Re: [R-sig-Geo] Error in Spatial lag model

2016-11-20 Thread Roger Bivand 

On Sun, 20 Nov 2016, Miluji Sb wrote:


Dear Roger,

Thank you for your quick reply.

#
print(spatial_knn2listw_obj)

Characteristics of weights list object:
Neighbour list object:
Number of regions: 10927
Number of nonzero links: 21854
Percentage nonzero weights: 0.01830329
Average number of links: 2
Non-symmetric neighbours list

Weights style: W
Weights constants summary:
 nnnS0  S1S2
W 10927 119399329 10927 10376.5 44660
#

The data is actually cross-sectional, is my mistake converting it
to pdata.frame? I have not tried the splm package, which is a mistake on my
part. I will try that now. Thanks.



If the data are not a spatial panel, then do not use splm, it is not 
relevant. If you have NAs in the response, you will need to address that 
once you can fit a model with complete cases. You may not have NAs in the 
covariates. I guess that the mistake was slag() and pdata.frame(), but 
your example is no help at all. Are you copying poor code from the 
internet? Why use k=2 (seems very ill-judged) - knn are intrinsically 
asymmetric, why 2?


Roger


Sincerely,

Milu

On Sun, Nov 20, 2016 at 8:29 PM, Roger Bivand  wrote:


On Sun, 20 Nov 2016, Miluji Sb wrote:

I have a dataset as below (with NAs). I am trying to run a spatial lagged

model

##
E2_mod_pdssat <- as.data.frame(gcp_t_p[,c(2,3)])
names(E2_mod_pdssat) <- c("Lon", "Lat")
row.names(E2_mod_pdssat) <- NULL

coords_matrix  <- as.matrix(E2_mod_pdssat) # create coordinate matrix
IDs <- row.names(as(E2_mod_pdssat, "data.frame"))

spatial_knn2nb_obj <- knn2nb(knearneigh(coords_matrix, k=2,
longlat=TRUE),
row.names=IDs)

# Now convert the nb to listw for use in spatial regression call.
# Spatial weights, illustrated with coding style "W" (row standardized)

spatial_knn2listw_obj <- nb2listw(spatial_knn2nb_obj, glist=NULL,
style="W",  zero.policy=TRUE)



Did you examine this object? What did the print method tell you?



E2_mod_pdssat_org_lon_lat <- E2_mod_pdssat_org[, c(2:3)] # The lon and lat
will be required



This object "_org" does not yet exist ...

E2_mod_pdssat_org <- E2_mod_pdssat_org[, -c(2,3)]  # Remove the Lon, Lat

columns that are not required

E2_mod_pdssat_pdata_frame <- pdata.frame(E2_mod_pdssat_org) # Convert data
frame to pdata.frame



So you omitted to say that the data are (unbalanced) panel data ...

All goes well until here but when I try to convert the explanatory

variables in the pdata.frame to spatial lagged variables

E2_mod_pdssat_X_lagged <-
as.data.frame(cbind(slag(E2_mod_pdssat_pdata_frame$tmean, listw =
spatial_knn2listw_obj),
slag(E2_mod_pdssat_pdata_frame$tmeansq, listw = spatial_knn2listw_obj),
slag(E2_mod_pdssat_pdata_frame$pmean, listw = spatial_knn2listw_obj),
slag(E2_mod_pdssat_pdata_frame$pmeansq, listw = spatial_knn2listw_obj)))

I get the following error "Error in lag.listw(listw, xt) : object lengths
differ". What am I doing wrong? I have also tried removing the NAs with
complete.cases.



You have defined weights for one object (possibly a cross section), and
then try to use them on a different object with a different number of rows.
If you really want to do this, you need a Kronecker product of the spatial
weights to take the panel structure of your data into account. Further, I
doubt strongly that you need to create WX manually, because spatial lags of
all the required variables are created by model fitting functions in the
splm package.

Roger



Any help will be greatly appreciated. Thank you.

