R Under development (unstable) (2025-11-25 r89063) -- "Unsuffered Consequences"
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> pkgname <- "iglm"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> library('iglm')
Loading required package: RcppProgress
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
> nameEx("count_statistics")
> ### * count_statistics
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: count_statistics
> ### Title: Compute Statistics
> ### Aliases: count_statistics
> 
> ### ** Examples
> 
> # Create a iglm.data object
> n_actors = 10
> neighborhood = matrix(1, nrow = n_actors, ncol = n_actors)
> type_x <- "binomial"
> type_y <- "binomial"
> x_attr_data <- rbinom(n_actors, 1, 0.5)
> y_attr_data <- rbinom(n_actors, 1, 0.5)
> z_net_data  <- matrix(0, nrow = n_actors, ncol = n_actors) 
> object = iglm.data(z_network = z_net_data, x_attribute = x_attr_data,
+  y_attribute = y_attr_data, neighborhood = neighborhood,
+  directed = FALSE,type_x = type_x,type_y = type_y)
> count_statistics(object ~ edges(mode = "local") + attribute_y + attribute_x)
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/subview_meat.hpp:1413:54: runtime error: reference binding to null pointer of type 'const double'
    #0 0x7bc05e849c49 in arma::subview<double>::colptr(unsigned long long) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/subview_meat.hpp:1413
    #1 0x7bc05e849c49 in arma::subview_col<double>::subview_col(arma::Mat<double> const&, unsigned long long) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/subview_meat.hpp:3267
    #2 0x7bc05e6da747 in arma::Mat<double>::col(unsigned long long) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:3450
    #3 0x7bc05e6da747 in mat_to_map(arma::Mat<double>, int, bool, std::unordered_map<int, std::unordered_set<int, std::hash<int>, std::equal_to<int>, std::allocator<int> >, std::hash<int>, std::equal_to<int>, std::allocator<std::pair<int const, std::unordered_set<int, std::hash<int>, std::equal_to<int>, std::allocator<int> > > > >&, std::unordered_map<int, std::unordered_set<int, std::hash<int>, std::equal_to<int>, std::allocator<int> >, std::hash<int>, std::equal_to<int>, std::allocator<std::pair<int const, std::unordered_set<int, std::hash<int>, std::equal_to<int>, std::allocator<int> > > > >&) ../inst/include/iglm/helper_functions.h:101
    #4 0x7bc05e6f1acb in Network::Network(int, bool, arma::Mat<double>) ../inst/include/iglm/network_class.h:35
    #5 0x7bc05e6f1acb in XZ_class::XZ_class(int, bool, arma::Mat<double>, arma::Col<double>, arma::Mat<double>, arma::Mat<double>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double) ../inst/include/iglm/xz_class.h:97
    #6 0x7bc05e6f1acb in XYZ_class::XYZ_class(int, bool, arma::Col<double>, arma::Col<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, double) ../inst/include/iglm/xyz_class.h:40
    #7 0x7bc05e6fd7f3 in xyz_count_global(arma::Mat<double>, arma::Col<double>, arma::Col<double>, arma::Mat<double>, arma::Mat<double>, bool, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, int, std::vector<arma::Mat<double>, std::allocator<arma::Mat<double> > >&, std::vector<double, std::allocator<double> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, double) /data/gannet/ripley/R/packages/tests-gcc-SAN/iglm/src/xyz_sampling.cpp:224
    #8 0x7bc05e5cbc91 in _iglm_xyz_count_global /data/gannet/ripley/R/packages/tests-gcc-SAN/iglm/src/RcppExports.cpp:43
    #9 0x00000074b9f5 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:813
    #10 0x0000008e26ca in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8664
    #11 0x0000008b8f0b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497
    #12 0x000000859282 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #13 0x00000086efca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389
    #14 0x00000087308a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302
    #15 0x000000859923 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324
    #16 0x000000859923 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280
    #17 0x0000009ff648 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264
    #18 0x0000009ff648 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317
    #19 0x000000a04a7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235
    #20 0x000000a0ec92 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242
    #21 0x00000041318f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #22 0x7fc07a8115f4 in __libc_start_call_main (/lib64/libc.so.6+0x35f4) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03)
    #23 0x7fc07a8116a7 in __libc_start_main@@GLIBC_2.34 (/lib64/libc.so.6+0x36a7) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03)
