* using log directory 'd:/RCompile/CRANincoming/R-devel/bispdep.Rcheck' * using R Under development (unstable) (2024-01-20 r85814 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'bispdep/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'bispdep' version '1.0-0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Carlos Melo ' New submission Possibly misspelled words in DESCRIPTION: Bivariate (3:8) Getis (18:58) autocorrelation (4:9, 18:305) autocorrelations (18:74) bivariate (3:53, 18:64, 18:287) scattergrams (18:106) Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. 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Current version is: 'Bivariate Spatial Dependence: statistics for bivariate spatial autocorrelation' In title case that is: 'Bivariate Spatial Dependence: Statistics for Bivariate Spatial Autocorrelation' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking serialization versions ... OK * checking whether package 'bispdep' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... 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 ... [10s] OK * checking Rd files ... NOTE checkRd: (-1) geary.bi.Rd:4: Lost braces; missing escapes or markup? 4 | \title{Compute Bivariate Geary's C_{xy}} | ^ checkRd: (-1) geary.bi.Rd:6: Lost braces; missing escapes or markup? 6 | A simple function to compute Bivariate Geary's C_{xy}; | ^ checkRd: (-1) gearybi.test.Rd:3: Lost braces; missing escapes or markup? 3 | \title{Bivariate Geary's C_{xy} test for spatial autocorrelation} | ^ checkRd: (-1) gearybi.test.Rd:25: Lost braces; missing escapes or markup? 25 | \item{statistic}{the value of the standard deviate of Geary's C_{xy}, in the order given in Cliff and Ord 1973, p. 21, which is (EC_{xy} - C_{xy}) / sqrt(VC_{xy}), that is with the sign reversed with respect to the more usual (C_{xy} - EC_{xy}) / sqrt(VC_{xy}); this means that the \dQuote{greater} alternative for the Bivariate Geary C_{xy} test corresponds to the \dQuote{greater} alternative for Bivariate Moran's I_{xy} test.} | ^ checkRd: (-1) gearybi.test.Rd:25: Lost braces; missing escapes or markup? 25 | \item{statistic}{the value of the standard deviate of Geary's C_{xy}, in the order given in Cliff and Ord 1973, p. 21, which is (EC_{xy} - C_{xy}) / sqrt(VC_{xy}), that is with the sign reversed with respect to the more usual (C_{xy} - EC_{xy}) / sqrt(VC_{xy}); this means that the \dQuote{greater} alternative for the Bivariate Geary C_{xy} test corresponds to the \dQuote{greater} alternative for Bivariate Moran's I_{xy} test.} | ^ checkRd: (-1) gearybi.test.Rd:25: Lost braces; missing escapes or markup? 25 | \item{statistic}{the value of the standard deviate of Geary's C_{xy}, in the order given in Cliff and Ord 1973, p. 21, which is (EC_{xy} - C_{xy}) / sqrt(VC_{xy}), that is with the sign reversed with respect to the more usual (C_{xy} - EC_{xy}) / sqrt(VC_{xy}); this means that the \dQuote{greater} alternative for the Bivariate Geary C_{xy} test corresponds to the \dQuote{greater} alternative for Bivariate Moran's I_{xy} test.} | ^ checkRd: (-1) gearybi.test.Rd:25: Lost braces; missing escapes or markup? 25 | \item{statistic}{the value of the standard deviate of Geary's C_{xy}, in the order given in Cliff and Ord 1973, p. 21, which is (EC_{xy} - C_{xy}) / sqrt(VC_{xy}), that is with the sign reversed with respect to the more usual (C_{xy} - EC_{xy}) / sqrt(VC_{xy}); this means that the \dQuote{greater} alternative for the Bivariate Geary C_{xy} test corresponds to the \dQuote{greater} alternative for Bivariate Moran's I_{xy} test.} | ^ checkRd: (-1) gearybi.test.Rd:25: Lost braces; missing escapes or markup? 