Sincerely,

Milu

## Data

E2_mod_pdssat_org <- dput(head(temp,5))
structure(list(iso3 = structure(c(30L, 30L, 30L, 1L, 30L), .Label = c(".",
".M", "AFG", "AGO", "ALB", "ARE", "ARG", "ARM", "AUS", "AUT",
"AZE", "BDI", "BEL", "BEN", "BFA", "BGD", "BGR", "BHS", "BIH",
"BLR", "BLZ", "BOL", "BRA", "BRN", "BTN", "BWA", "CAF", "CAN",
"CHE", "CHL", "CHN", "CIV", "CMR", "COD", "COG", "COL", "CRI",
"CUB", "CYP", "CZE", "DEU", "DJI", "DNK", "DOM", "DZA", "ECU",
"EGY", "ERI", "ESH", "ESP", "EST", "ETH", "FIN", "FJI", "FLK",
"FRA", "GAB", "GBR", "GEO", "GHA", "GIN", "GNB", "GNQ", "GRC",
"GRL", "GTM", "GUF", "GUY", "HND", "HRV", "HTI", "HUN", "IDN",
"IND", "IRL", "IRN", "IRQ", "ISL", "ISR", "ITA", "JAM", "JOR",
"JPN", "KAZ", "KEN", "KGZ", "KHM", "KIR", "KOR", "KWT", "LAO",
"LBN", "LBR", "LBY", "LCA", "LKA", "LSO", "LTU", "LUX", "LVA",
"MAR", "MDA", "MDG", "MEX", "MKD", "MLI", "MMR", "MNE", "MNG",
"MOZ", "MRT", "MWI", "MYS", "NCL", "NER", "NGA", "NIC", "NLD",
"NOR", "NPL", "NZL", "OMN", "PAK", "PAN", "PER", "PHL", "PNG",
"POL", "PRI", "PRK", "PRT", "PRY", "QAT", "ROU", "RUS", "RWA",
"SAU", "SDN", "SEN", "SJM", "SLB", "SLE", "SLV", "SOM", "SRB",
"SUR", "SVK", "SVN", "SWE", "SWZ", "SYR", "TCD", "TGO", "THA",
"TJK", "TKM", "TLS", "TUN", "TUR", "TWN", "TZA", "UGA", "UKR",
"URY", "USA", "UZB", "VEN", "VNM", "VUT", "YEM", "ZAF", "ZMB",
"ZWE"), class = "factor"), lon = c(-69L, -68L, -72L, -71L, -70L
), lat = c(-55L, -55L, -54L, -54L, -54L), tmean = c(NA, NA,
4.55847677595631,

Re: [R-sig-Geo] Error in Spatial lag model

2016-11-20 Thread Miluji Sb 
Dear Roger,

Thank you for your quick reply.

#
print(spatial_knn2listw_obj)

Characteristics of weights list object:
Neighbour list object:
Number of regions: 10927
Number of nonzero links: 21854
Percentage nonzero weights: 0.01830329
Average number of links: 2
Non-symmetric neighbours list

Weights style: W
Weights constants summary:
  nnnS0  S1S2
W 10927 119399329 10927 10376.5 44660
#

The data is actually cross-sectional, is my mistake converting it
to pdata.frame? I have not tried the splm package, which is a mistake on my
part. I will try that now. Thanks.

Sincerely,

Milu

On Sun, Nov 20, 2016 at 8:29 PM, Roger Bivand  wrote:

