Specified C++11: please drop specification unless essential
checkRd: (-1) fit_spm.Rd:73: Lost braces; missing escapes or markup?
    73 | algorithm to be used. For details, see {optim}.}
       |                                        ^
checkRd: (-1) fit_spm.Rd:76: Lost braces; missing escapes or markup?
    76 | the optimization algorithm to be used. For details, see {optim}.}
       |                                                         ^
checkRd: (-1) fit_spm.Rd:101: Lost braces; missing escapes or markup?
   101 | the control parameters from the {optim} function through the argument
       |                                 ^
Documented arguments not in \usage in Rd file 'aux_cs.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_gauss.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_gw.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_mat.Rd':
  ‘mat_list1’ ‘mat_list2’ ‘x’ ‘y’ ‘return_single’

Documented arguments not in \usage in Rd file 'aux_matern.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_pexp.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_spher.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_tapmat.Rd':
  ‘dists’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘smile-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predict_spm
> ### Title: Prediction over the same or a different set of regions (or
> ###   points).
> ### Aliases: predict_spm predict_spm.spm_fit predict_spm.sf
> 
> ### ** Examples
> 
> 
> data(liv_lsoa) ## loading the LSOA data
> data(liv_msoa) ## loading the MSOA data
> 
> msoa_spm <- sf_to_spm(sf_obj = liv_msoa, n_pts = 500,
+                       type = "regular", by_polygon = FALSE,
+                       poly_ids = "msoa11cd",
+                       var_ids = "leb_est")
> ## fitting model
> theta_st_msoa <- c("phi" = 1) # initial value for the range parameter
> 
> fit_msoa <-
+    fit_spm(x = msoa_spm,
+            theta_st = theta_st_msoa,
+            model = "matern",
+            nu = .5,
+            apply_exp  = TRUE,
+            opt_method = "L-BFGS-B",
+            control    = list(maxit = 500))
> 
> pred_lsoa <- predict_spm(x = liv_lsoa, spm_obj = fit_msoa, id_var = "lsoa11cd")
Error in `[.data.frame`(x, i) : undefined columns selected
Calls: predict_spm -> predict_spm.sf -> [ -> [.sf -> [ -> [.data.frame
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fit-and-pred.Rmd’ using rmarkdown

Quitting from lines 173-174 [predict-fit1] (fit-and-pred.Rmd)
Error: processing vignette 'fit-and-pred.Rmd' failed with diagnostics:
undefined columns selected
--- failed re-building ‘fit-and-pred.Rmd’

--- re-building ‘sai.Rmd’ using rmarkdown
--- finished re-building ‘sai.Rmd’

--- re-building ‘sf-to-spm.Rmd’ using rmarkdown

Quitting from lines 207-259 [sf-to-spm2] (sf-to-spm.Rmd)
Error: processing vignette 'sf-to-spm.Rmd' failed with diagnostics:
names do not match previous names
--- failed re-building ‘sf-to-spm.Rmd’

--- re-building ‘sp-cov-functions.Rmd’ using rmarkdown
--- finished re-building ‘sp-cov-functions.Rmd’

--- re-building ‘theory.Rmd’ using rmarkdown
--- finished re-building ‘theory.Rmd’

SUMMARY: processing the following files failed:
  ‘fit-and-pred.Rmd’ ‘sf-to-spm.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
checkRd: (-1) fit_spm.Rd:73: Lost braces; missing escapes or markup?
    73 | algorithm to be used. For details, see {optim}.}
       |                                        ^
checkRd: (-1) fit_spm.Rd:76: Lost braces; missing escapes or markup?
    76 | the optimization algorithm to be used. For details, see {optim}.}
       |                                                         ^
checkRd: (-1) fit_spm.Rd:101: Lost braces; missing escapes or markup?
   101 | the control parameters from the {optim} function through the argument
       |                                 ^
Documented arguments not in \usage in Rd file 'aux_cs.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_gauss.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_gw.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_mat.Rd':
  ‘mat_list1’ ‘mat_list2’ ‘x’ ‘y’ ‘return_single’

