spatstat/s2

R bindings for Google's s2 library for geometry on the sphere

spatstat

What is spatstat?

spatstat is a family of R packages for analysing spatial point pattern data (and other kinds of spatial data). It has extensive capabilities for exploratory analysis, statistical modelling, simulation and statistical inference.

See the website www.spatstat.org or read the book.

spatstat has been split into a family of packages

Originally there was a single package called spatstat. It grew so large that CRAN required us to split it into pieces.

The original spatstat has now been divided into a family of sub-packages:

Sub-package	CRAN page	GitHub repository	Description
spatstat.utils			Basic utilities
spatstat.data			Datasets
spatstat.sparse			Sparse arrays
spatstat.geom			Spatial data classes; geometrical operations
spatstat.random			Generation of random patterns
spatstat.explore			Exploratory Data Analysis of spatial data
spatstat.model			Parametric modelling and formal inference for spatial data
spatstat.linnet			Spatial analysis on a linear network
spatstat			Umbrella package

Click the green badge to visit the CRAN page which contains the current release of each sub-package. Click the blue badge to visit the GitHub repository for the current development version of the sub-package.

There still exists a package called spatstat, which is now an umbrella package that requires all the sub-packages listed above.

You can install and load the new spatstat family in virtually the same way as you would previously have installed and loaded the old spatstat package. When you install the new umbrella package spatstat, all the sub-packages listed above will be installed. When you load the new umbrella spatstat package in an R session, all the sub-packages listed above will be loaded or imported.

Extension packages

Additionally there are extension packages which contain more functionality. These packages are not automatically installed or loaded; the user must do that if these extra features are desired.

Extension package	CRAN page	GitHub repository	Description
spatstat.gui			Graphical interface
spatstat.Knet			linear networks
spatstat.local			Local (geographically weighted) models
spatstat.sphere	Not yet published		Spherical data

Family portrait

The pink box marked spatstat contains all the code that will be installed when you install the spatstat umbrella package, and loaded or imported when you load the spatstat umbrella package.

The blue boxes are extension packages which must be installed and loaded separately.

Future development

spatstat is the result of 30 years of software development and contains over 180,000 lines of code. It is still under development, motivated by the needs of researchers in many fields, and driven by innovations in statistical science. We welcome contributions of code, and suggestions for improvements.

s2's Issues

Linking to openssl 1.1 on Debian not working

The package doesn't compile on Debian with openssl 1.1 which can be tested with rhub::check (with the root of the s2 package as current working directory):

rhub::check(platform = "debian-gcc-devel")

