Last updated on 2025-07-05 22:50:38 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.6-9 | 12.36 | 138.22 | 150.58 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.6-9 | 8.11 | 90.83 | 98.94 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.6-9 | 237.59 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.6-9 | 243.83 | ERROR | |||
| r-devel-windows-x86_64 | 0.6-9 | 16.00 | 158.00 | 174.00 | NOTE | |
| r-patched-linux-x86_64 | 0.6-9 | 11.58 | 132.33 | 143.91 | ERROR | |
| r-release-linux-x86_64 | 0.6-9 | 11.65 | 158.33 | 169.98 | NOTE | |
| r-release-macos-arm64 | 0.6-9 | 71.00 | OK | |||
| r-release-macos-x86_64 | 0.6-9 | 153.00 | OK | |||
| r-release-windows-x86_64 | 0.6-9 | 15.00 | 165.00 | 180.00 | NOTE | |
| r-oldrel-macos-arm64 | 0.6-9 | 64.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.6-9 | 109.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.6-9 | 19.00 | 208.00 | 227.00 | OK |
Version: 0.6-9
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
getRtopParams.Rd: gstat
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64
Version: 0.6-9
Check: examples
Result: ERROR
Running examples in ‘rtop-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: useRtopWithIntamap
> ### Title: Integrates the rtop package with the 'intamap' package
> ### Aliases: useRtopWithIntamap
> ### Keywords: plot
>
> ### ** Examples
>
> library(intamap)
Error in library(intamap) : there is no package called ‘intamap’
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64
Version: 0.6-9
Check: tests
Result: ERROR
Running ‘rtop.R’ [11s/15s]
Running ‘rtop_sf.R’ [49s/67s]
Comparing ‘rtop_sf.Rout’ to ‘rtop_sf.Rout.save’ ... OK
Running the tests in ‘tests/rtop.R’ failed.
Complete output:
> set.seed(1501)
> #-----------------------------
> ## IGNORE_RDIFF_BEGIN
> library(rtop)
> if (interactive()) options(error = recover)
> # Read directly from shape-files in data directory
> rpath = system.file("extdata",package="rtop")
> library(sf)
Linking to GEOS 3.13.1, GDAL 3.10.3, PROJ 9.6.0; sf_use_s2() is TRUE
> observations = st_read(rpath, "observations")
Reading layer `observations' from data source
`/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rtop/extdata'
using driver `ESRI Shapefile'
Simple feature collection with 57 features and 7 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: 392041.1 ymin: 454983.1 xmax: 512819.5 ymax: 543984.4
Projected CRS: Lambert_Conformal_Conic
> predictionLocations = st_read(rpath, "predictionLocations")
Reading layer `predictionLocations' from data source
`/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rtop/extdata'
using driver `ESRI Shapefile'
Simple feature collection with 235 features and 5 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: 393416.8 ymin: 454919.1 xmax: 519903.3 ymax: 543984.4
Projected CRS: Lambert_Conformal_Conic
> ## IGNORE_RDIFF_END
>
>
> observations = as(observations, "Spatial")
> predictionLocations = as(predictionLocations, "Spatial")
> #Finding a few prediction locations of them
>
> observations = observations[1:30,]
> predictionLocations = predictionLocations[1:2,]
>
> observations$obs = observations$QSUMMER_OB/observations$AREASQKM
>
> # Setting some parameters
> params = list(gDist = TRUE, cloud = FALSE, rresol = 25, hresol = 3, debug.level = -1)
> # Build an object
> rtopObj = createRtopObject(observations,predictionLocations, params = params, formulaString = "obs ~ 1" )
> # Fit a variogram (function also creates it)
> rtopObj = rtopFitVariogram(rtopObj, iprint = -1)
> print(rtopObj$variogramModel, 3)
$model
[1] "Ex1"
$params
[1] 2.51e-04 4.26e+05 0.00e+00 1.01e-05 9.23e-01
attr(,"class")
[1] "rtopVariogramModel"
attr(,"SSErr")
[1] 0.557
attr(,"criterion")
[1] 0.0981
> #rtopObj = checkVario(rtopObj)
> rtopObj2 = rtopKrige(rtopObj, cv = TRUE)
[1] "Sampling points from 30 areas"
>
>
> print(attr(rtopObj2$varMatObs,"variogramModel"), 3)
$model
[1] "Ex1"
$params
[1] 2.51e-04 4.26e+05 0.00e+00 1.01e-05 9.23e-01
attr(,"class")
[1] "rtopVariogramModel"
attr(,"SSErr")
[1] 0.557
attr(,"criterion")
[1] 0.0981
>
> rtopObj3 = rtopKrige(rtopObj)
[1] "Sampling points from 30 areas"
[1] "Sampling points from 2 areas"
[1] "Creating prediction semivariance matrix. This can take some time."