Documented arguments not in \usage in Rd file 'aux_matern.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_pexp.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_spher.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_tapmat.Rd':
  ‘dists’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘smile-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predict_spm
> ### Title: Prediction over the same or a different set of regions (or
> ###   points).
> ### Aliases: predict_spm predict_spm.spm_fit predict_spm.sf
> 
> ### ** Examples
> 
> 
> data(liv_lsoa) ## loading the LSOA data
> data(liv_msoa) ## loading the MSOA data
> 
> msoa_spm <- sf_to_spm(sf_obj = liv_msoa, n_pts = 500,
+                       type = "regular", by_polygon = FALSE,
+                       poly_ids = "msoa11cd",
+                       var_ids = "leb_est")
> ## fitting model
> theta_st_msoa <- c("phi" = 1) # initial value for the range parameter
> 
> fit_msoa <-
+    fit_spm(x = msoa_spm,
+            theta_st = theta_st_msoa,
+            model = "matern",
+            nu = .5,
+            apply_exp  = TRUE,
+            opt_method = "L-BFGS-B",
+            control    = list(maxit = 500))
> 
> pred_lsoa <- predict_spm(x = liv_lsoa, spm_obj = fit_msoa, id_var = "lsoa11cd")
Error in `[.data.frame`(x, i) : undefined columns selected
Calls: predict_spm -> predict_spm.sf -> [ -> [.sf -> [ -> [.data.frame
Execution halted
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
checkRd: (-1) fit_spm.Rd:73: Lost braces; missing escapes or markup?
    73 | algorithm to be used. For details, see {optim}.}
       |                                        ^
checkRd: (-1) fit_spm.Rd:76: Lost braces; missing escapes or markup?
    76 | the optimization algorithm to be used. For details, see {optim}.}
       |                                                         ^
checkRd: (-1) fit_spm.Rd:101: Lost braces; missing escapes or markup?
   101 | the control parameters from the {optim} function through the argument
       |                                 ^
Documented arguments not in \usage in Rd file 'aux_cs.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_gauss.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_gw.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_mat.Rd':
  ‘mat_list1’ ‘mat_list2’ ‘x’ ‘y’ ‘return_single’

Documented arguments not in \usage in Rd file 'aux_matern.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_pexp.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_spher.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_tapmat.Rd':
  ‘dists’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘smile-Ex.R’ failed
The error most likely occurred in:

> ### Name: predict_spm
> ### Title: Prediction over the same or a different set of regions (or
> ###   points).
> ### Aliases: predict_spm predict_spm.spm_fit predict_spm.sf
> 
> ### ** Examples
> 
> 
> data(liv_lsoa) ## loading the LSOA data
> data(liv_msoa) ## loading the MSOA data
> 
> msoa_spm <- sf_to_spm(sf_obj = liv_msoa, n_pts = 500,
+                       type = "regular", by_polygon = FALSE,
+                       poly_ids = "msoa11cd",
+                       var_ids = "leb_est")
> ## fitting model
> theta_st_msoa <- c("phi" = 1) # initial value for the range parameter
> 
> fit_msoa <-
+    fit_spm(x = msoa_spm,
+            theta_st = theta_st_msoa,
+            model = "matern",
+            nu = .5,
+            apply_exp  = TRUE,
+            opt_method = "L-BFGS-B",
+            control    = list(maxit = 500))
> 
> pred_lsoa <- predict_spm(x = liv_lsoa, spm_obj = fit_msoa, id_var = "lsoa11cd")
Error in `[.data.frame`(x, i) : undefined columns selected
Calls: predict_spm -> predict_spm.sf -> [ -> [.sf -> [ -> [.data.frame
Execution halted
Specified C++11: please drop specification unless essential
checkRd: (-1) fit_spm.Rd:73: Lost braces; missing escapes or markup?
    73 | algorithm to be used. For details, see {optim}.}
       |                                        ^
checkRd: (-1) fit_spm.Rd:76: Lost braces; missing escapes or markup?
    76 | the optimization algorithm to be used. For details, see {optim}.}
       |                                                         ^
checkRd: (-1) fit_spm.Rd:101: Lost braces; missing escapes or markup?
   101 | the control parameters from the {optim} function through the argument
       |                                 ^
Documented arguments not in \usage in Rd file 'aux_cs.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_gauss.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_gw.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_mat.Rd':
  ‘mat_list1’ ‘mat_list2’ ‘x’ ‘y’ ‘return_single’

