Running examples in ‘netcom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: best_fit_optim
> ### Title: Empirical parameterization
> ### Aliases: best_fit_optim
> 
> ### ** Examples
> 
> # Import netcom
> library(netcom)
> 
> # Adjacency matrix
> size <- 10
> network <- matrix(sample(c(0,1), size = size^2, replace = TRUE), nrow = size, ncol = size)
> 
> # Calculate how similar the input network is to Small-World networks with 
> # a rewiring probability of 0.28.
> best_fit_optim(
+      parameter = 0.28, 
+      process = "SW", 
+      network = network, 
+      net_size = 12, 
+      net_kind = "matrix", 
+      mechanism_kind = "grow", 
+      resolution = 100, 
+      resolution_min = 0.01, 
+      resolution_max = 0.99, 
+      reps = 3, 
+      power_max = 5, 
+      connectance_max = 0.5, 
+      divergence_max = 0.5, 
+      mutation_max = 0.5, 
+      cores = 1, 
+      directed = TRUE, 
+      method = "DD", 
+      cause_orientation = "row", 
+      DD_kind = c(
+          "in", "out", "entropy_in", "entropy_out", 
+          "clustering_coefficient", "page_rank", "communities"
+      ), 
+      DD_weight = 1, 
+      max_norm = FALSE,
+      verbose = FALSE
+ )
Error in igraph::transitivity(igraph_graph, type = "weighted") : 
  At vendor/cigraph/src/properties/triangles.c:886 : Barrat's weighted transitivity measure works only if the graph has no multi-edges. Invalid value
Calls: best_fit_optim -> compare_Target -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 200-215 [Classify networks] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
At vendor/cigraph/src/properties/triangles.c:886 : Barrat's weighted transitivity measure works only if the graph has no multi-edges. Invalid value
--- failed re-building ‘tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘netcom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: best_fit_optim
> ### Title: Empirical parameterization
> ### Aliases: best_fit_optim
> 
> ### ** Examples
> 
> # Import netcom
> library(netcom)
> 
> # Adjacency matrix
> size <- 10
> network <- matrix(sample(c(0,1), size = size^2, replace = TRUE), nrow = size, ncol = size)
> 
> # Calculate how similar the input network is to Small-World networks with 
> # a rewiring probability of 0.28.
> best_fit_optim(
+      parameter = 0.28, 
+      process = "SW", 
+      network = network, 
+      net_size = 12, 
+      net_kind = "matrix", 
+      mechanism_kind = "grow", 
+      resolution = 100, 
+      resolution_min = 0.01, 
+      resolution_max = 0.99, 
+      reps = 3, 
+      power_max = 5, 
+      connectance_max = 0.5, 
+      divergence_max = 0.5, 
+      mutation_max = 0.5, 
+      cores = 1, 
+      directed = TRUE, 
+      method = "DD", 
+      cause_orientation = "row", 
+      DD_kind = c(
+          "in", "out", "entropy_in", "entropy_out", 
+          "clustering_coefficient", "page_rank", "communities"
+      ), 
+      DD_weight = 1, 
+      max_norm = FALSE,
+      verbose = FALSE
+ )
Error in igraph::transitivity(igraph_graph, type = "weighted") : 
  At vendor/cigraph/src/properties/triangles.c:885 : Barrat's weighted transitivity measure works only if the graph has no multi-edges. Invalid value
Calls: best_fit_optim -> compare_Target -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 200-215 [Classify networks] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
At vendor/cigraph/src/properties/triangles.c:885 : Barrat's weighted transitivity measure works only if the graph has no multi-edges. Invalid value
--- failed re-building ‘tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘ggraph’ ‘reshape2’
  All declared Imports should be used.
Running examples in ‘netcom-Ex.R’ failed
The error most likely occurred in:

> ### Name: best_fit_optim
> ### Title: Empirical parameterization
> ### Aliases: best_fit_optim
> 
> ### ** Examples
> 
> # Import netcom
> library(netcom)
> 
> # Adjacency matrix
> size <- 10
> network <- matrix(sample(c(0,1), size = size^2, replace = TRUE), nrow = size, ncol = size)
> 
> # Calculate how similar the input network is to Small-World networks with 
> # a rewiring probability of 0.28.
> best_fit_optim(
+      parameter = 0.28, 
+      process = "SW", 
+      network = network, 
+      net_size = 12, 
+      net_kind = "matrix", 
+      mechanism_kind = "grow", 
+      resolution = 100, 
+      resolution_min = 0.01, 
+      resolution_max = 0.99, 
+      reps = 3, 
+      power_max = 5, 
+      connectance_max = 0.5, 
+      divergence_max = 0.5, 
+      mutation_max = 0.5, 
+      cores = 1, 
+      directed = TRUE, 
+      method = "DD", 
+      cause_orientation = "row", 
+      DD_kind = c(
+          "in", "out", "entropy_in", "entropy_out", 
+          "clustering_coefficient", "page_rank", "communities"
+      ), 
+      DD_weight = 1, 
+      max_norm = FALSE,
+      verbose = FALSE
+ )
Error in igraph::transitivity(igraph_graph, type = "weighted") : 
  At vendor/cigraph/src/properties/triangles.c:886 : Barrat's weighted transitivity measure works only if the graph has no multi-edges. Invalid value
Calls: best_fit_optim -> compare_Target -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 200-215 [Classify networks] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
At vendor/cigraph/src/properties/triangles.c:886 : Barrat's weighted transitivity measure works only if the graph has no multi-edges. Invalid value
--- failed re-building ‘tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘ggraph’ ‘reshape2’
  All declared Imports should be used.
Running examples in ‘netcom-Ex.R’ failed
The error most likely occurred in:

> ### Name: best_fit_optim
> ### Title: Empirical parameterization
> ### Aliases: best_fit_optim
> 
> ### ** Examples
> 
> # Import netcom
> library(netcom)
> 
> # Adjacency matrix
> size <- 10
> network <- matrix(sample(c(0,1), size = size^2, replace = TRUE), nrow = size, ncol = size)
> 
> # Calculate how similar the input network is to Small-World networks with 
> # a rewiring probability of 0.28.
> best_fit_optim(
+      parameter = 0.28, 
+      process = "SW", 
+      network = network, 
+      net_size = 12, 
+      net_kind = "matrix", 
+      mechanism_kind = "grow", 
+      resolution = 100, 
+      resolution_min = 0.01, 
+      resolution_max = 0.99, 
+      reps = 3, 
+      power_max = 5, 
+      connectance_max = 0.5, 
+      divergence_max = 0.5, 
+      mutation_max = 0.5, 
+      cores = 1, 
+      directed = TRUE, 
+      method = "DD", 
+      cause_orientation = "row", 
+      DD_kind = c(
+          "in", "out", "entropy_in", "entropy_out", 
+          "clustering_coefficient", "page_rank", "communities"
+      ), 
+      DD_weight = 1, 
+      max_norm = FALSE,
+      verbose = FALSE
+ )
Error in igraph::transitivity(igraph_graph, type = "weighted") : 
  At vendor/cigraph/src/properties/triangles.c:885 : Barrat's weighted transitivity measure works only if the graph has no multi-edges. Invalid value
Calls: best_fit_optim -> compare_Target -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 200-215 [Classify networks] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
At vendor/cigraph/src/properties/triangles.c:885 : Barrat's weighted transitivity measure works only if the graph has no multi-edges. Invalid value
--- failed re-building ‘tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in 'netcom-Ex.R' failed
The error most likely occurred in:

> ### Name: best_fit_optim
> ### Title: Empirical parameterization
> ### Aliases: best_fit_optim
> 
> ### ** Examples
> 
> # Import netcom
> library(netcom)
> 
> # Adjacency matrix
> size <- 10
> network <- matrix(sample(c(0,1), size = size^2, replace = TRUE), nrow = size, ncol = size)
> 
> # Calculate how similar the input network is to Small-World networks with 
> # a rewiring probability of 0.28.
> best_fit_optim(
+      parameter = 0.28, 
+      process = "SW", 
+      network = network, 
+      net_size = 12, 
+      net_kind = "matrix", 
+      mechanism_kind = "grow", 
+      resolution = 100, 
+      resolution_min = 0.01, 
+      resolution_max = 0.99, 
+      reps = 3, 
+      power_max = 5, 
+      connectance_max = 0.5, 
+      divergence_max = 0.5, 
+      mutation_max = 0.5, 
+      cores = 1, 
+      directed = TRUE, 
+      method = "DD", 
+      cause_orientation = "row", 
+      DD_kind = c(
+          "in", "out", "entropy_in", "entropy_out", 
+          "clustering_coefficient", "page_rank", "communities"
+      ), 
+      DD_weight = 1, 
+      max_norm = FALSE,
+      verbose = FALSE
+ )
Error in igraph::transitivity(igraph_graph, type = "weighted") : 
  At vendor/cigraph/src/properties/triangles.c:885 : Barrat's weighted transitivity measure works only if the graph has no multi-edges. Invalid value
Calls: best_fit_optim -> compare_Target -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building 'tutorial.Rmd' using rmarkdown

Quitting from lines 200-215 [Classify networks] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
At vendor/cigraph/src/properties/triangles.c:885 : Barrat's weighted transitivity measure works only if the graph has no multi-edges. Invalid value
--- failed re-building 'tutorial.Rmd'

SUMMARY: processing the following file failed:
  'tutorial.Rmd'

