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.