Documented arguments not in \usage in Rd file 'aux_matern.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_pexp.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_spher.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_tapmat.Rd':
  ‘dists’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘smile-Ex.R’ failed
The error most likely occurred in:

> ### Name: predict_spm
> ### Title: Prediction over the same or a different set of regions (or
> ###   points).
> ### Aliases: predict_spm predict_spm.spm_fit predict_spm.sf
> 
> ### ** Examples
> 
> 
> data(liv_lsoa) ## loading the LSOA data
> data(liv_msoa) ## loading the MSOA data
> 
> msoa_spm <- sf_to_spm(sf_obj = liv_msoa, n_pts = 500,
+                       type = "regular", by_polygon = FALSE,
+                       poly_ids = "msoa11cd",
+                       var_ids = "leb_est")
> ## fitting model
> theta_st_msoa <- c("phi" = 1) # initial value for the range parameter
> 
> fit_msoa <-
+    fit_spm(x = msoa_spm,
+            theta_st = theta_st_msoa,
+            model = "matern",
+            nu = .5,
+            apply_exp  = TRUE,
+            opt_method = "L-BFGS-B",
+            control    = list(maxit = 500))
> 
> pred_lsoa <- predict_spm(x = liv_lsoa, spm_obj = fit_msoa, id_var = "lsoa11cd")
Error in `[.data.frame`(x, i) : undefined columns selected
Calls: predict_spm -> predict_spm.sf -> [ -> [.sf -> [ -> [.data.frame
Execution halted
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
    libs   1.0Mb
checkRd: (-1) fit_spm.Rd:73: Lost braces; missing escapes or markup?
    73 | algorithm to be used. For details, see {optim}.}
       |                                        ^
checkRd: (-1) fit_spm.Rd:76: Lost braces; missing escapes or markup?
    76 | the optimization algorithm to be used. For details, see {optim}.}
       |                                                         ^
checkRd: (-1) fit_spm.Rd:101: Lost braces; missing escapes or markup?
   101 | the control parameters from the {optim} function through the argument
       |                                 ^
Documented arguments not in \usage in Rd file 'aux_cs.Rd':
  'dists'

Documented arguments not in \usage in Rd file 'aux_gauss.Rd':
  'dists'

Documented arguments not in \usage in Rd file 'aux_gw.Rd':
  'dists'

Documented arguments not in \usage in Rd file 'aux_mat.Rd':
  'mat_list1' 'mat_list2' 'x' 'y' 'return_single'

Documented arguments not in \usage in Rd file 'aux_matern.Rd':
  'dists'

Documented arguments not in \usage in Rd file 'aux_pexp.Rd':
  'dists'

Documented arguments not in \usage in Rd file 'aux_spher.Rd':
  'dists'

Documented arguments not in \usage in Rd file 'aux_tapmat.Rd':
  'dists'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Running examples in 'smile-Ex.R' failed
The error most likely occurred in:

> ### Name: predict_spm
> ### Title: Prediction over the same or a different set of regions (or
> ###   points).
> ### Aliases: predict_spm predict_spm.spm_fit predict_spm.sf
> 
> ### ** Examples
> 
> 
> data(liv_lsoa) ## loading the LSOA data
> data(liv_msoa) ## loading the MSOA data
> 
> msoa_spm <- sf_to_spm(sf_obj = liv_msoa, n_pts = 500,
+                       type = "regular", by_polygon = FALSE,
+                       poly_ids = "msoa11cd",
+                       var_ids = "leb_est")
> ## fitting model
> theta_st_msoa <- c("phi" = 1) # initial value for the range parameter
> 
> fit_msoa <-
+    fit_spm(x = msoa_spm,
+            theta_st = theta_st_msoa,
+            model = "matern",
+            nu = .5,
+            apply_exp  = TRUE,
+            opt_method = "L-BFGS-B",
+            control    = list(maxit = 500))
> 
> pred_lsoa <- predict_spm(x = liv_lsoa, spm_obj = fit_msoa, id_var = "lsoa11cd")
Error in `[.data.frame`(x, i) : undefined columns selected
Calls: predict_spm -> predict_spm.sf -> [ -> [.sf -> [ -> [.data.frame
Execution halted
Error(s) in re-building vignettes:
--- re-building 'fit-and-pred.Rmd' using rmarkdown