25 | \item{statistic}{the value of the standard deviate of Geary's C_{xy}, in the order given in Cliff and Ord 1973, p. 21, which is (EC_{xy} - C_{xy}) / sqrt(VC_{xy}), that is with the sign reversed with respect to the more usual (C_{xy} - EC_{xy}) / sqrt(VC_{xy}); this means that the \dQuote{greater} alternative for the Bivariate Geary C_{xy} test corresponds to the \dQuote{greater} alternative for Bivariate Moran's I_{xy} test.} | ^ checkRd: (-1) gearybi.test.Rd:25: Lost braces; missing escapes or markup? 25 | \item{statistic}{the value of the standard deviate of Geary's C_{xy}, in the order given in Cliff and Ord 1973, p. 21, which is (EC_{xy} - C_{xy}) / sqrt(VC_{xy}), that is with the sign reversed with respect to the more usual (C_{xy} - EC_{xy}) / sqrt(VC_{xy}); this means that the \dQuote{greater} alternative for the Bivariate Geary C_{xy} test corresponds to the \dQuote{greater} alternative for Bivariate Moran's I_{xy} test.} | ^ checkRd: (-1) gearybi.test.Rd:25: Lost braces; missing escapes or markup? 25 | \item{statistic}{the value of the standard deviate of Geary's C_{xy}, in the order given in Cliff and Ord 1973, p. 21, which is (EC_{xy} - C_{xy}) / sqrt(VC_{xy}), that is with the sign reversed with respect to the more usual (C_{xy} - EC_{xy}) / sqrt(VC_{xy}); this means that the \dQuote{greater} alternative for the Bivariate Geary C_{xy} test corresponds to the \dQuote{greater} alternative for Bivariate Moran's I_{xy} test.} | ^ checkRd: (-1) gearybi.test.Rd:25: Lost braces; missing escapes or markup? 25 | \item{statistic}{the value of the standard deviate of Geary's C_{xy}, in the order given in Cliff and Ord 1973, p. 21, which is (EC_{xy} - C_{xy}) / sqrt(VC_{xy}), that is with the sign reversed with respect to the more usual (C_{xy} - EC_{xy}) / sqrt(VC_{xy}); this means that the \dQuote{greater} alternative for the Bivariate Geary C_{xy} test corresponds to the \dQuote{greater} alternative for Bivariate Moran's I_{xy} test.} | ^ checkRd: (-1) gearybi.test.Rd:25: Lost braces; missing escapes or markup? 25 | \item{statistic}{the value of the standard deviate of Geary's C_{xy}, in the order given in Cliff and Ord 1973, p. 21, which is (EC_{xy} - C_{xy}) / sqrt(VC_{xy}), that is with the sign reversed with respect to the more usual (C_{xy} - EC_{xy}) / sqrt(VC_{xy}); this means that the \dQuote{greater} alternative for the Bivariate Geary C_{xy} test corresponds to the \dQuote{greater} alternative for Bivariate Moran's I_{xy} test.} | ^ checkRd: (-1) gearybi.test.Rd:27: Lost braces; missing escapes or markup? 27 | \item{estimate}{the value of the observed BIvariate Geary's C_{xy}, its expectation and | ^ checkRd: (-1) getis.cluster.Rd:67: Lost braces; missing escapes or markup? 67 | \item Bivariate Moran's I_{xy}: \code{\link{moran.bi}} | ^ checkRd: (-1) getis.cluster.Rd:68: Lost braces; missing escapes or markup? 68 | \item Plot Bivariate Moran's I_{xy}: \code{\link{moranbi.plot}} | ^ checkRd: (-1) getis.cluster.Rd:69: Lost braces; missing escapes or markup? 69 | \item Bivariate Moran's I_{xy} Test: \code{\link{moranbi.test}} | ^ checkRd: (-1) getis.cluster.Rd:70: Lost braces; missing escapes or markup? 70 | \item Bivariate Local Moran's I_{xy} and Test: \code{\link{localmoran.bi}} | ^ checkRd: (-1) localmoran.bi.Rd:4: Lost braces; missing escapes or markup? 4 | \title{BiLISA - Bivariate Local Indicators of Spatial Association Moran's I_{xy} statistic} | ^ checkRd: (-1) moran.bi.Rd:3: Lost braces; missing escapes or markup? 3 | \title{Compute Bivariate Moran's I_{xy}} | ^ checkRd: (-1) moran.bi.Rd:5: Lost braces; missing escapes or markup? 