> On Sun, 20 Nov 2016, Miluji Sb wrote:
>
> I have a dataset as below (with NAs). I am trying to run a spatial lagged
>> model
>>
>> ##
>> E2_mod_pdssat <- as.data.frame(gcp_t_p[,c(2,3)])
>> names(E2_mod_pdssat) <- c("Lon", "Lat")
>> row.names(E2_mod_pdssat) <- NULL
>>
>> coords_matrix  <- as.matrix(E2_mod_pdssat) # create coordinate matrix
>> IDs <- row.names(as(E2_mod_pdssat, "data.frame"))
>>
>> spatial_knn2nb_obj <- knn2nb(knearneigh(coords_matrix, k=2,
>> longlat=TRUE),
>> row.names=IDs)
>>
>> # Now convert the nb to listw for use in spatial regression call.
>> # Spatial weights, illustrated with coding style "W" (row standardized)
>>
>> spatial_knn2listw_obj <- nb2listw(spatial_knn2nb_obj, glist=NULL,
>> style="W",  zero.policy=TRUE)
>>
>
> Did you examine this object? What did the print method tell you?
>
>
>> E2_mod_pdssat_org_lon_lat <- E2_mod_pdssat_org[, c(2:3)] # The lon and lat
>> will be required
>>
>
> This object "_org" does not yet exist ...
>
> E2_mod_pdssat_org <- E2_mod_pdssat_org[, -c(2,3)]  # Remove the Lon, Lat
>> columns that are not required
>>
>> E2_mod_pdssat_pdata_frame <- pdata.frame(E2_mod_pdssat_org) # Convert data
>> frame to pdata.frame
>>
>>
> So you omitted to say that the data are (unbalanced) panel data ...
>
> All goes well until here but when I try to convert the explanatory
>> variables in the pdata.frame to spatial lagged variables
>>
>> E2_mod_pdssat_X_lagged <-
>> as.data.frame(cbind(slag(E2_mod_pdssat_pdata_frame$tmean, listw =
>> spatial_knn2listw_obj),
>> slag(E2_mod_pdssat_pdata_frame$tmeansq, listw = spatial_knn2listw_obj),
>> slag(E2_mod_pdssat_pdata_frame$pmean, listw = spatial_knn2listw_obj),
>> slag(E2_mod_pdssat_pdata_frame$pmeansq, listw = spatial_knn2listw_obj)))
>>
>> I get the following error "Error in lag.listw(listw, xt) : object lengths
>> differ". What am I doing wrong? I have also tried removing the NAs with
>> complete.cases.
>>
>
> You have defined weights for one object (possibly a cross section), and
> then try to use them on a different object with a different number of rows.
> If you really want to do this, you need a Kronecker product of the spatial
> weights to take the panel structure of your data into account. Further, I
> doubt strongly that you need to create WX manually, because spatial lags of
> all the required variables are created by model fitting functions in the
> splm package.
>
> Roger
>
>
>> Any help will be greatly appreciated. Thank you.
>>
>> Sincerely,
>>
>> Milu
>>
>> ## Data
>>
>> E2_mod_pdssat_org <- dput(head(temp,5))
>> structure(list(iso3 = structure(c(30L, 30L, 30L, 1L, 30L), .Label = c(".",
>> ".M", "AFG", "AGO", "ALB", "ARE", "ARG", "ARM", "AUS", "AUT",
>> "AZE", "BDI", "BEL", "BEN", "BFA", "BGD", "BGR", "BHS", "BIH",
>> "BLR", "BLZ", "BOL", "BRA", "BRN", "BTN", "BWA", "CAF", "CAN",
>> "CHE", "CHL", "CHN", "CIV", "CMR", "COD", "COG", "COL", "CRI",
>> "CUB", "CYP", "CZE", "DEU", "DJI", "DNK", "DOM", "DZA", "ECU",
>> "EGY", "ERI", "ESH", "ESP", "EST", "ETH", "FIN", "FJI", "FLK",
>> "FRA", "GAB", "GBR", "GEO", "GHA", "GIN", "GNB", "GNQ", "GRC",
>> "GRL", "GTM", "GUF", "GUY", "HND", "HRV", "HTI", "HUN", "IDN",
>> "IND", "IRL", "IRN", "IRQ", "ISL", "ISR", "ITA", "JAM", "JOR",
>> "JPN", "KAZ", "KEN", "KGZ", "KHM", "KIR", "KOR", "KWT", "LAO",
>> "LBN", "LBR", "LBY", "LCA", "LKA", "LSO", "LTU", "LUX", "LVA",
>> "MAR", "MDA", "MDG", "MEX", "MKD", "MLI", "MMR", "MNE", "MNG",
>> "MOZ", "MRT", "MWI", "MYS", "NCL", "NER", "NGA", "NIC", "NLD",
>> "NOR", "NPL", "NZL", "OMN", "PAK", "PAN", "PER", "PHL", "PNG",
>> "POL", "PRI", "PRK", "PRT", "PRY", "QAT", "ROU", "RUS", "RWA",
>> "SAU", "SDN", "SEN", "SJM", "SLB", "SLE", "SLV", "SOM", "SRB",
>> "SUR", "SVK", "SVN", "SWE", "SWZ", "SYR", "TCD", "TGO", "THA",
>> "TJK", "TKM", "TLS", "TUN", "TUR", "TWN", "TZA", "UGA", "UKR",
>> "URY", "USA", "UZB", "VEN", "VNM", "VUT", "YEM", "ZAF", "ZMB",
>> "ZWE"), class = "factor"), lon = c(-69L, -68L, -72L, -71L, -70L
>> ), lat = c(-55L, -55L, -54L, -54L, -54L), tmean = c(NA, NA,
>> 4.55847677595631,
>> 4.06015710382516, 3.71010245901642), pmean = c(NA, NA, 2.45569896697998,
>> 1.6384220123291, 1.43925595283508), lngdp = c(-0.102380074560642,
>> -2.3195972442627, 0.0122363297268748, -0.483756244182587,
>> -6.29744625091553
>> ), tmeansq = c(NA, NA, 20.7797107696533,