Quitting from lines 173-174 [predict-fit1] (fit-and-pred.Rmd)
Error: processing vignette 'fit-and-pred.Rmd' failed with diagnostics:
undefined columns selected
--- failed re-building 'fit-and-pred.Rmd'

--- re-building 'sai.Rmd' using rmarkdown
--- finished re-building 'sai.Rmd'

--- re-building 'sf-to-spm.Rmd' using rmarkdown

Quitting from lines 207-259 [sf-to-spm2] (sf-to-spm.Rmd)
Error: processing vignette 'sf-to-spm.Rmd' failed with diagnostics:
names do not match previous names
--- failed re-building 'sf-to-spm.Rmd'

--- re-building 'sp-cov-functions.Rmd' using rmarkdown
--- finished re-building 'sp-cov-functions.Rmd'

--- re-building 'theory.Rmd' using rmarkdown
--- finished re-building 'theory.Rmd'

SUMMARY: processing the following files failed:
  'fit-and-pred.Rmd' 'sf-to-spm.Rmd'

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
checkRd: (-1) fit_spm.Rd:73: Lost braces; missing escapes or markup?
    73 | algorithm to be used. For details, see {optim}.}
       |                                        ^
checkRd: (-1) fit_spm.Rd:76: Lost braces; missing escapes or markup?
    76 | the optimization algorithm to be used. For details, see {optim}.}
       |                                                         ^
checkRd: (-1) fit_spm.Rd:101: Lost braces; missing escapes or markup?
   101 | the control parameters from the {optim} function through the argument
       |                                 ^
Documented arguments not in \usage in Rd file 'aux_cs.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_gauss.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_gw.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_mat.Rd':
  ‘mat_list1’ ‘mat_list2’ ‘x’ ‘y’ ‘return_single’

Documented arguments not in \usage in Rd file 'aux_matern.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_pexp.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_spher.Rd':
  ‘dists’

Documented arguments not in \usage in Rd file 'aux_tapmat.Rd':
  ‘dists’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘smile-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predict_spm
> ### Title: Prediction over the same or a different set of regions (or
> ###   points).
> ### Aliases: predict_spm predict_spm.spm_fit predict_spm.sf
> 
> ### ** Examples
> 
> 
> data(liv_lsoa) ## loading the LSOA data
> data(liv_msoa) ## loading the MSOA data
> 
> msoa_spm <- sf_to_spm(sf_obj = liv_msoa, n_pts = 500,
+                       type = "regular", by_polygon = FALSE,
+                       poly_ids = "msoa11cd",
+                       var_ids = "leb_est")
> ## fitting model
> theta_st_msoa <- c("phi" = 1) # initial value for the range parameter
> 
> fit_msoa <-
+    fit_spm(x = msoa_spm,
+            theta_st = theta_st_msoa,
+            model = "matern",
+            nu = .5,
+            apply_exp  = TRUE,
+            opt_method = "L-BFGS-B",
+            control    = list(maxit = 500))
> 
> pred_lsoa <- predict_spm(x = liv_lsoa, spm_obj = fit_msoa, id_var = "lsoa11cd")
Error in `[.data.frame`(x, i) : undefined columns selected
Calls: predict_spm -> predict_spm.sf -> [ -> [.sf -> [ -> [.data.frame
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fit-and-pred.Rmd’ using rmarkdown

Quitting from lines 173-174 [predict-fit1] (fit-and-pred.Rmd)
Error: processing vignette 'fit-and-pred.Rmd' failed with diagnostics:
undefined columns selected
--- failed re-building ‘fit-and-pred.Rmd’

--- re-building ‘sai.Rmd’ using rmarkdown
--- finished re-building ‘sai.Rmd’