>
>
> varmat = varMat(observations, predictionLocations, variogramModel = rtopObj$variogramModel,
+ gDistEst = TRUE, gDistPred = TRUE, rresol = 25, hresol = 3)
[1] "Sampling points from 30 areas"
[1] "Sampled on average 54.2 points from 30 areas"
[1] "Sampling points from 2 areas"
[1] "Sampled on average 77 points from 2 areas"
>
> all.equal(varmat$varMatObs, rtopObj2$varMatObs)
[1] TRUE
> rtopObj4 = rtopKrige(rtopObj2)
[1] "Sampling points from 2 areas"
[1] "Creating prediction semivariance matrix. This can take some time."
>
> #debug(rtop:::rtopDisc.SpatialPolygons)
> # rtopObj5 = rtopKrige(rtopObj, params = list(cnAreas = 5, cDlim = 10, nclus = 2))
>
> print(summary(rtopObj2$predictions))
Length Class Mode
30 SpatialPolygonsDataFrame S4
> print(summary(rtopObj3$predictions))
Length Class Mode
2 SpatialPolygonsDataFrame S4
> print(summary(rtopObj4$predictions))
Length Class Mode
2 SpatialPolygonsDataFrame S4
> print(all.equal(rtopObj4$predictions, rtopObj3$predictions))
[1] TRUE
> #spplot(rtopObj$predictions,col.regions = bpy.colors(), c("var1.pred","var1.var"))
>
> # Cross-validation
> #spplot(rtopObj2$predictions,col.regions = bpy.colors(), c("observed","var1.pred"))
> print(cor(rtopObj2$predictions$observed,rtopObj2$predictions$var1.pred))
[1] 0.1678744
>
>
>
>
> set.seed(1501)
> library(intamap)
Error in library(intamap) : there is no package called 'intamap'
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.6-9
Check: tests
Result: ERROR
Running ‘rtop.R’ [6s/7s]
Running ‘rtop_sf.R’ [29s/35s]
Comparing ‘rtop_sf.Rout’ to ‘rtop_sf.Rout.save’ ... OK
Running the tests in ‘tests/rtop.R’ failed.
