Running ‘RFsimulate.R’ [12s/13s]
  Running ‘krige.R’ [9s/11s]
  Running ‘lgcp.R’
  Running ‘lgm.R’ [18s/22s]
  Running ‘lgmRaster.R’ [192s/137s]
  Running ‘likfitLgm.R’ [11s/14s]
  Running ‘matern.R’
  Running ‘maternGmrfPrec.R’ [12s/14s]
  Running ‘profLlgm.R’ [15s/15s]
  Running ‘simLgcp.R’ [10s/13s]
  Running ‘stackRasterList.R’
Running the tests in ‘tests/lgcp.R’ failed.
Complete output:
  > options("rgdal_show_exportToProj4_warnings"="none") 
  > if(Sys.info()['sysname'] =='Linux' &
  +   requireNamespace("INLA", quietly=TRUE)) {   
  +   INLA::inla.setOption(inla.call = 
  +       system.file(paste(
  +           "bin/linux/",          
  +           ifelse(
  +             .Machine$sizeof.pointer == 4, 
  +             "32", "64"),
  +           'bit/inla.static', sep=''),
  +         package="INLA")) 
  + }
  > 
  > 
  > havePackages = c(
  +     'INLA' = requireNamespace('INLA', quietly=TRUE)
  + )
  > 
  > print(havePackages)
  INLA 
  TRUE 
  > 
  > # as in example
  > require('geostatsp')
  Loading required package: geostatsp
  Loading required package: Matrix
  Loading required package: raster
  Loading required package: sp
  > myPoints = SpatialPoints(cbind(rbeta(100,2,2), rbeta(100,3,4)))
  > myPoints@bbox = cbind(c(0,0), c(1,1))
  > 
  > mycov = raster(matrix(rbinom(100, 1, 0.5), 10, 10), 0, 1, 0, 1)
  > names(mycov)="x1"
  > 
  > if(all(havePackages)) {
  +   
  + res = lgcp(
  +     formula=~factor(x1),
  +     data=myPoints, 
  +     grid=20, 
  +     covariates=mycov,
  + 		priorCI=list(sd=c(u=0.1, alpha = 0.01), range=c(0.4, 0.41))
  + )
  + 
  + knitr::kable(res$parameters$summary, digits=3)
  + 
  + plot(res$raster[["predict.exp"]])
  + plot(myPoints,add=TRUE,col="#0000FF30",cex=0.5)
  + 
  + 	
  + # intercept only
  + 
  + res = lgcp(
  +     data=myPoints, 
  +     grid=20, 
  +     covariates=mycov,
  + 		formula=~1,
  + 		priorCI=list(sd=c(0.9, 1.1), range=c(0.4, 0.41))
  + )
  + 
  + knitr::kable(res$parameters$summary, digits=3)
  + 
  + plot(res$raster[["predict.exp"]])
  + plot(myPoints,add=TRUE,col="#0000FF30",cex=0.5)
  + 
  + if(interactive()  | Sys.info()['user'] =='patrick') {
  + 
  + # some missing values
  + 
  + temp = values(mycov)
  + temp[1:4] = NA
  + values(mycov) = temp
  + 
  + res = lgcp(data=myPoints, grid=20, covariates=mycov,
  + 		formula=~factor(x1),
  + 		priorCI=list(sd=c(0.9, 1.1), range=c(0.4, 0.41))
  + )
  + 
  + plot(res$raster[["predict.exp"]])
  + plot(myPoints,add=TRUE,col="#0000FF30",cex=0.5)
  + 
  + data('murder')
  + data('torontoPop')
  + myCov = list(
  +     pop=torontoPdens,
  +     inc = log(torontoIncome)
  + )
  + 
  + formula = ~ inc + offset(pop, log=TRUE)
  + 
  + resL=lgcp(formula, data=murder, 
  +     grid=squareRaster(murder, 30),
  +     covariates=myCov,
  +     border=torontoBorder)
  + 
  + resO = lgcp( ~ inc + pop, 
  +     data=murder, 
  +     grid=squareRaster(murder, 30),
  +     covariates=list(inc=myCov$inc, pop=log(myCov$pop)),
  +     border=torontoBorder)
  + 
  + rbind(resL$param$summary, resO$param$summary)
  + 
  + 
  + 
  + }	
  + }
  Error in (function (formula, family = "gaussian", contrasts = NULL, data,  : 
    f(space). Covariate does not match 'values' 380 times. Indexes for mismatch:2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400. This is not what you want. Use NA values in the covariate!