--- re-building ‘sf-to-spm.Rmd’ using rmarkdown

Quitting from lines 207-259 [sf-to-spm2] (sf-to-spm.Rmd)
Error: processing vignette 'sf-to-spm.Rmd' failed with diagnostics:
names do not match previous names
--- failed re-building ‘sf-to-spm.Rmd’

--- re-building ‘sp-cov-functions.Rmd’ using rmarkdown
--- finished re-building ‘sp-cov-functions.Rmd’

--- re-building ‘theory.Rmd’ using rmarkdown
--- finished re-building ‘theory.Rmd’

SUMMARY: processing the following files failed:
  ‘fit-and-pred.Rmd’ ‘sf-to-spm.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Running examples in ‘smile-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predict_spm
> ### Title: Prediction over the same or a different set of regions (or
> ###   points).
> ### Aliases: predict_spm predict_spm.spm_fit predict_spm.sf
> 
> ### ** Examples
> 
> 
> data(liv_lsoa) ## loading the LSOA data
> data(liv_msoa) ## loading the MSOA data
> 
> msoa_spm <- sf_to_spm(sf_obj = liv_msoa, n_pts = 500,
+                       type = "regular", by_polygon = FALSE,
+                       poly_ids = "msoa11cd",
+                       var_ids = "leb_est")
> ## fitting model
> theta_st_msoa <- c("phi" = 1) # initial value for the range parameter
> 
> fit_msoa <-
+    fit_spm(x = msoa_spm,
+            theta_st = theta_st_msoa,
+            model = "matern",
+            nu = .5,
+            apply_exp  = TRUE,
+            opt_method = "L-BFGS-B",
+            control    = list(maxit = 500))
> 
> pred_lsoa <- predict_spm(x = liv_lsoa, spm_obj = fit_msoa, id_var = "lsoa11cd")
Error in `[.data.frame`(x, i) : undefined columns selected
Calls: predict_spm -> predict_spm.sf -> [ -> [.sf -> [ -> [.data.frame
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fit-and-pred.Rmd’ using rmarkdown

Quitting from lines 173-174 [predict-fit1] (fit-and-pred.Rmd)
Error: processing vignette 'fit-and-pred.Rmd' failed with diagnostics:
undefined columns selected
--- failed re-building ‘fit-and-pred.Rmd’

--- re-building ‘sai.Rmd’ using rmarkdown
--- finished re-building ‘sai.Rmd’

--- re-building ‘sf-to-spm.Rmd’ using rmarkdown

Quitting from lines 207-259 [sf-to-spm2] (sf-to-spm.Rmd)
Error: processing vignette 'sf-to-spm.Rmd' failed with diagnostics:
names do not match previous names
--- failed re-building ‘sf-to-spm.Rmd’

--- re-building ‘sp-cov-functions.Rmd’ using rmarkdown
--- finished re-building ‘sp-cov-functions.Rmd’

--- re-building ‘theory.Rmd’ using rmarkdown
--- finished re-building ‘theory.Rmd’

SUMMARY: processing the following files failed:
  ‘fit-and-pred.Rmd’ ‘sf-to-spm.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.2Mb
Specified C++11: please drop specification unless essential
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.2Mb
Specified C++11: please drop specification unless essential
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.1Mb
Running examples in 'smile-Ex.R' failed
The error most likely occurred in:

> ### Name: predict_spm
> ### Title: Prediction over the same or a different set of regions (or
> ###   points).
> ### Aliases: predict_spm predict_spm.spm_fit predict_spm.sf
> 
> ### ** Examples
> 
> 
> data(liv_lsoa) ## loading the LSOA data
> data(liv_msoa) ## loading the MSOA data
> 
> msoa_spm <- sf_to_spm(sf_obj = liv_msoa, n_pts = 500,
+                       type = "regular", by_polygon = FALSE,
+                       poly_ids = "msoa11cd",
+                       var_ids = "leb_est")
> ## fitting model
> theta_st_msoa <- c("phi" = 1) # initial value for the range parameter
> 
> fit_msoa <-
+    fit_spm(x = msoa_spm,
+            theta_st = theta_st_msoa,
+            model = "matern",
+            nu = .5,
+            apply_exp  = TRUE,
+            opt_method = "L-BFGS-B",
+            control    = list(maxit = 500))
> 
> pred_lsoa <- predict_spm(x = liv_lsoa, spm_obj = fit_msoa, id_var = "lsoa11cd")
Error in `[.data.frame`(x, i) : undefined columns selected
Calls: predict_spm -> predict_spm.sf -> [ -> [.sf -> [ -> [.data.frame
Execution halted
Error(s) in re-building vignettes:
--- re-building 'fit-and-pred.Rmd' using rmarkdown

