Cause of error in spdep::errorsarlm

Hi

Please remember to keep the r-sig-geo on the list.

See ?formula. I guess that somewhere under the hood of glm()
as.formula() is called. Checking the code of glm() you can see that
model.frame() is called. From ?model.frame one notice that:

    If either 'formula' or 'data' is already a model frame (a data
    frame with a '"terms"' attribute) and the other is missing, the
    model frame is returned.  Unless 'formula' is a terms object,
    'as.formula' and then 'terms' is called on it.  (If you wish to
    use the 'keep.order' argument of 'terms.formula', pass a terms
    object rather than a formula.)

All this happens in glm() but not in errorsarlm():

my_formula    <- "resp ~  pred1 + pred2"
SAR.mod           <- errorsarlm(my_formula, data=df, listw=weight_list)

Error: $ operator is invalid for atomic vectors

traceback()

3: terms.default(formula, data = data)
2: terms(formula, data = data)
1: errorsarlm(my_formula, data = df, listw = weight_list)

class(my_formula)

[1] "character"

class(resp ~  pred1 + pred2)

[1] "formula"

In errorsarlm() terms() is called with my_formula and data and since formula is a string an error is raised.

In the man page of errorsarlm() one sees:

formula: a symbolic description of the model to be fit. The details of
         model specification are given for 'lm()'

And in ?lm we see:

formula: an object of class '"formula"' (or one that can be coerced to
         that class): a symbolic description of the model to be
         fitted.  The details of model specification are given under
         'Details'.

So strictly speaking errorsarlm() should be able to handle a formula defined as a string (maintainer on cc).


Yours sincerely / Med venlig hilsen


Frede Aakmann T?gersen
Specialist, M.Sc., Ph.D.
Plant Performance & Modeling

Technology & Service Solutions
T +45 9730 5135
M +45 2547 6050
frtog at vestas.com
http://www.vestas.com

Company reg. name: Vestas Wind Systems A/S This e-mail is subject to 
our e-mail disclaimer statement.
Please refer to www.vestas.com/legal/notice If you have received this 
e-mail in error please contact the sender.

-----Original Message-----
From: Dan Rosauer [mailto:dan.rosauer at anu.edu.au]
Sent: 5. november 2014 07:59
To: Frede Aakmann T?gersen
Subject: RE: Cause of error in spdep::errorsarlm

That worked.  Thank you!

But I don't understand.  Normally if you try to assign unquoted text 
to a variable, it check if the text refers to named objects, and if not gives an error.

And the quoted version worked perfectly for GLM models.

So problem solved, and something learned.

cheers
Dan

~~~~~~~~~~~~~~~~~~~~~~
Dan Rosauer
Postdoctoral Researcher
Moritz Lab
Ecology, Evolution & Genetics
Research School of Biology
Gould Building, Daley Road
Australian National University
Canberra ACT 0200

+61 413 950 275 (mobile)
+61 2 6125 1028 (office)
dan.rosauer at anu.edu.au

sites.google.com/site/danielrosauer




-----Original Message-----
From: Frede Aakmann T?gersen [mailto:frtog at vestas.com]
Sent: Wednesday, 5 November 2014 5:19 PM
To: Dan Rosauer; r-sig-geo at r-project.org
Subject: RE: Cause of error in spdep::errorsarlm

Hi Dan

Remove the " from your formula. It should be

my_formula    <- resp ~  pred1 + pred2


Yours sincerely / Med venlig hilsen


Frede Aakmann T?gersen
Specialist, M.Sc., Ph.D.
Plant Performance & Modeling

Technology & Service Solutions
T +45 9730 5135
M +45 2547 6050
frtog at vestas.com
http://www.vestas.com

Company reg. name: Vestas Wind Systems A/S This e-mail is subject to 
our e- mail disclaimer statement.
Please refer to www.vestas.com/legal/notice If you have received this 
e-mail in error please contact the sender.

-----Original Message-----
From: r-sig-geo-bounces at r-project.org [mailto:r-sig-geo-bounces at r- 
project.org] On Behalf Of Dan Rosauer
Sent: 5. november 2014 03:21
To: r-sig-geo at r-project.org
Subject: [R-sig-Geo] Cause of error in spdep::errorsarlm

Hi Roger et al

I hope someone can help me with the following error with a call to 
the spdep function errorsarlm()

Calling the function returns this:  Error: $ operator is invalid for 
atomic vectors

Things I have already tried:
* testing with real and simulated data - error occurs
* running it on windows and linux - error is identical
* omitting various arguments to the function to see which one is the 
cause - error occurs with or without the data or listw arguments.  
So it apparently triggers this error before it even gets to the 
problem of the missing arguments, and apparently they don't relate 
to the actual content of the data or spatial weights.

Here is a test script which generates the error:

######################
library(spdep)

# create a sample data frame
df            <- data.frame(lat=runif(100,0,3),long=runif(100,0,3),
pred1=runif(100,0,1), pred2=runif(100,0,1), resp=runif(100,0,10))

cat("\nPreparing neighbourhood weights for SARLM\n\n")
coords        <-as.matrix(cbind(df$long, df$lat))
cont.nb       <- dnearneigh(coords,d1=0, d2=100,longlat=TRUE)
weight_list   <- nb2listw(cont.nb, glist=NULL, style="W", zero.policy=TRUE)

my_formula    <- "resp ~  pred1 + pred2"

# this line gives the error: $ operator is invalid for atomic vectors
SAR.mod           <- errorsarlm(my_formula, data=df, listw=weight_list)
######################

The R version is 3.1.0, and spdep 0.5-77

Any advice on how to fix this problem would be much appreciated.

The best possibility is that I've made a dumb mistake which can be 
easily fixed... :-)

thanks

Dan


~~~~~~~~~~~~~~~~~~~~~~
Dan Rosauer
Postdoctoral Researcher
Moritz Lab
Ecology, Evolution & Genetics
Research School of Biology
Gould Building, Daley Road
Australian National University
Canberra ACT 0200

+61 413 950 275 (mobile)
+61 2 6125 1028 (office)
dan.rosauer at anu.edu.au

sites.google.com/site/danielrosauer