5 | A simple function to compute bivariate Moran's I_{xy}, called by \code{moranbi.test} and \code{moranbi.mc}; | ^ checkRd: (-1) moran.cluster.Rd:75: Lost braces; missing escapes or markup? 75 | \item Bivariate Moran's I_{xy}: \code{\link{moran.bi}} | ^ checkRd: (-1) moran.cluster.Rd:76: Lost braces; missing escapes or markup? 76 | \item Plot Bivariate Moran's I_{xy}: \code{\link{moranbi.plot}} | ^ checkRd: (-1) moran.cluster.Rd:77: Lost braces; missing escapes or markup? 77 | \item Bivariate Moran's I_{xy} Test: \code{\link{moranbi.test}} | ^ checkRd: (-1) moranbi.cluster.Rd:80: Lost braces; missing escapes or markup? 80 | \item Bivariate Moran's I_{xy}: \code{\link{moran.bi}} | ^ checkRd: (-1) moranbi.cluster.Rd:81: Lost braces; missing escapes or markup? 81 | \item Plot Bivariate Moran's I_{xy}: \code{\link{moranbi.plot}} | ^ checkRd: (-1) moranbi.cluster.Rd:82: Lost braces; missing escapes or markup? 82 | \item Bivariate Moran's I_{xy} Test: \code{\link{moranbi.test}} | ^ checkRd: (-1) moranbi.mc.Rd:3: Lost braces; missing escapes or markup? 3 | \title{Permutation test for bivariate Moran's I_{xy} statistic} | ^ checkRd: (-1) moranbi.mc.Rd:5: Lost braces; missing escapes or markup? 5 | A permutation test for bivariate Moran's I_{xy} statistic calculated by using nsim random permutations of \code{x} and \code{y} for the given spatial weighting scheme, to establish the rank of the observed statistic in relation to the nsim simulated values. | ^ checkRd: (-1) moranbi.test.Rd:3: Lost braces; missing escapes or markup? 3 | \title{Moran's I_{xy} test for bivariate spatial autocorrelation} | ^ checkRd: (-1) moranbi.test.Rd:5: Lost braces; missing escapes or markup? 5 | Moran's I_{xy} test for bivariate spatial autocorrelation using a spatial weights matrix in weights list form. The assumptions underlying the test are sensitive to the form of the graph of neighbour relationships and other factors, and results may be checked against those of \code{moranbi.mc} permutations. | ^ checkRd: (-1) moranbi.test.Rd:28: Lost braces; missing escapes or markup? 28 | \item{statistic}{the value of the standard deviate of Moran's I_{xy}.} | ^ checkRd: (-1) moranbi.test.Rd:30: Lost braces; missing escapes or markup? 30 | \item{estimate}{the value of the observed Moran's I_{xy}, its expectation and variance under the method assumption.} | ^ checkRd: (-1) moranbi.test.Rd:35: Lost braces; missing escapes or markup? 35 | \note{Var(I_{xy}) is taken from Cliff and Ord (1969, p. 28), and | ^ checkRd: (-1) moranbi.test.Rd:38: Lost braces; missing escapes or markup? 38 | see Tutorial workbook Chapter 22; VI_{xy} is the second crude moment minus the | ^ checkRd: (-1) moranbir.test.Rd:3: Lost braces; missing escapes or markup? 3 | \title{Moran's I_{xy} test using Monte Carlo permutations for bivariate spatial autocorrelation} | ^ checkRd: (-1) moranbir.test.Rd:5: Lost braces; missing escapes or markup? 5 | Moran's _{xy} test for bivariate spatial autocorrelation using a spatial weights matrix in weights list form. Constructs a plot of the empirical density from the simulations (Monte Carlo permutations) and superimposes Moran's bivariate I_{xy} index. | ^ checkRd: (-1) moranbir.test.Rd:5: Lost braces; missing escapes or markup? 5 | Moran's _{xy} test for bivariate spatial autocorrelation using a spatial weights matrix in weights list form. Constructs a plot of the empirical density from the simulations (Monte Carlo permutations) and superimposes Moran's bivariate I_{xy} index. | ^ checkRd: (-1) moranbir.test.Rd:36: Lost braces; missing escapes or markup? 