Complete output:
> set.seed(1501)
> #-----------------------------
> ## IGNORE_RDIFF_BEGIN
> library(rtop)
> if (interactive()) options(error = recover)
> # Read directly from shape-files in data directory
> rpath = system.file("extdata",package="rtop")
> library(sf)
Linking to GEOS 3.13.1, GDAL 3.10.3, PROJ 9.6.0; sf_use_s2() is TRUE
> observations = st_read(rpath, "observations")
Reading layer `observations' from data source
`/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rtop/extdata'
using driver `ESRI Shapefile'
Simple feature collection with 57 features and 7 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: 392041.1 ymin: 454983.1 xmax: 512819.5 ymax: 543984.4
Projected CRS: Lambert_Conformal_Conic
> predictionLocations = st_read(rpath, "predictionLocations")
Reading layer `predictionLocations' from data source
`/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rtop/extdata'
using driver `ESRI Shapefile'
Simple feature collection with 235 features and 5 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: 393416.8 ymin: 454919.1 xmax: 519903.3 ymax: 543984.4
Projected CRS: Lambert_Conformal_Conic
> ## IGNORE_RDIFF_END
>
>
> observations = as(observations, "Spatial")
> predictionLocations = as(predictionLocations, "Spatial")
> #Finding a few prediction locations of them
>
> observations = observations[1:30,]
> predictionLocations = predictionLocations[1:2,]
>
> observations$obs = observations$QSUMMER_OB/observations$AREASQKM
>
> # Setting some parameters
> params = list(gDist = TRUE, cloud = FALSE, rresol = 25, hresol = 3, debug.level = -1)
> # Build an object
> rtopObj = createRtopObject(observations,predictionLocations, params = params, formulaString = "obs ~ 1" )
> # Fit a variogram (function also creates it)
> rtopObj = rtopFitVariogram(rtopObj, iprint = -1)
> print(rtopObj$variogramModel, 3)
$model
[1] "Ex1"
$params
[1] 2.51e-04 4.26e+05 0.00e+00 1.01e-05 9.23e-01
attr(,"class")
[1] "rtopVariogramModel"
attr(,"SSErr")
[1] 0.557
attr(,"criterion")
[1] 0.0981
> #rtopObj = checkVario(rtopObj)
> rtopObj2 = rtopKrige(rtopObj, cv = TRUE)
[1] "Sampling points from 30 areas"
>
>
> print(attr(rtopObj2$varMatObs,"variogramModel"), 3)
$model
[1] "Ex1"
$params
[1] 2.51e-04 4.26e+05 0.00e+00 1.01e-05 9.23e-01
attr(,"class")
[1] "rtopVariogramModel"
attr(,"SSErr")
[1] 0.557
attr(,"criterion")
[1] 0.0981
>
> rtopObj3 = rtopKrige(rtopObj)
[1] "Sampling points from 30 areas"
[1] "Sampling points from 2 areas"
[1] "Creating prediction semivariance matrix. This can take some time."
>
>
> varmat = varMat(observations, predictionLocations, variogramModel = rtopObj$variogramModel,
+ gDistEst = TRUE, gDistPred = TRUE, rresol = 25, hresol = 3)
[1] "Sampling points from 30 areas"
[1] "Sampled on average 54.2 points from 30 areas"
[1] "Sampling points from 2 areas"
[1] "Sampled on average 77 points from 2 areas"
>
> all.equal(varmat$varMatObs, rtopObj2$varMatObs)
[1] TRUE
> rtopObj4 = rtopKrige(rtopObj2)
[1] "Sampling points from 2 areas"
[1] "Creating prediction semivariance matrix. This can take some time."
>
> #debug(rtop:::rtopDisc.SpatialPolygons)
> # rtopObj5 = rtopKrige(rtopObj, params = list(cnAreas = 5, cDlim = 10, nclus = 2))
>
> print(summary(rtopObj2$predictions))
Length Class Mode
30 SpatialPolygonsDataFrame S4
> print(summary(rtopObj3$predictions))
Length Class Mode
2 SpatialPolygonsDataFrame S4
> print(summary(rtopObj4$predictions))
Length Class Mode
2 SpatialPolygonsDataFrame S4
> print(all.equal(rtopObj4$predictions, rtopObj3$predictions))
[1] TRUE
> #spplot(rtopObj$predictions,col.regions = bpy.colors(), c("var1.pred","var1.var"))
>
> # Cross-validation
> #spplot(rtopObj2$predictions,col.regions = bpy.colors(), c("observed","var1.pred"))
> print(cor(rtopObj2$predictions$observed,rtopObj2$predictions$var1.pred))
[1] 0.1678744
>
>
>
>
> set.seed(1501)
> library(intamap)
Error in library(intamap) : there is no package called 'intamap'
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.6-9
Check: examples
Result: ERROR
Running examples in ‘rtop-Ex.R’ failed
The error most likely occurred in:
> ### Name: useRtopWithIntamap
> ### Title: Integrates the rtop package with the 'intamap' package
> ### Aliases: useRtopWithIntamap
> ### Keywords: plot
>
> ### ** Examples
>
> library(intamap)
Error in library(intamap) : there is no package called ‘intamap’
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.6-9
Check: tests
Result: ERROR
Running ‘rtop.R’ [18s/24s]
Running ‘rtop_sf.R’ [78s/99s]
Comparing ‘rtop_sf.Rout’ to ‘rtop_sf.Rout.save’ ... OK
Running the tests in ‘tests/rtop.R’ failed.