Quitting from lines 173-174 [predict-fit1] (fit-and-pred.Rmd)
Error: processing vignette 'fit-and-pred.Rmd' failed with diagnostics:
undefined columns selected
--- failed re-building 'fit-and-pred.Rmd'

--- re-building 'sai.Rmd' using rmarkdown
--- finished re-building 'sai.Rmd'

--- re-building 'sf-to-spm.Rmd' using rmarkdown

Quitting from lines 207-259 [sf-to-spm2] (sf-to-spm.Rmd)
Error: processing vignette 'sf-to-spm.Rmd' failed with diagnostics:
names do not match previous names
--- failed re-building 'sf-to-spm.Rmd'

--- re-building 'sp-cov-functions.Rmd' using rmarkdown
--- finished re-building 'sp-cov-functions.Rmd'

--- re-building 'theory.Rmd' using rmarkdown
--- finished re-building 'theory.Rmd'

SUMMARY: processing the following files failed:
  'fit-and-pred.Rmd' 'sf-to-spm.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.1Mb
Running examples in 'smile-Ex.R' failed
The error most likely occurred in:

> ### Name: predict_spm
> ### Title: Prediction over the same or a different set of regions (or
> ###   points).
> ### Aliases: predict_spm predict_spm.spm_fit predict_spm.sf
> 
> ### ** Examples
> 
> 
> data(liv_lsoa) ## loading the LSOA data
> data(liv_msoa) ## loading the MSOA data
> 
> msoa_spm <- sf_to_spm(sf_obj = liv_msoa, n_pts = 500,
+                       type = "regular", by_polygon = FALSE,
+                       poly_ids = "msoa11cd",
+                       var_ids = "leb_est")
> ## fitting model
> theta_st_msoa <- c("phi" = 1) # initial value for the range parameter
> 
> fit_msoa <-
+    fit_spm(x = msoa_spm,
+            theta_st = theta_st_msoa,
+            model = "matern",
+            nu = .5,
+            apply_exp  = TRUE,
+            opt_method = "L-BFGS-B",
+            control    = list(maxit = 500))
> 
> pred_lsoa <- predict_spm(x = liv_lsoa, spm_obj = fit_msoa, id_var = "lsoa11cd")
Error in `[.data.frame`(x, i) : undefined columns selected
Calls: predict_spm -> predict_spm.sf -> [ -> [.sf -> [ -> [.data.frame
Execution halted
Error(s) in re-building vignettes:
--- re-building 'fit-and-pred.Rmd' using rmarkdown

Quitting from lines 173-174 [predict-fit1] (fit-and-pred.Rmd)
Error: processing vignette 'fit-and-pred.Rmd' failed with diagnostics:
undefined columns selected
--- failed re-building 'fit-and-pred.Rmd'

--- re-building 'sai.Rmd' using rmarkdown
--- finished re-building 'sai.Rmd'

--- re-building 'sf-to-spm.Rmd' using rmarkdown

Quitting from lines 207-259 [sf-to-spm2] (sf-to-spm.Rmd)
Error: processing vignette 'sf-to-spm.Rmd' failed with diagnostics:
names do not match previous names
--- failed re-building 'sf-to-spm.Rmd'

--- re-building 'sp-cov-functions.Rmd' using rmarkdown
--- finished re-building 'sp-cov-functions.Rmd'

--- re-building 'theory.Rmd' using rmarkdown
--- finished re-building 'theory.Rmd'

SUMMARY: processing the following files failed:
  'fit-and-pred.Rmd' 'sf-to-spm.Rmd'

Error: Vignette re-building failed.
Execution halted