36 | Compare the observed bivariate Moran's I_{xy} (moran.bi function) with the expected value empirical density. The expected value is -cor(x,y)/(n-1), where n is the number of rows/samples (number of polygons), and represents the null hyphothesis (Ho) of no spatial Autocorrelation (bivariate Moran's I_{xy} coefficient around zero). This expected value density is constructed with Monte Carlo simulations. Values significant below of -cor(x,y)/(n-1) represents negative spatial autocorrelation (generally negative values of observed bivariate Moran's I_{xy}), and values significant above of -cor(x,y)/(n-1) represents positive spatial autocorrelation (generally positive values of observed bivariate Moran's Ixy). | ^ checkRd: (-1) moranbir.test.Rd:36: Lost braces; missing escapes or markup? 36 | Compare the observed bivariate Moran's I_{xy} (moran.bi function) with the expected value empirical density. The expected value is -cor(x,y)/(n-1), where n is the number of rows/samples (number of polygons), and represents the null hyphothesis (Ho) of no spatial Autocorrelation (bivariate Moran's I_{xy} coefficient around zero). This expected value density is constructed with Monte Carlo simulations. Values significant below of -cor(x,y)/(n-1) represents negative spatial autocorrelation (generally negative values of observed bivariate Moran's I_{xy}), and values significant above of -cor(x,y)/(n-1) represents positive spatial autocorrelation (generally positive values of observed bivariate Moran's Ixy). | ^ checkRd: (-1) moranbir.test.Rd:36: Lost braces; missing escapes or markup? 36 | Compare the observed bivariate Moran's I_{xy} (moran.bi function) with the expected value empirical density. The expected value is -cor(x,y)/(n-1), where n is the number of rows/samples (number of polygons), and represents the null hyphothesis (Ho) of no spatial Autocorrelation (bivariate Moran's I_{xy} coefficient around zero). This expected value density is constructed with Monte Carlo simulations. Values significant below of -cor(x,y)/(n-1) represents negative spatial autocorrelation (generally negative values of observed bivariate Moran's I_{xy}), and values significant above of -cor(x,y)/(n-1) represents positive spatial autocorrelation (generally positive values of observed bivariate Moran's Ixy). | ^ checkRd: (-1) moranbir.test.Rd:29: Lost braces; missing escapes or markup? 29 | \item{Observed}{the value of the observed Moran's I_{xy}.} | ^ checkRd: (-1) moranbir.test.Rd:30: Lost braces; missing escapes or markup? 30 | \item{Expected}{the expected value of Moran's I_{xy}.} | ^ checkRd: (-1) moranbir.test.Rd:32: Lost braces; missing escapes or markup? 32 | \item{Values}{corresponds to the N simulated values of Moran's I_{xy} coefficient for bivariate autocorrelation.} | ^ checkRd: (-1) spcorrelogram.bi.Rd:7: Lost braces; missing escapes or markup? 7 | Bivariate spatial correlograms for Moran's I_{xy} and the autocorrelation coefficient, with print and plot helper functions. | ^ checkRd: (-1) spcorrelogram.bi.Rd:22: Lost braces; missing escapes or markup? 22 | \item{method}{"corr" for correlation, "I" for Moran's I_{xy}, "C" for Geary's C_{xy}} | ^ checkRd: (-1) spcorrelogram.bi.Rd:22: Lost braces; missing escapes or markup? 22 | \item{method}{"corr" for correlation, "I" for Moran's I_{xy}, "C" for Geary's C_{xy}} | ^ checkRd: (-1) spcorrelogram.bi.Rd:38: Lost braces; missing escapes or markup? 