Complete output:
> set.seed(1501)
> #-----------------------------
> ## IGNORE_RDIFF_BEGIN
> library(rtop)
> if (interactive()) options(error = recover)
> # Read directly from shape-files in data directory
> rpath = system.file("extdata",package="rtop")
> library(sf)
Linking to GEOS 3.13.0, GDAL 3.10.3, PROJ 9.6.2; sf_use_s2() is TRUE
> observations = st_read(rpath, "observations")
Reading layer `observations' from data source
`/data/gannet/ripley/R/packages/tests-clang/rtop.Rcheck/rtop/extdata'
using driver `ESRI Shapefile'
Simple feature collection with 57 features and 7 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: 392041.1 ymin: 454983.1 xmax: 512819.5 ymax: 543984.4
Projected CRS: Lambert_Conformal_Conic
> predictionLocations = st_read(rpath, "predictionLocations")
Reading layer `predictionLocations' from data source
`/data/gannet/ripley/R/packages/tests-clang/rtop.Rcheck/rtop/extdata'
using driver `ESRI Shapefile'
Simple feature collection with 235 features and 5 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: 393416.8 ymin: 454919.1 xmax: 519903.3 ymax: 543984.4
Projected CRS: Lambert_Conformal_Conic
> ## IGNORE_RDIFF_END
>
>
> observations = as(observations, "Spatial")
> predictionLocations = as(predictionLocations, "Spatial")
> #Finding a few prediction locations of them
>
> observations = observations[1:30,]
> predictionLocations = predictionLocations[1:2,]
>
> observations$obs = observations$QSUMMER_OB/observations$AREASQKM
>
> # Setting some parameters
> params = list(gDist = TRUE, cloud = FALSE, rresol = 25, hresol = 3, debug.level = -1)
> # Build an object
> rtopObj = createRtopObject(observations,predictionLocations, params = params, formulaString = "obs ~ 1" )
> # Fit a variogram (function also creates it)
> rtopObj = rtopFitVariogram(rtopObj, iprint = -1)
> print(rtopObj$variogramModel, 3)
$model
[1] "Ex1"
$params
[1] 2.51e-04 4.26e+05 0.00e+00 1.01e-05 9.23e-01
attr(,"class")
[1] "rtopVariogramModel"
attr(,"SSErr")
[1] 0.557
attr(,"criterion")
[1] 0.0981
> #rtopObj = checkVario(rtopObj)
> rtopObj2 = rtopKrige(rtopObj, cv = TRUE)
[1] "Sampling points from 30 areas"
>
>
> print(attr(rtopObj2$varMatObs,"variogramModel"), 3)
$model
[1] "Ex1"
$params
[1] 2.51e-04 4.26e+05 0.00e+00 1.01e-05 9.23e-01
attr(,"class")
[1] "rtopVariogramModel"
attr(,"SSErr")
[1] 0.557
attr(,"criterion")
[1] 0.0981
>
> rtopObj3 = rtopKrige(rtopObj)
[1] "Sampling points from 30 areas"
[1] "Sampling points from 2 areas"
[1] "Creating prediction semivariance matrix. This can take some time."
