fdapde/fdapde-r

The R wrapper to the fdaPDE library for physics-informed spatial and functional data analysis.

fdaPDE-R

The R wrapper to the fdaPDE library

fdapde-r's Issues

package fail to install on mac-os systems (`apple-clang`)

Installing the R package on a mac-os system makes the compilation fail. Error reported:

In file included from R_Model.cpp:23:
   In file included from fdaPDE/fdaPDE/models.h:20:
   In file included from fdaPDE/fdaPDE/models/model_base.h:20:
   In file included from fdaPDE/fdaPDE/core/fdaPDE/mesh.h:20:
   fdaPDE/fdaPDE/core/fdaPDE/mesh/mesh.h:202:56: error: declaration of 'N' shadows template parameter
       static constexpr bool is_manifold = is_manifold<M, N>::value;
                                                          ^
   fdaPDE/fdaPDE/core/fdaPDE/mesh/mesh.h:59:22: note: template parameter is declared here
   template <int M, int N> class Mesh {
                        ^
   fdaPDE/fdaPDE/core/fdaPDE/mesh/mesh.h:202:56: error: default initialization of an object of const type 'const bool'
       static constexpr bool is_manifold = is_manifold<M, N>::value;
                                                          ^
                                                            = false
   fdaPDE/fdaPDE/core/fdaPDE/mesh/mesh.h:202:57: error: expected ';' at end of declaration list
       static constexpr bool is_manifold = is_manifold<M, N>::value;
                                                           ^
                                                           ;
   In file included from R_Model.cpp:23:
   In file included from fdaPDE/fdaPDE/models.h:20:
   In file included from fdaPDE/fdaPDE/models/model_base.h:21:
   In file included from fdaPDE/fdaPDE/core/fdaPDE/utils.h:24:
   fdaPDE/fdaPDE/core/fdaPDE/utils/type_erasure.h:222:28: error: use 'template' keyword to treat 'fn_ptrs' as a dependent template name
           size_ = (size<typename I::fn_ptrs<T_>>::value + ...);
                                     ^
                                     template 
   fdaPDE/fdaPDE/core/fdaPDE/utils/type_erasure.h:225:55: error: use 'template' keyword to treat 'fn_ptrs' as a dependent template name
           init_vtable<0, T_>(typename merge<typename I::fn_ptrs<T_>...>::type(), vtable_);
                                                         ^
                                                         template 
   fdaPDE/fdaPDE/core/fdaPDE/utils/type_erasure.h:230:67: error: use 'template' keyword to treat 'fn_ptrs' as a dependent template name
               base_ += size<typename std::decay<decltype(i)>::type::fn_ptrs<T_>>::value;
                                                                     ^
                                                                     template 
   In file included from R_Model.cpp:23:
   In file included from fdaPDE/fdaPDE/models.h:20:
   In file included from fdaPDE/fdaPDE/models/model_base.h:22:
   In file included from fdaPDE/fdaPDE/core/fdaPDE/pde.h:20:
   In file included from fdaPDE/fdaPDE/core/fdaPDE/pde/pde.h:29:
   fdaPDE/fdaPDE/core/fdaPDE/pde/differential_operators.h:48:51: error: template template argument has different template parameters than its corresponding template template parameter
       static constexpr bool value = has_instance_of<dT, decltype(std::declval<E>().get_operator_type())>::value;
                                                     ^
   fdaPDE/fdaPDE/core/fdaPDE/pde/differential_operators.h:36:1: note: too many template parameters in template template argument
   FDAPDE_DEFINE_DIFFERENTIAL_OPERATOR(dT,          dt         );
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   fdaPDE/fdaPDE/core/fdaPDE/pde/differential_operators.h:28:5: note: expanded from macro 'FDAPDE_DEFINE_DIFFERENTIAL_OPERATOR'
       template <typename T, typename... Ts> class OP { };                                                                \
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   fdaPDE/fdaPDE/core/fdaPDE/utils/traits.h:58:11: note: previous template template parameter is here
   template <template <typename F> typename E, typename Tuple> struct has_instance_of { };
             ^~~~~~~~~~~~~~~~~~~~~
   In file included from R_Model.cpp:23:
   In file included from fdaPDE/fdaPDE/models.h:20:
   In file included from fdaPDE/fdaPDE/models/model_base.h:22:
   In file included from fdaPDE/fdaPDE/core/fdaPDE/pde.h:20:
   In file included from fdaPDE/fdaPDE/core/fdaPDE/pde/pde.h:29:
   fdaPDE/fdaPDE/core/fdaPDE/pde/differential_operators.h:48:27: error: default initialization of an object of const type 'const bool'
       static constexpr bool value = has_instance_of<dT, decltype(std::declval<E>().get_operator_type())>::value;
                             ^
                                   = false