38 | The print function also calculates the standard deviates of Bivariate Moran's I_{xy} or Geary's C_{xy} and a two-sided probability value, optionally using \code{p.adjust} to correct by the nymber of lags. The plot function plots a bar from the estimated value of Bivariate Moran's I_{xy}, or Geary's C_{xy} to +/- twice the square root of its variance (in previous releases only once, not twice). The table includes the count of included observations in brackets after the lag order. Care must be taken when interpreting the results, since increasing the order of the lag tends to include fewer observations. | ^ checkRd: (-1) spcorrelogram.bi.Rd:38: Lost braces; missing escapes or markup? 38 | The print function also calculates the standard deviates of Bivariate Moran's I_{xy} or Geary's C_{xy} and a two-sided probability value, optionally using \code{p.adjust} to correct by the nymber of lags. The plot function plots a bar from the estimated value of Bivariate Moran's I_{xy}, or Geary's C_{xy} to +/- twice the square root of its variance (in previous releases only once, not twice). The table includes the count of included observations in brackets after the lag order. Care must be taken when interpreting the results, since increasing the order of the lag tends to include fewer observations. | ^ checkRd: (-1) spcorrelogram.bi.Rd:38: Lost braces; missing escapes or markup? 38 | The print function also calculates the standard deviates of Bivariate Moran's I_{xy} or Geary's C_{xy} and a two-sided probability value, optionally using \code{p.adjust} to correct by the nymber of lags. The plot function plots a bar from the estimated value of Bivariate Moran's I_{xy}, or Geary's C_{xy} to +/- twice the square root of its variance (in previous releases only once, not twice). The table includes the count of included observations in brackets after the lag order. Care must be taken when interpreting the results, since increasing the order of the lag tends to include fewer observations. | ^ checkRd: (-1) spcorrelogram.bi.Rd:38: Lost braces; missing escapes or markup? 38 | The print function also calculates the standard deviates of Bivariate Moran's I_{xy} or Geary's C_{xy} and a two-sided probability value, optionally using \code{p.adjust} to correct by the nymber of lags. The plot function plots a bar from the estimated value of Bivariate Moran's I_{xy}, or Geary's C_{xy} to +/- twice the square root of its variance (in previous releases only once, not twice). The table includes the count of included observations in brackets after the lag order. Care must be taken when interpreting the results, since increasing the order of the lag tends to include fewer observations. | ^ * checking Rd metadata ... OK * checking Rd line widths ... 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 examples ... ERROR Running examples in 'bispdep-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: connectivity.map > ### Title: Map of spatial connectivity > ### Aliases: connectivity.map > ### Keywords: spatial connectivity > > ### ** Examples > > library(spdep) > columbus <- st_read(system.file("shapes/columbus.shp", package="spData")[1], quiet=TRUE) > #Queen neighbours > col_nbq1 <- poly2nb(columbus) # queen, order 1 > col.lags10 <- nblag(col_nbq1, 10) # queen, up to order 10 > connectivity.map(col.lags10[[1]],columbus,"COLUMBUS_I",obs=25,col="green",cex=0.5) > > coords <- st_geometry(st_centroid(columbus$geometry)) > col.k4 <- knn2nb(knearneigh(coords,4)) > connectivity.map(col.k4,columbus,"COLUMBUS_I",obs=25,col="green",cex=0.5) > > trinb=tri2nb(coords) Warning in sn2listw(df1) : style is M (missing); style should be set to a valid value > connectivity.map(trinb,columbus,"COLUMBUS_I",obs=25,col="green",cex=0.5) > > soinb=graph2nb(soi.graph(trinb,coords)) Error in soi.graph(trinb, coords) : dbscan required Calls: graph2nb -> soi.graph Execution halted * checking PDF version of manual ... [14s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs