Check results for 'StrucDiv'

using R version 4.3.0 beta (2023-04-08 r84203)
using platform: x86_64-apple-darwin20 (64-bit)
R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0
running under: macOS Ventura 13.3
using session charset: UTF-8
checking for file ‘StrucDiv/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘StrucDiv’ version ‘0.2.1’
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘StrucDiv’ can be installed ... [225s/304s] OK See the install log for details.
used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
used SDK: ‘MacOSX11.3.sdk’
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 11.4Mb sub-directories of 1Mb or more: libs 10.4Mb
checking package directory ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking R files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [5s/7s] OK
checking whether the package can be loaded with stated dependencies ... [5s/7s] OK
checking whether the package can be unloaded cleanly ... [5s/5s] OK
checking whether the namespace can be loaded with stated dependencies ... [5s/7s] OK
checking whether the namespace can be unloaded cleanly ... [5s/7s] OK
checking loading without being on the library search path ... [5s/7s] OK
checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [11s/15s] OK
checking Rd files ... [0s/0s] OK
checking Rd metadata ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
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checking for unstated dependencies in examples ... OK
checking contents of ‘data’ directory ... OK
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checking LazyData ... OK
checking data for ASCII and uncompressed saves ... OK
checking line endings in C/C++/Fortran sources/headers ... OK
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checking compilation flags in Makevars ... OK
checking for GNU extensions in Makefiles ... OK
checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
checking use of PKG_*FLAGS in Makefiles ... OK
checking compiled code ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [5s/6s] OK
checking differences from ‘StrucDiv-Ex.Rout’ to ‘StrucDiv-Ex.Rout.save’ ... OK 43,61c43,57 < > ## Not run: < > ##D # Construct a small raster file containing realizations of normal random variables: < > ##D a <- raster::raster(matrix(rnorm(648), 18, 36)) < > ##D raster::plot(a) < > ##D # Calculate contrast: < > ##D contrast_a <- strucDiv(a, wsl = 3, fun = contrast) < > ##D raster::plot(contrast_a) < > ##D < > ##D # Calculate dissimilarity: < > ##D b <- raster::raster(matrix(rnorm(100), 10, 10)) < > ##D raster::plot(b) < > ##D dissim_b <- strucDiv(b, wsl = 5, angle = "horizontal", fun = dissimilarity) < > ##D raster::plot(dissim_b) < > ##D < > ##D # Calculate structural diversity entropy with delta = 2 on NDVI data binned to 15 gray levels < > ##D ndvi.15gl <- raster::raster(ndvi.15gl) < > ##D sde_ndvi15 <- strucDiv(ndvi.15gl, wsl = 3, fun = entropy, delta = 2) < > ##D raster::plot(sde_ndvi15) < > ## End(Not run) --- > > # Construct a small raster file containing realizations of normal random variables: > > a <- raster::raster(matrix(rnorm(648), 18, 36)) > > raster::plot(a) > > # Calculate contrast: > > contrast_a <- strucDiv(a, wsl = 3, fun = contrast, na.handling = na.omit, rank = FALSE) > Extracting values from raster file > Calculating gray level co-occurrence matrix > 0% 10 20 30 40 50 60 70 80 90 100% > [----|----|----|----|----|----|----|----|----|----| > **************************************************| > Calculating horizontal structural diversity > 0% 10 20 30 40 50 60 70 80 90 100% > [----|----|----|----|----|----|----|----|----|----| > **************************************************| > > raster::plot(contrast_a) 62a59,73 > > # Calculate dissimilarity: > > b <- raster::raster(matrix(rnorm(100), 10, 10)) > > raster::plot(b) > > dissim_b <- strucDiv(b, wsl = 5, dist = 1, angle = "all", fun = dissimilarity, > + na.handling = na.pass, rank = FALSE) > Extracting values from raster file > Calculating gray level co-occurrence matrix > 0% 10 20 30 40 50 60 70 80 90 100% > [----|----|----|----|----|----|----|----|----|----| > **************************************************| > **************************************************************Calculating horizontal structural diversity > 0% 10 20 30 40 50 60 70 80 90 100% > [----|----|----|----|----|----|----|----|----|----| > **************************************************| > **************************************************************> raster::plot(dissim_b) 63a75,88 > > # Calculate structural diversity entropy with delta = 2 on NDVI data binned to 15 gray levels > > ndvi.15gl <- raster::raster(ndvi.15gl) > > sde_ndvi15 <- strucDiv(ndvi.15gl, wsl = 3, fun = entropy, delta = 2, na.handling = na.pass, > + rank = FALSE) > Extracting values from raster file > Calculating gray level co-occurrence matrix > 0% 10 20 30 40 50 60 70 80 90 100% > [----|----|----|----|----|----|----|----|----|----| > **************************************************| > Calculating horizontal structural diversity > 0% 10 20 30 40 50 60 70 80 90 100% > [----|----|----|----|----|----|----|----|----|----| > **************************************************| > > raster::plot(sde_ndvi15) 64a90,92 > > > > > > 79,89c107,111 < > ## Not run: < > ##D # Calculate entropy on simulated random patch data < > ##D a <- raster::raster(matrix(rnorm(100), 10, 10)) < > ##D sdivDom <- strucDivDom(a, angle = "vertical", fun = entropyDom) < > ##D # Structural diversity value of the domain < > ##D div <- sdivDom$div < > ##D # Gray level co-occurrence matrix < > ##D glcm <- sdivDom$GLCM < > ##D # Diversity matrix < > ##D divmat <- sdivDom$divMat < > ## End(Not run) --- > > # Calculate entropy on NDVI data binned to 15 gray levels > > ndvi15 <- raster::raster(ndvi.15gl) > > ndvi15Dom <- strucDivDom(ndvi15, fun = entropyDom) > > ndvi15GLCM <- ndvi15Dom$GLCM > > ndvi15Div <- ndvi15Dom$div 92a115 > > 106,125c129,170 < > ## Not run: < > ##D # Construct a small raster file containing realizations of normal random variables: < > ##D a <- raster::raster(matrix(rnorm(400), 20, 20)) < > ##D raster::plot(a) < > ##D # Calculate structural diversity entropy with delta = 2, double moving window scheme < > ##D sde_1 <- strucDivNest(a, wslI = 3, wslO = 5, angle = "horizontal", fun = entropy, delta = 2) < > ##D raster::plot(sde_1) < > ##D < > ##D # Calculate structural diversity entropy with delta = 1, block nesting scheme < > ##D b <- raster::raster(matrix(rnorm(2500), 50, 50)) < > ##D raster::plot(b) < > ##D sde_b <- strucDivNest(b, wslI = 3, dimB = c(10, 10), oLap = 4, priorB = TRUE, fun = entropy, < > ##D delta = 1) < > ##D raster::plot(sde_b) < > ##D < > ##D # Calculate entropy on simulated random patch, domain nesting scheme < > ##D patch <- raster::raster(patch) < > ##D entropy_patch <- strucDivNest(patch, wslI = 5, domain = TRUE, angle = "vertical", fun = entropy) < > ##D raster::plot(entropy_patch) < > ## End(Not run) --- > > # Construct a small raster file containing realizations of normal random variables: > > a <- raster::raster(matrix(rnorm(648), 18, 36)) > > raster::plot(a) > > # Calculate structural diversity entropy with delta = 2, double moving window scheme > > sde_a <- strucDivNest(a, wslI = 3, wslO = 7, fun = entropy, delta = 2, na.handling = na.omit, > + rank = FALSE) > Extracting values from raster file > Calculating gray level co-occurrence matrix > 0% 10 20 30 40 50 60 70 80 90 100% > [----|----|----|----|----|----|----|----|----|----| > **************************************************| > Calculating horizontal structural diversity > 0% 10 20 30 40 50 60 70 80 90 100% > [----|----|----|----|----|----|----|----|----|----| > **************************************************| > > raster::plot(sde_a) > > > > # Calculate structural diversity entropy with delta = 1, block nesting scheme > > b <- raster::raster(matrix(rnorm(2500), 50, 50)) > > raster::plot(b) > > sde_b <- strucDivNest(b, wslI = 3, dimB = c(10, 10), oLap = 4, priorB = TRUE, fun = entropy, > + delta = 1, na.handling = na.pass, rank = FALSE) > > | > | | 0% > > raster::plot(sde_b) > > > > # Calculate entropy on NDVI data binned to 15 gray levels, domain nesting scheme > > ndvi.15gl <- raster::raster(ndvi.15gl) > > entropyNest_ndvi15 <- strucDivNest(ndvi.15gl, wslI = 5, domain = TRUE, fun = entropy, > + na.handling = na.pass, rank = FALSE) > Extracting values from raster file > Calculating gray level co-occurrence matrix > 0% 10 20 30 40 50 60 70 80 90 100% > [----|----|----|----|----|----|----|----|----|----| > **************************************************| > Calculating horizontal structural diversity > 0% 10 20 30 40 50 60 70 80 90 100% > [----|----|----|----|----|----|----|----|----|----| > **************************************************| > > raster::plot(entropyNest_ndvi15) > >
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [6s/8s] OK Running ‘testthat.R’ [5s/8s] Comparing ‘testthat.Rout’ to ‘testthat.Rout.save’ ... OK
checking for unstated dependencies in vignettes ... OK
checking package vignettes in ‘inst/doc’ ... OK
checking running R code from vignettes ... [0s/0s] NONE ‘StrucDiv.Rmd’ using ‘UTF-8’... [0s/0s] OK
checking re-building of vignette outputs ... [8s/11s] OK
checking PDF version of manual ... [4s/5s] OK
DONE Status: 2 NOTEs
using check arguments '--no-clean-on-error '