Re: [R-sig-Geo] Error in Spatial lag model

2016-11-20 Thread Roger Bivand 

On Sun, 20 Nov 2016, Miluji Sb wrote:


I have a dataset as below (with NAs). I am trying to run a spatial lagged
model

##
E2_mod_pdssat <- as.data.frame(gcp_t_p[,c(2,3)])
names(E2_mod_pdssat) <- c("Lon", "Lat")
row.names(E2_mod_pdssat) <- NULL

coords_matrix  <- as.matrix(E2_mod_pdssat) # create coordinate matrix
IDs <- row.names(as(E2_mod_pdssat, "data.frame"))

spatial_knn2nb_obj <- knn2nb(knearneigh(coords_matrix, k=2, longlat=TRUE),
row.names=IDs)

# Now convert the nb to listw for use in spatial regression call.
# Spatial weights, illustrated with coding style "W" (row standardized)

spatial_knn2listw_obj <- nb2listw(spatial_knn2nb_obj, glist=NULL,
style="W",  zero.policy=TRUE)


Did you examine this object? What did the print method tell you?



E2_mod_pdssat_org_lon_lat <- E2_mod_pdssat_org[, c(2:3)] # The lon and lat
will be required


This object "_org" does not yet exist ...


E2_mod_pdssat_org <- E2_mod_pdssat_org[, -c(2,3)]  # Remove the Lon, Lat
columns that are not required

E2_mod_pdssat_pdata_frame <- pdata.frame(E2_mod_pdssat_org) # Convert data
frame to pdata.frame



So you omitted to say that the data are (unbalanced) panel data ...


All goes well until here but when I try to convert the explanatory
variables in the pdata.frame to spatial lagged variables

E2_mod_pdssat_X_lagged <-
as.data.frame(cbind(slag(E2_mod_pdssat_pdata_frame$tmean, listw =
spatial_knn2listw_obj),
slag(E2_mod_pdssat_pdata_frame$tmeansq, listw = spatial_knn2listw_obj),
slag(E2_mod_pdssat_pdata_frame$pmean, listw = spatial_knn2listw_obj),
slag(E2_mod_pdssat_pdata_frame$pmeansq, listw = spatial_knn2listw_obj)))

I get the following error "Error in lag.listw(listw, xt) : object lengths
differ". What am I doing wrong? I have also tried removing the NAs with
complete.cases.


You have defined weights for one object (possibly a cross section), and 
then try to use them on a different object with a different number of 
rows. If you really want to do this, you need a Kronecker product of the 
spatial weights to take the panel structure of your data into account. 
Further, I doubt strongly that you need to create WX manually, because 
spatial lags of all the required variables are created by model fitting 
functions in the splm package.


Roger



Any help will be greatly appreciated. Thank you.

