Check results for 'StrucDiv'

using R version 4.4.0 alpha (2024-03-31 r86238)
using platform: aarch64-apple-darwin20
R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0
running under: macOS Ventura 13.4
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 ... [113s/117s] OK See the install log for details.
used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
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 11.1Mb sub-directories of 1Mb or more: libs 10.1Mb
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 code files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [3s/3s] OK
checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
checking whether the package can be unloaded cleanly ... [3s/3s] OK
checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
checking loading without being on the library search path ... [3s/3s] 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 ... [7s/7s] 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
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking contents of ‘data’ directory ... OK
checking data for non-ASCII characters ... [0s/0s] OK
checking LazyData ... OK
checking data for ASCII and uncompressed saves ... OK
checking line endings in C/C++/Fortran sources/headers ... OK
checking line endings in Makefiles ... OK
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 ... [3s/3s] 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 ... [4s/4s] OK Running ‘testthat.R’ [3s/4s] Comparing ‘testthat.Rout’ to ‘testthat.Rout.save’ ... OK
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [6s/6s] OK
checking PDF version of manual ... [4s/4s] OK
DONE Status: 2 NOTEs
using check arguments '--no-clean-on-error '