The problem arises when exactfloat.cc is compiled

g++ -std=gnu++11 -I/opt/R-devel/lib/R/include -DNDEBUG -DS2_USE_EXACTFLOAT -DHASH_NAMESPACE=std -DNDEBUG -I./geometry -I./geometry/s2 -I/usr/local/include -I"/home/docker/R/Rcpp/include"  -pthread -fpic  -Wall -pedantic -c geometry/util/math/exactfloat/exactfloat.cc -o geometry/util/math/exactfloat/exactfloat.o
In file included from geometry/util/math/exactfloat/exactfloat.cc:3:0:
./geometry/util/math/exactfloat/exactfloat.h:502:10: error: field ‘bn_’ has incomplete type ‘BIGNUM {aka bignum_st}’
   BIGNUM bn_;
          ^~~
In file included from /usr/include/openssl/bn.h:32:0,
                 from ./geometry/util/math/exactfloat/exactfloat.h:108,
                 from geometry/util/math/exactfloat/exactfloat.cc:3:
/usr/include/openssl/ossl_typ.h:80:16: note: forward declaration of ‘BIGNUM {aka struct bignum_st}’
 typedef struct bignum_st BIGNUM;
                ^~~~~~~~~
In file included from geometry/util/math/exactfloat/exactfloat.cc:3:0:
./geometry/util/math/exactfloat/exactfloat.h: In constructor ‘ExactFloat::ExactFloat()’:
./geometry/util/math/exactfloat/exactfloat.h:562:15: error: ‘BN_init’ was not declared in this scope
   BN_init(&bn_);
               ^
geometry/util/math/exactfloat/exactfloat.cc: In function ‘int BN_ext_count_low_zero_bits(const BIGNUM*)’:
geometry/util/math/exactfloat/exactfloat.cc:75:25: error: invalid use of incomplete type ‘const BIGNUM {aka const struct bignum_st}’
   for (int i = 0; i < bn->top; ++i) {
                         ^~
In file included from /usr/include/openssl/bn.h:32:0,
                 from ./geometry/util/math/exactfloat/exactfloat.h:108,
                 from geometry/util/math/exactfloat/exactfloat.cc:3:
/usr/include/openssl/ossl_typ.h:80:16: note: forward declaration of ‘BIGNUM {aka struct bignum_st}’
 typedef struct bignum_st BIGNUM;
                ^~~~~~~~~
geometry/util/math/exactfloat/exactfloat.cc:76:20: error: invalid use of incomplete type ‘const BIGNUM {aka const struct bignum_st}’
     BN_ULONG w = bn->d[i];
                    ^~
In file included from /usr/include/openssl/bn.h:32:0,
                 from ./geometry/util/math/exactfloat/exactfloat.h:108,
                 from geometry/util/math/exactfloat/exactfloat.cc:3:
/usr/include/openssl/ossl_typ.h:80:16: note: forward declaration of ‘BIGNUM {aka struct bignum_st}’
 typedef struct bignum_st BIGNUM;
                ^~~~~~~~~
geometry/util/math/exactfloat/exactfloat.cc: In constructor ‘ExactFloat::ExactFloat(double)’:
geometry/util/math/exactfloat/exactfloat.cc:90:15: error: ‘BN_init’ was not declared in this scope
   BN_init(&bn_);
               ^
geometry/util/math/exactfloat/exactfloat.cc: In constructor ‘ExactFloat::ExactFloat(int)’:
geometry/util/math/exactfloat/exactfloat.cc:113:15: error: ‘BN_init’ was not declared in this scope
   BN_init(&bn_);
               ^
geometry/util/math/exactfloat/exactfloat.cc: In copy constructor ‘ExactFloat::ExactFloat(const ExactFloat&)’:
geometry/util/math/exactfloat/exactfloat.cc:125:15: error: ‘BN_init’ was not declared in this scope
   BN_init(&bn_);
               ^

Adding AppendAllNeighbors functionality

Thank you for this package. Thus far I have used it for pretty basic grouping of spatial points. I'm now trying to apply spatial operations (distances calculations etc.) on a global dataset, where the comparisons are only important for points within the vicinity of one another. I would like to perform an initial join using neighboring s2cells and then apply the spatial calculations just for those points in neighboring s2cells. I had a quick look and I didn't seen an implementation of AppendAllNeighbors in the package. Is there any thought to adding this or any of the neighbor functions (GetEdgeNeighbors, GetVertexNeighbors)? That would be incredibly useful.

CPPFLAGS vs CXXFLAGS

From your Makevars files it seems you are confusing CPPFLAGS with CXXFLAGS / CXX1XFLAGS.

• CPPFLAGS: C/C++ preprocessor flags. These are applied both to c and c++ preprocessor. Usually this only includes flags that start with -D and -I.
• CFLAGS / CXXFLAGS / CXX1XFLAGS: Compiler flags for the c/c++/c++11 compiler that are not in the preprocessor. Things like -g -o -pthread. You should rarely set these as R automatically uses the appropriate defaults.

As a package author you do not have to manually pass any CXXFLAGS or CXX1X flags in your Makevars. R does that automatically: c++ code is always compiled with CXXFLAGS (or CXX1XFLAGS when CXX_STD = CXX11)

Hence the configure script should only set the CPPFLAGS which are system dependent based on how libssl was compiled and where it resides on the user system.

Google's S2 Repo

I think Google have updated / released their s2 repo and are now maintaining it

• Blog post announcing it: https://opensource.googleblog.com/2017/12/announcing-s2-library-geometry-on-sphere.html
• homepage: https://opensource.googleblog.com/2017/12/announcing-s2-library-geometry-on-sphere.html
• source code: https://github.com/google/s2geometry

Is it worth moving to this one, rather than the fork of the older one that's no longer maintained?

S2CellIdFromLatLng method is missing

Hello,
I have forked the project and added the code to support the S2CellIdFromLatLng.
Is there any instructions or script for making the package/library?

Thank you in advance.