>
>
> varmat = varMat(observations, predictionLocations, variogramModel = rtopObj$variogramModel,
+ gDistEst = TRUE, gDistPred = TRUE, rresol = 25, hresol = 3)
[1] "Sampling points from 30 areas"
[1] "Sampled on average 54.2 points from 30 areas"
[1] "Sampling points from 2 areas"
[1] "Sampled on average 77 points from 2 areas"
>
> all.equal(varmat$varMatObs, rtopObj2$varMatObs)
[1] TRUE
> rtopObj4 = rtopKrige(rtopObj2)
[1] "Sampling points from 2 areas"
[1] "Creating prediction semivariance matrix. This can take some time."
>
> #debug(rtop:::rtopDisc.SpatialPolygons)
> # rtopObj5 = rtopKrige(rtopObj, params = list(cnAreas = 5, cDlim = 10, nclus = 2))
>
> print(summary(rtopObj2$predictions))
Length Class Mode
30 SpatialPolygonsDataFrame S4
> print(summary(rtopObj3$predictions))
Length Class Mode
2 SpatialPolygonsDataFrame S4
> print(summary(rtopObj4$predictions))
Length Class Mode
2 SpatialPolygonsDataFrame S4
> print(all.equal(rtopObj4$predictions, rtopObj3$predictions))
[1] TRUE
> #spplot(rtopObj$predictions,col.regions = bpy.colors(), c("var1.pred","var1.var"))
>
> # Cross-validation
> #spplot(rtopObj2$predictions,col.regions = bpy.colors(), c("observed","var1.pred"))
> print(cor(rtopObj2$predictions$observed,rtopObj2$predictions$var1.pred))
[1] 0.1678744
>
>
>
>
> set.seed(1501)
> library(intamap)
Error in library(intamap) : there is no package called 'intamap'
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.6-9
Check: tests
Result: ERROR
Running ‘rtop.R’ [19s/36s]
Running ‘rtop_sf.R’ [77s/111s]
Comparing ‘rtop_sf.Rout’ to ‘rtop_sf.Rout.save’ ... OK
Running the tests in ‘tests/rtop.R’ failed.
Complete output:
> set.seed(1501)
> #-----------------------------
> ## IGNORE_RDIFF_BEGIN
> library(rtop)
> if (interactive()) options(error = recover)
> # Read directly from shape-files in data directory
> rpath = system.file("extdata",package="rtop")
> library(sf)
Linking to GEOS 3.13.0, GDAL 3.10.3, PROJ 9.6.2; sf_use_s2() is TRUE
> observations = st_read(rpath, "observations")
Reading layer `observations' from data source
`/data/gannet/ripley/R/packages/tests-devel/rtop.Rcheck/rtop/extdata'
using driver `ESRI Shapefile'
Simple feature collection with 57 features and 7 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: 392041.1 ymin: 454983.1 xmax: 512819.5 ymax: 543984.4
Projected CRS: Lambert_Conformal_Conic
> predictionLocations = st_read(rpath, "predictionLocations")
Reading layer `predictionLocations' from data source
`/data/gannet/ripley/R/packages/tests-devel/rtop.Rcheck/rtop/extdata'
using driver `ESRI Shapefile'
Simple feature collection with 235 features and 5 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: 393416.8 ymin: 454919.1 xmax: 519903.3 ymax: 543984.4
Projected CRS: Lambert_Conformal_Conic
> ## IGNORE_RDIFF_END
>
>
> observations = as(observations, "Spatial")
> predictionLocations = as(predictionLocations, "Spatial")
> #Finding a few prediction locations of them
>
> observations = observations[1:30,]
> predictionLocations = predictionLocations[1:2,]
>
> observations$obs = observations$QSUMMER_OB/observations$AREASQKM
>
> # Setting some parameters
> params = list(gDist = TRUE, cloud = FALSE, rresol = 25, hresol = 3, debug.level = -1)
> # Build an object
> rtopObj = createRtopObject(observations,predictionLocations, params = params, formulaString = "obs ~ 1" )
> # Fit a variogram (function also creates it)
> rtopObj = rtopFitVariogram(rtopObj, iprint = -1)
> print(rtopObj$variogramModel, 3)
$model
[1] "Ex1"
$params
[1] 2.51e-04 4.26e+05 0.00e+00 1.01e-05 9.23e-01
attr(,"class")
[1] "rtopVariogramModel"
attr(,"SSErr")
[1] 0.557
attr(,"criterion")
[1] 0.0981
> #rtopObj = checkVario(rtopObj)
> rtopObj2 = rtopKrige(rtopObj, cv = TRUE)
[1] "Sampling points from 30 areas"
>
>
> print(attr(rtopObj2$varMatObs,"variogramModel"), 3)
$model
[1] "Ex1"
$params
[1] 2.51e-04 4.26e+05 0.00e+00 1.01e-05 9.23e-01
attr(,"class")
[1] "rtopVariogramModel"
attr(,"SSErr")
[1] 0.557
attr(,"criterion")
[1] 0.0981
>
> rtopObj3 = rtopKrige(rtopObj)
[1] "Sampling points from 30 areas"
[1] "Sampling points from 2 areas"
[1] "Creating prediction semivariance matrix. This can take some time."