    #24 0x000000413b54 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413b54) (BuildId: d72f18244a1aebdcb6b557766816e31e8f422f5c)

/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/access.hpp:26:100: runtime error: reference binding to null pointer of type 'double'
    #0 0x7bc05e849af1 in double& arma::access::rw<double>(double const&) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/access.hpp:26
    #1 0x7bc05e849af1 in arma::subview<double>::colptr(unsigned long long) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/subview_meat.hpp:1413
    #2 0x7bc05e849af1 in arma::subview_col<double>::subview_col(arma::Mat<double> const&, unsigned long long) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/subview_meat.hpp:3267
    #3 0x7bc05e6da747 in arma::Mat<double>::col(unsigned long long) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:3450
    #4 0x7bc05e6da747 in mat_to_map(arma::Mat<double>, int, bool, std::unordered_map<int, std::unordered_set<int, std::hash<int>, std::equal_to<int>, std::allocator<int> >, std::hash<int>, std::equal_to<int>, std::allocator<std::pair<int const, std::unordered_set<int, std::hash<int>, std::equal_to<int>, std::allocator<int> > > > >&, std::unordered_map<int, std::unordered_set<int, std::hash<int>, std::equal_to<int>, std::allocator<int> >, std::hash<int>, std::equal_to<int>, std::allocator<std::pair<int const, std::unordered_set<int, std::hash<int>, std::equal_to<int>, std::allocator<int> > > > >&) ../inst/include/iglm/helper_functions.h:101
    #5 0x7bc05e6f1acb in Network::Network(int, bool, arma::Mat<double>) ../inst/include/iglm/network_class.h:35
    #6 0x7bc05e6f1acb in XZ_class::XZ_class(int, bool, arma::Mat<double>, arma::Col<double>, arma::Mat<double>, arma::Mat<double>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double) ../inst/include/iglm/xz_class.h:97
    #7 0x7bc05e6f1acb in XYZ_class::XYZ_class(int, bool, arma::Col<double>, arma::Col<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, double) ../inst/include/iglm/xyz_class.h:40
    #8 0x7bc05e6fd7f3 in xyz_count_global(arma::Mat<double>, arma::Col<double>, arma::Col<double>, arma::Mat<double>, arma::Mat<double>, bool, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, int, std::vector<arma::Mat<double>, std::allocator<arma::Mat<double> > >&, std::vector<double, std::allocator<double> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, double) /data/gannet/ripley/R/packages/tests-gcc-SAN/iglm/src/xyz_sampling.cpp:224
    #9 0x7bc05e5cbc91 in _iglm_xyz_count_global /data/gannet/ripley/R/packages/tests-gcc-SAN/iglm/src/RcppExports.cpp:43
    #10 0x00000074b9f5 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:813
    #11 0x0000008e26ca in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8664
    #12 0x0000008b8f0b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497
    #13 0x000000859282 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #14 0x00000086efca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389
    #15 0x00000087308a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302
    #16 0x000000859923 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324
    #17 0x000000859923 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280
    #18 0x0000009ff648 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264
    #19 0x0000009ff648 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317
    #20 0x000000a04a7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235
    #21 0x000000a0ec92 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242
    #22 0x00000041318f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #23 0x7fc07a8115f4 in __libc_start_call_main (/lib64/libc.so.6+0x35f4) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03)
    #24 0x7fc07a8116a7 in __libc_start_main@@GLIBC_2.34 (/lib64/libc.so.6+0x36a7) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03)
    #25 0x000000413b54 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413b54) (BuildId: d72f18244a1aebdcb6b557766816e31e8f422f5c)

edges(mode = 'local')           attribute_y           attribute_x 
                    0                     5                     6 
> 
> 
> 
> cleanEx()
> nameEx("iglm")
> ### * iglm
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: iglm
> ### Title: Construct a iglm Model Specification Object
> ### Aliases: iglm iglm_object
> 
> ### ** Examples
> 
> # Example usage:
> library(iglm)
> # Create a iglm.data data object (example)
> n_actors <- 50
> neighborhood <- matrix(1, nrow = n_actors, ncol = n_actors)
> xyz_obj <- iglm.data(neighborhood = neighborhood, directed = FALSE,
+                    type_x = "binomial", type_y = "binomial")
> # Define ground truth coefficients
> gt_coef <- c("edges_local" = 3, "attribute_y" = -1, "attribute_x" = -1)
