adding vignette desribing recent changes in poly2nb from #162, subgraph and no-neighbour (island) handling
adding prototype of LICD ESDA function licd_multi and hotspot method
add read.swmdbf2listw #163 for reading DBF files exported from ArcGIS representing SWM objects; note that there will be problems when the observation IDs are not known, see help file
#162 add option for no-neighbour checking for poly2nb - default report whether no-neighbour observations are present
#162 change the default snap= argument to poly2nb to 10mm
Condition on forthcoming tmap 4
#160 handle n.comp.nb delay in print.nb and elsewhere when the total number of neighbours is large
#157 migrate ESRI Shapefile to GPKG files; convert bhicv.shp to GPKG
#155 Throw error if hotspot despatched on object without a "quadr" attribute
#154 turn on s2 in vignette
add scale argument to geary.test, geary.mc and geary #151, and appropriate tests
Introduce error in knearneigh for k less than the largest count of identical points; if encountered, increase k
remove spurious warning in knearneigh for longlat geometries
fix https://github.com/edzer/sdsr/issues/121, wrong assignment of old test names in lmRStests
fix #144 in plot.nb and nb2lines
change lm.LMtests to lm.RStests and re-name Lagrange multiplier to Rao's score; add GNM_ prefix to test names if the input object inherits from SlX created by spatialreg::lmSLX (Koley, forthcoming)
add SD.RStests implementation of Rao's score tests for spatial Durbin models (Koley and Bera, 2024) and for SDEM models (Koley, forthcoming)
#143 row.names pass-through in poly2nb corrected, harmonised row.names pass-through also in nbdists and dnearneigh
#139 add na.action argument to geary.test, geary.mc and globalG.test
add style to sn2listw use in tri2nb
functions creating nb objects now warn if the object has a sub-graph count of > 1 and get.SubgraphOption is TRUE (default FALSE): complement.nb, diffnb, dnearneigh, droplinks, edit.nb, graph2nb, knn2nb, nb2blocknb, nblag, nblag_cumul, poly2nb, read.gal, read.gwt2nb, setdiff.nb, tolerance.nb, tri2nb, union.nb
summary.nb, print.nb, summary.listw and print.listw now report the subgraph count from n.comp.nb if it is more than one
subset.nb now reports if the subgraph count of the neighbour object increases on subsetting
adding a zero.policy attribute to functions creating listw objects: nb2listw, sn2listw, mat2listw, nb2listwdist. Default zero.policy= argument updated to use attr(., "zero.policy") in summary.listw, print.listw, moran, moran.test, moran.mc, moran.plot, geary.mc, geary, geary.test, globalG.test, joincount.test, joincount.mc, joincount.multi, localC, localC_perm, localmoran, localmoran_perm, localG, localG_perm, lee, lee.test, lee.mc, lm.morantest, lm.LMtests, sp.mantel.mc, listw2star, lag.listw, lm.morantest, lm.LMtests, subset.listw, EBImoran.mc, LOSH, LOSH.mc, LOSH.cs, lm.morantest.exactand lm.morantest.sad
confusing error message in moran.plot() if no-neighbour cases, but zero.policy=FALSE
replace rgrass7 with rgrass in vignette
fix #133 (edit.nb affected by not attaching sp)
mat2listw() warning if no style= argument given, or if M" is given https://github.com/r-spatial/spatialreg/issues/24, https://github.com/r-spatial/spatialreg/issues/23.
remaining users of run_perm() - localC(), localmoran_bv() and local_joincount_uni() get no_repeat_in_row= arguments.
Address 2) in #124; localG_perm() and localmoran_perm() get no_repeat_in_row= arguments to use conditional permutation without replacement by sample vectors; the default implementation uses sampling with replacement, which is acceptable across simulation draws, but arguably less acceptable within draws. Feedback would be valued.
Address 1) in #124; localG_perm() and localG() now return the same analytical standard deviates. The standard deviates from the simulated distributions are now returned in attr(., "internals")[,"StdDev.Gi"] from localG_perm(), as are p-values, etc.
move sp from Depends to Imports, to reduce the visual impression that sp objects are required for spdep; sf objects are now preferred, but sp objects can be used as before, although users may need to attach sp expliciitly.
fix #121 and #123; correcting returned values for localG_perm() when estimating the G-star measure (fix self x values and weights)
address #120, moving documentation of listw2U() from ?lm.morantest to ?nb2listw
addressing #119 for interpretation of moran_bv() results
adding #116, René Westerholt
fix #113, too low R version for grDevices::hcl.colors()
addressing #111 by Josiah Parry
PRs from René Westerholt, ending with #109, for the local GS measure
#103 refactoring local joincount test by Josiah Parry
add hotspot methods for localmoran (analytical, permutation, Saddlepoint and exact), localC (univariate and multivariate) and localG (analytical and permutation)
#95 add "two.sided" to lee.mc(), same for sp.mantel.mc(), EBImoran.mc(), joincount.mc(), geary.mc()
#92, #93, #94, #96, #97 contributions of prototype bivariate Moran, local bivariate Moran and local joincount and bivariate joincount tests by Josiah Parry
#91 tolerance.nb() update by F. Guillaume Blanchet
updating coercion for Matrix 1.4-2
fix ncpus issue in dontrun examples
remove suggested packages rgdal, rgeos, maptools
permit use of data.frame or tibble as matrix for functions creating neighbour objects from 2D points (preferred use an object inheriting from ``"SpatialPoints"or"sfc"`)
fix #87 wrong logic in infinite weights in nb2listwdist()
https://github.com/r-spatial/s2/pull/174 speeds up dnearneigh() for geographical coordinates without using s2::s2_closest_edges().
Adapting vignettes for absence of rgdal and maptools
added remove.self(), thanks to Josiah Parry #83.
unescape underscores in help pages.
replace deprecated S-compatibility macros DOUBLE_
#81 improved dnearneigh() help page.
#79 remove "htest" class from LOSH.mc() output object.
Added GA SI article to citations.
Replace rainbow() by hcl.colors(..., "Set 2") in plot.skater().
Add link to R-sig-geo thread on EBlocal() NaN estimates when many counts are zero on help page.
Revise and add documentation for object returned by localC_perm() #68 #72 #73 #74 #75 #76
localmoran.sad(), localmoran.exact() and localmoran.exact.alt() will now use multiple compute nodes if needed; if Omega is used, multiple cores may need more memory #77
For s2 > 1.0.7, use indexed distances in dnearneigh() https://github.com/r-spatial/s2/pull/162.
Recent changes in poly2nb() had reduced and most recently (1.1-8) removed the use of snap= in finding candidate neighbours; many thanks to Matilda Brown for a clear and well-documented issue #65
Add local Geary's C #66 thanks to Josiah Parry, discussion on further work on #68
localmoran_perm() returns both look-up and folded rank p-values
In poly2nb(), reverted removal of legacy interpreted overlapping envelope code for sp objects that cannot be coerced to sf without rgeos.
Add Fortran character handling USE_FC_LEN_T WRE §6.6.1.
Checks OK with forthcoming deldir 1.0-0.
Fixes #62 clarifying dnearneigh() help page
knearneigh() and nbdists(); added prototype adaptation to s2 for unprojected coordinates, used if sf_use_s2() is TRUE which became the default for sf 1.0.0 https://github.com/r-spatial/s2/issues/125. These are activated by default.
dnearneigh() can choose the prototype s2 approach if sf_use_s2() is TRUE and use_s2=TRUE for unprojected coordinates; from https://github.com/r-spatial/s2/issues/125 it seems that distance thresholds at present use brute-force rather than spatial indexing. Use is not activated by default.
poly2nb() now uses sf::st_intersects() to find candidate neighbours unless findInBounds= is not NULL. With spatial indexing, this is very fast and scales well for large data sets. If sf_use_s2() is TRUE, sf::st_intersects() passes the geometries to s2::s2_intersects_matrix(), which also uses spatial indexing and is very fast, scaling well for large data sets.
localmoran() and localmoran_perm() return cluster quadrants in an attribute for three splits, zeros, means and medians on the variable of interest and its spatial lag.
localmoran_perm() returns the skewness and kurtosis of the permutation samples.
#55 related to #20 and cycling order in setting up grids provoked re-design of interface to cell2nb(), with passing of "GridTopology" or "SpatialGrid" objects as unnamed first or x= argument. Coerce "RasterLayer" or similar raster, terra or stars objects to sp class objects first if need be.
In working with renewing the arguments to cell2nb(), it was useful to add tinytest support, which is now present for this function and may be extended to other functions for creating "nb" objects.
#58 contributed by Jeff Sauer and Levi Wolf (from https://doi.org/10.31219/osf.io/ugkhp) providing conditional standard deviates for local Moran's I
Error in assignment to matrix detected by CRAN check in SIDS vignette, section on median polish
Changes to continuous integration and vignettes.
Error in poly2nb(, queen=FALSE) in sf grids (double counting of closed polygon start/end points), https://github.com/r-spatial/spdep/issues/50, thanks to Christopher Kenny.
Adding local Moran and local G conditional permutation: localmoran_perm() and localG_perm().
Adding nb2listwdist() contributed by René Westerholt.
Adding use of sf through GEOS to find polygon contiguity candidates in poly2nb() if geometry count >= 500 - uses intersections in polygon envelopes.
#38, #53 removing RANN, adding dbscan suggestions for fast dnearneigh() and knearneigh() via use_kd_tree= argument for fast planar neighbour set finding in 2D and 3D. Affects soi.graph() too, which had used RANN.
#54 avoid partial matching in glist= handling.
Disambiguating spdep and spatialreg model output object class names prior to making spdep model fitting functions defunct.