  Error in plot.window(...) : need finite 'xlim' values
  Calls: plot -> plot -> plot.default -> localWindow -> plot.window
  In addition: Warning messages:
  1: In kable_pipe(x = character(0), caption = NULL, escape = TRUE) :
    The table should have a header (column names)
  2: In min(x) : no non-missing arguments to min; returning Inf
  3: In max(x) : no non-missing arguments to max; returning -Inf
  4: In min(x) : no non-missing arguments to min; returning Inf
  5: In max(x) : no non-missing arguments to max; returning -Inf
  Execution halted
Running the tests in ‘tests/simLgcp.R’ failed.
Complete output:
  > options("rgdal_show_exportToProj4_warnings"="none") 
  > library('geostatsp')
  Loading required package: Matrix
  Loading required package: raster
  Loading required package: sp
  > mymodel = c(mean=-1.5, variance=1, 
  + 				range=2, shape=2)
  > 
  > myraster = raster(nrows=15,ncols=15,xmn=0,xmx=10,ymn=0,ymx=10)
  > 
  > # some covariates, deliberately with a different resolution than myraster
  > covA = covB = myoffset = raster(extent(myraster), 10, 10)
  > values(covA) = as.vector(matrix(1:10, 10, 10))
  > values(covB) = as.vector(matrix(1:10, 10, 10, byrow=TRUE))
  > values(myoffset) = round(seq(-1, 1, len=ncell(myoffset)))
  > 
  > myCovariate = list(a=covA, b=covB, offsetFooBar = myoffset)
  > 
  > set.seed(0)
  > myLgcp=simLgcp(mymodel, myCovariate, 
  +     betas=c(a=-0.1, b=0.25), 
  + 	offset='offsetFooBar',
  + 	rasterTemplate=myraster)
  New output format of RFsimulate: S4 object of class 'RFsp';
  for a bare, but faster array format use 'RFoptions(spConform=FALSE)'.
  > 
  > if(requireNamespace("INLA", quietly=TRUE)) {
  + res = lgcp(data=myLgcp$events, 
  + 		formula = ~ a + b + offset(offsetFooBar),
  + 		grid=squareRaster(myoffset, 15), 
  + 		covariates=myCovariate,
  + 		priorCI=list(sd=c(0.9, 1.1), range=c(0.4, 0.41)),
  + 		control.mode=list(theta=c(0.022, -0.5),restart=TRUE)
  + )
  + 
  + res$parameters$summary[,c(1,3,5)]
  + 
  + lgcpRoc =  spatialRoc(
  +   fit=res, 
  + 	rr=c(2,3), 
  + 	truth=myLgcp, 
  + 	random=FALSE)
  + 
  + head(lgcpRoc)
  + 
  + plot(lgcpRoc[,'onemspec'] , 
  + 	lgcpRoc[,'2'], 
  + 	type='o', 
  + 	xlim=c(0,1), ylim=c(0,1),
  + 	ylab='sensitivity', xlab='1-specificity'
  + )
  + 
  + }
  Error in (function (formula, family = "gaussian", contrasts = NULL, data,  : 
    f(space). Covariate does not match 'values' 210 times. Indexes for mismatch:2 3 4 5 6 7 8 9 10 11 12 13 14 15 17 18 19 20 21 22 23 24 25 26 27 28 29 30 32 33 34 35 36 37 38 39 40 41 42 43 44 45 47 48 49 50 51 52 53 54 55 56 57 58 59 60 62 63 64 65 66 67 68 69 70 71 72 73 74 75 77 78 79 80 81 82 83 84 85 86 87 88 89 90 92 93 94 95 96 97 98 99 100 101 102 103 104 105 107 108 109 110 111 112 113 114 115 116 117 118 119 120 122 123 124 125 126 127 128 129 130 131 132 133 134 135 137 138 139 140 141 142 143 144 145 146 147 148 149 150 152 153 154 155 156 157 158 159 160 161 162 163 164 165 167 168 169 170 171 172 173 174 175 176 177 178 179 180 182 183 184 185 186 187 188 189 190 191 192 193 194 195 197 198 199 200 201 202 203 204 205 206 207 208 209 210 212 213 214 215 216 217 218 219 220 221 222 223 224 225. This is not what you want. Use NA values in the covariate!
  Error in (function (classes, fdef, mtable)  : 
    unable to find an inherited method for function 'rasterize' for signature '"list", "RasterLayer"'
  Calls: spatialRoc -> spatialRocPolyTemplate -> rasterize -> <Anonymous>
  Execution halted