Sincerely,

Milu

## Data

E2_mod_pdssat_org <- dput(head(temp,5))
structure(list(iso3 = structure(c(30L, 30L, 30L, 1L, 30L), .Label = c(".",
".M", "AFG", "AGO", "ALB", "ARE", "ARG", "ARM", "AUS", "AUT",
"AZE", "BDI", "BEL", "BEN", "BFA", "BGD", "BGR", "BHS", "BIH",
"BLR", "BLZ", "BOL", "BRA", "BRN", "BTN", "BWA", "CAF", "CAN",
"CHE", "CHL", "CHN", "CIV", "CMR", "COD", "COG", "COL", "CRI",
"CUB", "CYP", "CZE", "DEU", "DJI", "DNK", "DOM", "DZA", "ECU",
"EGY", "ERI", "ESH", "ESP", "EST", "ETH", "FIN", "FJI", "FLK",
"FRA", "GAB", "GBR", "GEO", "GHA", "GIN", "GNB", "GNQ", "GRC",
"GRL", "GTM", "GUF", "GUY", "HND", "HRV", "HTI", "HUN", "IDN",
"IND", "IRL", "IRN", "IRQ", "ISL", "ISR", "ITA", "JAM", "JOR",
"JPN", "KAZ", "KEN", "KGZ", "KHM", "KIR", "KOR", "KWT", "LAO",
"LBN", "LBR", "LBY", "LCA", "LKA", "LSO", "LTU", "LUX", "LVA",
"MAR", "MDA", "MDG", "MEX", "MKD", "MLI", "MMR", "MNE", "MNG",
"MOZ", "MRT", "MWI", "MYS", "NCL", "NER", "NGA", "NIC", "NLD",
"NOR", "NPL", "NZL", "OMN", "PAK", "PAN", "PER", "PHL", "PNG",
"POL", "PRI", "PRK", "PRT", "PRY", "QAT", "ROU", "RUS", "RWA",
"SAU", "SDN", "SEN", "SJM", "SLB", "SLE", "SLV", "SOM", "SRB",
"SUR", "SVK", "SVN", "SWE", "SWZ", "SYR", "TCD", "TGO", "THA",
"TJK", "TKM", "TLS", "TUN", "TUR", "TWN", "TZA", "UGA", "UKR",
"URY", "USA", "UZB", "VEN", "VNM", "VUT", "YEM", "ZAF", "ZMB",
"ZWE"), class = "factor"), lon = c(-69L, -68L, -72L, -71L, -70L
), lat = c(-55L, -55L, -54L, -54L, -54L), tmean = c(NA, NA,
4.55847677595631,
4.06015710382516, 3.71010245901642), pmean = c(NA, NA, 2.45569896697998,
1.6384220123291, 1.43925595283508), lngdp = c(-0.102380074560642,
-2.3195972442627, 0.0122363297268748, -0.483756244182587, -6.29744625091553
), tmeansq = c(NA, NA, 20.7797107696533, 16.4848766326904, 13.7648601531982
), pmeansq = c(NA, NA, 6.03045749664307, 2.68442678451538, 2.07145762443542
)), .Names = c("iso3", "lon", "lat", "tmean", "pmean", "lngdp",
"tmeansq", "pmeansq"), row.names = c("1", "2", "3", "4", "5"), class =
"data.frame")

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Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 91 00
e-mail: roger.biv...@nhh.no
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[R-sig-Geo] Error in Spatial lag model

2016-11-20 Thread Miluji Sb 
I have a dataset as below (with NAs). I am trying to run a spatial lagged
model

##
E2_mod_pdssat <- as.data.frame(gcp_t_p[,c(2,3)])
names(E2_mod_pdssat) <- c("Lon", "Lat")
row.names(E2_mod_pdssat) <- NULL

coords_matrix  <- as.matrix(E2_mod_pdssat) # create coordinate matrix
IDs <- row.names(as(E2_mod_pdssat, "data.frame"))

spatial_knn2nb_obj <- knn2nb(knearneigh(coords_matrix, k=2, longlat=TRUE),
row.names=IDs)

# Now convert the nb to listw for use in spatial regression call.
# Spatial weights, illustrated with coding style "W" (row standardized)

spatial_knn2listw_obj <- nb2listw(spatial_knn2nb_obj, glist=NULL,
style="W",  zero.policy=TRUE)

E2_mod_pdssat_org_lon_lat <- E2_mod_pdssat_org[, c(2:3)] # The lon and lat
will be required
E2_mod_pdssat_org <- E2_mod_pdssat_org[, -c(2,3)]  # Remove the Lon, Lat
columns that are not required

E2_mod_pdssat_pdata_frame <- pdata.frame(E2_mod_pdssat_org) # Convert data
frame to pdata.frame

All goes well until here but when I try to convert the explanatory
variables in the pdata.frame to spatial lagged variables

E2_mod_pdssat_X_lagged <-
as.data.frame(cbind(slag(E2_mod_pdssat_pdata_frame$tmean, listw =
spatial_knn2listw_obj),
slag(E2_mod_pdssat_pdata_frame$tmeansq, listw = spatial_knn2listw_obj),
slag(E2_mod_pdssat_pdata_frame$pmean, listw = spatial_knn2listw_obj),
slag(E2_mod_pdssat_pdata_frame$pmeansq, listw = spatial_knn2listw_obj)))

I get the following error "Error in lag.listw(listw, xt) : object lengths
differ". What am I doing wrong? I have also tried removing the NAs with
complete.cases.

Any help will be greatly appreciated. Thank you.

Sincerely,

Milu

## Data

E2_mod_pdssat_org <- dput(head(temp,5))
structure(list(iso3 = structure(c(30L, 30L, 30L, 1L, 30L), .Label = c(".",
".M", "AFG", "AGO", "ALB", "ARE", "ARG", "ARM", "AUS", "AUT",
"AZE", "BDI", "BEL", "BEN", "BFA", "BGD", "BGR", "BHS", "BIH",
"BLR", "BLZ", "BOL", "BRA", "BRN", "BTN", "BWA", "CAF", "CAN",
"CHE", "CHL", "CHN", "CIV", "CMR", "COD", "COG", "COL", "CRI",
"CUB", "CYP", "CZE", "DEU", "DJI", "DNK", "DOM", "DZA", "ECU",
"EGY", "ERI", "ESH", "ESP", "EST", "ETH", "FIN", "FJI", "FLK",
"FRA", "GAB", "GBR", "GEO", "GHA", "GIN", "GNB", "GNQ", "GRC",
"GRL", "GTM", "GUF", "GUY", "HND", "HRV", "HTI", "HUN", "IDN",
"IND", "IRL", "IRN", "IRQ", "ISL", "ISR", "ITA", "JAM", "JOR",
"JPN", "KAZ", "KEN", "KGZ", "KHM", "KIR", "KOR", "KWT", "LAO",
"LBN", "LBR", "LBY", "LCA", "LKA", "LSO", "LTU", "LUX", "LVA",
"MAR", "MDA", "MDG", "MEX", "MKD", "MLI", "MMR", "MNE", "MNG",
"MOZ", "MRT", "MWI", "MYS", "NCL", "NER", "NGA", "NIC", "NLD",
"NOR", "NPL", "NZL", "OMN", "PAK", "PAN", "PER", "PHL", "PNG",
"POL", "PRI", "PRK", "PRT", "PRY", "QAT", "ROU", "RUS", "RWA",
"SAU", "SDN", "SEN", "SJM", "SLB", "SLE", "SLV", "SOM", "SRB",
"SUR", "SVK", "SVN", "SWE", "SWZ", "SYR", "TCD", "TGO", "THA",
"TJK", "TKM", "TLS", "TUN", "TUR", "TWN", "TZA", "UGA", "UKR",
"URY", "USA", "UZB", "VEN", "VNM", "VUT", "YEM", "ZAF", "ZMB",
"ZWE"), class = "factor"), lon = c(-69L, -68L, -72L, -71L, -70L
), lat = c(-55L, -55L, -54L, -54L, -54L), tmean = c(NA, NA,
4.55847677595631,
4.06015710382516, 3.71010245901642), pmean = c(NA, NA, 2.45569896697998,
1.6384220123291, 1.43925595283508), lngdp = c(-0.102380074560642,
-2.3195972442627, 0.0122363297268748, -0.483756244182587, -6.29744625091553
), tmeansq = c(NA, NA, 20.7797107696533, 16.4848766326904, 13.7648601531982
), pmeansq = c(NA, NA, 6.03045749664307, 2.68442678451538, 2.07145762443542
)), .Names = c("iso3", "lon", "lat", "tmean", "pmean", "lngdp",
"tmeansq", "pmeansq"), row.names = c("1", "2", "3", "4", "5"), class =
"data.frame")

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