> gt_coef_pop <- rnorm(n = n_actors, -2, 1)
> # Define MCMC sampler
> sampler_new <- sampler.iglm(n_burn_in = 100, n_simulation = 10,
+                                sampler.x = sampler.net_attr(n_proposals = n_actors * 10, seed = 13),
+                                sampler.y = sampler.net_attr(n_proposals = n_actors * 10, seed = 32),
+                                sampler.z = sampler.net_attr(n_proposals = sum(neighborhood > 0
+                                ) * 10, seed = 134),
+                                init_empty = FALSE)
> # Create iglm model specification
> model_tmp_new <- iglm(formula = xyz_obj ~ edges(mode = "local") +
+                           attribute_y + attribute_x + popularity,
+                           coef = gt_coef,
+                           coef_popularity = gt_coef_pop,
+                           sampler = sampler_new,
+                           control = control.iglm(accelerated = FALSE,
+                           max_it = 200, display_progress = FALSE, var = TRUE))
> # Simulate from the model
> model_tmp_new$simulate()
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
> model_tmp_new$set_target(model_tmp_new$get_samples()[[1]])
> 
> # Estimate model parameters
> model_tmp_new$estimate()
> 
> # Model Assessment
> model_tmp_new$model_assessment(formula = ~  degree_distribution )
> # model_tmp_new$results$plot(model_assessment = TRUE)
>                                                    
> 
> 
> 
> cleanEx()
> nameEx("iglm.data")
> ### * iglm.data
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: iglm.data
> ### Title: Constructor for the iglm.data R6 object
> ### Aliases: iglm.data
> 
> ### ** Examples
> 
> data(state_twitter)
> state_twitter$iglm.data$degree_distribution(prob = FALSE, plot = TRUE)
> state_twitter$iglm.data$geodesic_distances_distribution(prob = FALSE, plot = TRUE)
> state_twitter$iglm.data$density_x()
> state_twitter$iglm.data$density_y()
> 
> # Generate a small iglm data object either via adjacency matrix or edgelist
> tmp_adjacency <- iglm.data(z_network = matrix(c(0,1,1,0,
+                                                 1,0,0,1,
+                                                 1,0,0,1,
+                                                 0,1,1,0), nrow=4, byrow=TRUE),
+                            directed = FALSE,
+                            n_actor = 4,
+                            type_x = "binomial",
+                            type_y = "binomial")
> 
> 
> tmp_edgelist <- iglm.data(z_network = tmp_adjacency$z_network, 
+                           directed = FALSE,
+                        n_actor = 4,
+                        type_x = "binomial",
+                        type_y = "binomial")
> 
> tmp_edgelist$density_z()
> tmp_adjacency$density_z()
> 
> 
> 
> cleanEx()
> nameEx("sampler.iglm")
> ### * sampler.iglm
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: sampler.iglm
> ### Title: Constructor for a iglm Sampler
> ### Aliases: sampler.iglm
> 
> ### ** Examples
> 
> n_actors <- 50
> sampler_new <- sampler.iglm(n_burn_in = 100, n_simulation = 10,
+                                sampler.x = sampler.net_attr(n_proposals = n_actors * 10, seed = 13),
+                                sampler.y = sampler.net_attr(n_proposals = n_actors * 10, seed = 32),
+                                sampler.z = sampler.net_attr(n_proposals = n_actors^2, seed = 134),
+                                init_empty = FALSE)
> sampler_new
Sampler settings
------------------------------------------------------------
Core parameters
  n_simulation :10
  n_burn_in    :100
  init_empty   :FALSE
  gibbs        :FALSE

Sub-samplers
  sampler.x:
    Number of proposals : 500
    Random seed         : 13
  sampler.y:
    Number of proposals : 500
    Random seed         : 32
  sampler.z:
    Number of proposals : 2500
    Random seed         : 134
> # Change some values of the  sampler 
> sampler_new$n_simulation                                
[1] 10
> sampler_new$set_n_simulation(100)
> sampler_new$n_simulation                                
[1] 100
> 
> 
> 
> cleanEx()
> nameEx("sampler.net_attr")
> ### * sampler.net_attr
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: sampler.net_attr
> ### Title: Constructor for Single Component Sampler Settings
> ### Aliases: sampler.net_attr
> 
> ### ** Examples
> 
> # Default settings
> sampler_comp_default <- sampler.net_attr()
> sampler_comp_default
  Number of proposals : 10000
  Random seed         : 548676
> 
> # Custom settings
> sampler_comp_custom <- sampler.net_attr(n_proposals = 50000, seed = 123)
> sampler_comp_custom
  Number of proposals : 50000
  Random seed         : 123
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  44.5 1.261 46.497 0 0 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')