>
>
> varmat = varMat(observations, predictionLocations, variogramModel = rtopObj$variogramModel,
+ gDistEst = TRUE, gDistPred = TRUE, rresol = 25, hresol = 3)
[1] "Sampling points from 30 areas"
[1] "Sampled on average 54.2 points from 30 areas"
[1] "Sampling points from 2 areas"
[1] "Sampled on average 77 points from 2 areas"
>
> all.equal(varmat$varMatObs, rtopObj2$varMatObs)
[1] TRUE
> rtopObj4 = rtopKrige(rtopObj2)
[1] "Sampling points from 2 areas"
[1] "Creating prediction semivariance matrix. This can take some time."
>
> #debug(rtop:::rtopDisc.SpatialPolygons)
> # rtopObj5 = rtopKrige(rtopObj, params = list(cnAreas = 5, cDlim = 10, nclus = 2))
>
> print(summary(rtopObj2$predictions))
Length Class Mode
30 SpatialPolygonsDataFrame S4
> print(summary(rtopObj3$predictions))
Length Class Mode
2 SpatialPolygonsDataFrame S4
> print(summary(rtopObj4$predictions))
Length Class Mode
2 SpatialPolygonsDataFrame S4
> print(all.equal(rtopObj4$predictions, rtopObj3$predictions))
[1] TRUE
> #spplot(rtopObj$predictions,col.regions = bpy.colors(), c("var1.pred","var1.var"))
>
> # Cross-validation
> #spplot(rtopObj2$predictions,col.regions = bpy.colors(), c("observed","var1.pred"))
> print(cor(rtopObj2$predictions$observed,rtopObj2$predictions$var1.pred))
[1] 0.1678744
>
>
>
>
> set.seed(1501)
> library(intamap)
Error in library(intamap) : there is no package called 'intamap'
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.6-9
Check: tests
Result: ERROR
Running ‘rtop.R’ [10s/11s]
Running ‘rtop_sf.R’ [48s/60s]
Comparing ‘rtop_sf.Rout’ to ‘rtop_sf.Rout.save’ ... OK
Running the tests in ‘tests/rtop.R’ failed.