Problem seems related to some apple-clang aspects which are ignored when compiling with gcc.

Compiler details:

─  installing source package ‘fdaPDE2’ ...
   ** using staged installation
   ** libs
   using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
   using C++17
   using SDK: ‘MacOSX14.0.sdk’

`optimizer = "bfgs"` causes segfault in GCV lambda selection

When using BFGS as optimization method, the R wrapper crashes with cause 'memory not mapped'

MWE

data("unit_square", package = "fdaPDE2")
unit_square <- Mesh(unit_square)
df <- ## some data...

model <- SRPDE(y ~ f, domain = unit_square, data = df)
## fit with BFGS optimization
model$fit(lambda = gcv(
    optimizer = "bfgs",
    lambda = 1e-4,
    step = 1e-6
))

The problem is releated to the R wrapper, as performing a BFGS optimization of the GCV from the C++ layer does not cause any segfault.

You can reproduce the test gcv_srpde_newton_test, laplacian_nonparametric_samplingatnodes_newton_fd_exact with BFGS in place of Netwon, and obtain the correct result using a wolfe line search approach for the adaptive step.

auto GCV = model.gcv<ExactEDF>();
GCV.set_step(4e-08);
// optimize GCV
BFGS<fdapde::Dynamic> opt(10, 0.05, 1);
DVector<double> pt = SVector<1>(6.25e-06);
opt.optimize(GCV, pt, WolfeLineSearch());

Missing expected type for the first argument of function FunctionSpace()

FunctionSpace() does not complain when an object of a type different from MeshObject is passed as the first argument. Instead, it returns an error that is not clear.

Code

library(fdaPDE2)

data("unit_square", package = "fdaPDE2")
domain <- Mesh(unit_square)

Vh <- FunctionSpace(domain, fe_order = 1)

Error

> data("unit_square", package = "fdaPDE2")
> domain <- Mesh(unit_square)
> 
> ## the functional space of finite element functions of order 1, over the unit square
> Vh <- FunctionSpace(unit_square, fe_order = 1)
Error in eval(parse(text = paste("cpp_lagrange_basis_", mesh$domain_type,  : 
  object 'cpp_lagrange_basis__fe1' not found

Add support for standardized and well-known input data format (stop using `matrix` everywhere!)

fdaPDE must be able to support many different data format as input, well established in the R language and scientific community. Is quiet annoying to input data in low-level matrix or array data formats. This is true for statistical data, but also for the domain geometry (this is a critical aspect which must be fixed sooner or later).

This issue wants to keep a list of all data format we should (or wish) support to enhance the fdaPDE usage. Each iter reports the data format, its supporting R package and possibly some specific documentation:

• netCDF: widely used format for exchanging or distributing climate data, and has also been adopted in other fields, particularly in bioinformatics, and in other disciplines where large multidimensional arrays of data are generated (https://pjbartlein.github.io/REarthSysSci/netCDF.html). Supporting packages: ncdf4, raster.
• raster: a raster is a spatial (geographic) data structure that divides a region into rectangles called “cells” (or “pixels”) that can store one or more values for each of these cells. (https://cran.r-project.org/web/packages/raster/raster.pdf). Supporting packages: raster, terra (https://github.com/rspatial/terra)
• data.frame: data frames are one of the basic dataset structures for the R language. Also support for modern packages like tibble would be nice (https://tibble.tidyverse.org/).