FALSE, slotVal) :
       no function to return from, jumping to top level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
Error in `slot<-`(.Object, slotName, check = FALSE, slotVal) :
       no function to return from, jumping to top level
In addition: Warning message:
NA/Inf replaced by maximum positive value in: optimize(sar.error.f.M,
interval = interval, maximum = TRUE,
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

I also tried the following

adr_rd.saerror<-errorsarlm(LN_PRICE~., data=adr_rd_ols, wts2500,
zero.policy=TRUE, method="SparseM")

I got the following

Error in getClass(Class, where = topenv(parent.frame())) :
       "matrix.csr" is not a defined class
In addition: Warning message:
'asMatrixCsrListw' is deprecated.
Use 'as_dgRMatrix_listw' instead.
See help("Deprecated") and help("spdep-deprecated").

Again, I don't understand the error. How should I run the errorsarlm
function?

Thanks in advance.
Debs.

--

Debarchana Ghosh
PHD Candidate | Research Assistant
Department of Geography
University of Minnesota.
PH: 8143607580
www.tc.umn.edu/~ghos0033/ <http://www.tc.umn.edu/%7Eghos0033/>

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Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no
Dear Spatial R group,

I disclose that I have been more active in image segmentation than spatial
statistics of late so please bear with me if this question is too pedantic.
I have a field collected marked point pattern of tree crown size classes.
The point data consists of the X,Y coordinates of the center of the tree
crown projected onto CT State Plane Datum and the estimated crown size class
(described as a radius measured in feet).  There are 8 possible size
classes: 4, 6, 8, 10, 12, 14, 16 and 20 feet.  I have produced a marked
point pattern data set with the same crown size class attribute from an
automatic crown detection algorithm using remotely sensed data.  I would
like to test how similar (or different if that turns out to be the case) the
two marked point patterns are to each other, ie, how well the size class
spatial location and distributions match.  I know this is not a perfect
match as there are 516 field measured points and 568 remotely sensed points.
However, I am looking for a metric to assess how closely the simulated size
class distribution patterns emulate the field measured patterns.

Any suggestions are truly appreciated.
Thanks,

Andrew Niccolai
Doctoral Candidate
Yale University
office (203) 432-5144
cell (860) 402-6079