Complete output:
> set.seed(1501)
> #-----------------------------
> ## IGNORE_RDIFF_BEGIN
> library(rtop)
> if (interactive()) options(error = recover)
> # Read directly from shape-files in data directory
> rpath = system.file("extdata",package="rtop")
> library(sf)
Linking to GEOS 3.13.1, GDAL 3.10.3, PROJ 9.6.0; sf_use_s2() is TRUE
> observations = st_read(rpath, "observations")
Reading layer `observations' from data source
`/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rtop/extdata'
using driver `ESRI Shapefile'
Simple feature collection with 57 features and 7 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: 392041.1 ymin: 454983.1 xmax: 512819.5 ymax: 543984.4
Projected CRS: Lambert_Conformal_Conic
> predictionLocations = st_read(rpath, "predictionLocations")
Reading layer `predictionLocations' from data source
`/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rtop/extdata'
using driver `ESRI Shapefile'
Simple feature collection with 235 features and 5 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: 393416.8 ymin: 454919.1 xmax: 519903.3 ymax: 543984.4
Projected CRS: Lambert_Conformal_Conic
> ## IGNORE_RDIFF_END
>
>
> observations = as(observations, "Spatial")
> predictionLocations = as(predictionLocations, "Spatial")
> #Finding a few prediction locations of them
>
> observations = observations[1:30,]
> predictionLocations = predictionLocations[1:2,]
>
> observations$obs = observations$QSUMMER_OB/observations$AREASQKM
>
> # Setting some parameters
> params = list(gDist = TRUE, cloud = FALSE, rresol = 25, hresol = 3, debug.level = -1)
> # Build an object
> rtopObj = createRtopObject(observations,predictionLocations, params = params, formulaString = "obs ~ 1" )
> # Fit a variogram (function also creates it)
> rtopObj = rtopFitVariogram(rtopObj, iprint = -1)
> print(rtopObj$variogramModel, 3)
$model
[1] "Ex1"
$params
[1] 2.51e-04 4.26e+05 0.00e+00 1.01e-05 9.23e-01
attr(,"class")
[1] "rtopVariogramModel"
attr(,"SSErr")
[1] 0.557
attr(,"criterion")
[1] 0.0981
> #rtopObj = checkVario(rtopObj)
> rtopObj2 = rtopKrige(rtopObj, cv = TRUE)
[1] "Sampling points from 30 areas"
>
>
> print(attr(rtopObj2$varMatObs,"variogramModel"), 3)
$model
[1] "Ex1"
$params
[1] 2.51e-04 4.26e+05 0.00e+00 1.01e-05 9.23e-01
attr(,"class")
[1] "rtopVariogramModel"
attr(,"SSErr")
[1] 0.557
attr(,"criterion")
[1] 0.0981
>
> rtopObj3 = rtopKrige(rtopObj)
[1] "Sampling points from 30 areas"
[1] "Sampling points from 2 areas"
[1] "Creating prediction semivariance matrix. This can take some time."
>
>
> varmat = varMat(observations, predictionLocations, variogramModel = rtopObj$variogramModel,
+ gDistEst = TRUE, gDistPred = TRUE, rresol = 25, hresol = 3)
[1] "Sampling points from 30 areas"
[1] "Sampled on average 54.2 points from 30 areas"
[1] "Sampling points from 2 areas"
[1] "Sampled on average 77 points from 2 areas"
>
> all.equal(varmat$varMatObs, rtopObj2$varMatObs)
[1] TRUE
> rtopObj4 = rtopKrige(rtopObj2)
[1] "Sampling points from 2 areas"
[1] "Creating prediction semivariance matrix. This can take some time."
>
> #debug(rtop:::rtopDisc.SpatialPolygons)
> # rtopObj5 = rtopKrige(rtopObj, params = list(cnAreas = 5, cDlim = 10, nclus = 2))
>
> print(summary(rtopObj2$predictions))
Length Class Mode
30 SpatialPolygonsDataFrame S4
> print(summary(rtopObj3$predictions))
Length Class Mode
2 SpatialPolygonsDataFrame S4
> print(summary(rtopObj4$predictions))
Length Class Mode
2 SpatialPolygonsDataFrame S4
> print(all.equal(rtopObj4$predictions, rtopObj3$predictions))
[1] TRUE
> #spplot(rtopObj$predictions,col.regions = bpy.colors(), c("var1.pred","var1.var"))
>
> # Cross-validation
> #spplot(rtopObj2$predictions,col.regions = bpy.colors(), c("observed","var1.pred"))
> print(cor(rtopObj2$predictions$observed,rtopObj2$predictions$var1.pred))
[1] 0.1678744
>
>
>
>
> set.seed(1501)
> library(intamap)
Error in library(intamap) : there is no package called 'intamap'
Execution halted
Flavor: r-patched-linux-x86_64