Error: Vignette re-building failed.
Execution halted
Running examples in ‘netcom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: best_fit_optim
> ### Title: Empirical parameterization
> ### Aliases: best_fit_optim
> 
> ### ** Examples
> 
> # Import netcom
> library(netcom)
> 
> # Adjacency matrix
> size <- 10
> network <- matrix(sample(c(0,1), size = size^2, replace = TRUE), nrow = size, ncol = size)
> 
> # Calculate how similar the input network is to Small-World networks with 
> # a rewiring probability of 0.28.
> best_fit_optim(
+      parameter = 0.28, 
+      process = "SW", 
+      network = network, 
+      net_size = 12, 
+      net_kind = "matrix", 
+      mechanism_kind = "grow", 
+      resolution = 100, 
+      resolution_min = 0.01, 
+      resolution_max = 0.99, 
+      reps = 3, 
+      power_max = 5, 
+      connectance_max = 0.5, 
+      divergence_max = 0.5, 
+      mutation_max = 0.5, 
+      cores = 1, 
+      directed = TRUE, 
+      method = "DD", 
+      cause_orientation = "row", 
+      DD_kind = c(
+          "in", "out", "entropy_in", "entropy_out", 
+          "clustering_coefficient", "page_rank", "communities"
+      ), 
+      DD_weight = 1, 
+      max_norm = FALSE,
+      verbose = FALSE
+ )
Error in igraph::transitivity(igraph_graph, type = "weighted") : 
  At vendor/cigraph/src/properties/triangles.c:885 : Barrat's weighted transitivity measure works only if the graph has no multi-edges. Invalid value
Calls: best_fit_optim -> compare_Target -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 200-215 [Classify networks] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
At vendor/cigraph/src/properties/triangles.c:885 : Barrat's weighted transitivity measure works only if the graph has no multi-edges. Invalid value
--- failed re-building ‘tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘netcom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: best_fit_optim
> ### Title: Empirical parameterization
> ### Aliases: best_fit_optim
> 
> ### ** Examples
> 
> # Import netcom
> library(netcom)
> 
> # Adjacency matrix
> size <- 10
> network <- matrix(sample(c(0,1), size = size^2, replace = TRUE), nrow = size, ncol = size)
> 
> # Calculate how similar the input network is to Small-World networks with 
> # a rewiring probability of 0.28.
> best_fit_optim(
+      parameter = 0.28, 
+      process = "SW", 
+      network = network, 
+      net_size = 12, 
+      net_kind = "matrix", 
+      mechanism_kind = "grow", 
+      resolution = 100, 
+      resolution_min = 0.01, 
+      resolution_max = 0.99, 
+      reps = 3, 
+      power_max = 5, 
+      connectance_max = 0.5, 
+      divergence_max = 0.5, 
+      mutation_max = 0.5, 
+      cores = 1, 
+      directed = TRUE, 
+      method = "DD", 
+      cause_orientation = "row", 
+      DD_kind = c(
+          "in", "out", "entropy_in", "entropy_out", 
+          "clustering_coefficient", "page_rank", "communities"
+      ), 
+      DD_weight = 1, 
+      max_norm = FALSE,
+      verbose = FALSE
+ )
Error in igraph::transitivity(igraph_graph, type = "weighted") : 
  At vendor/cigraph/src/properties/triangles.c:885 : Barrat's weighted transitivity measure works only if the graph has no multi-edges. Invalid value
Calls: best_fit_optim -> compare_Target -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Quitting from lines 200-215 [Classify networks] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
At vendor/cigraph/src/properties/triangles.c:885 : Barrat's weighted transitivity measure works only if the graph has no multi-edges. Invalid value
--- failed re-building ‘tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in 'netcom-Ex.R' failed
The error most likely occurred in:

> ### Name: best_fit_optim
> ### Title: Empirical parameterization
> ### Aliases: best_fit_optim
> 
> ### ** Examples
> 
> # Import netcom
> library(netcom)
> 
> # Adjacency matrix
> size <- 10
> network <- matrix(sample(c(0,1), size = size^2, replace = TRUE), nrow = size, ncol = size)
> 
> # Calculate how similar the input network is to Small-World networks with 
> # a rewiring probability of 0.28.
> best_fit_optim(
+      parameter = 0.28, 
+      process = "SW", 
+      network = network, 
+      net_size = 12, 
+      net_kind = "matrix", 
+      mechanism_kind = "grow", 
+      resolution = 100, 
+      resolution_min = 0.01, 
+      resolution_max = 0.99, 
+      reps = 3, 
+      power_max = 5, 
+      connectance_max = 0.5, 
+      divergence_max = 0.5, 
+      mutation_max = 0.5, 
+      cores = 1, 
+      directed = TRUE, 
+      method = "DD", 
+      cause_orientation = "row", 
+      DD_kind = c(
+          "in", "out", "entropy_in", "entropy_out", 
+          "clustering_coefficient", "page_rank", "communities"
+      ), 
+      DD_weight = 1, 
+      max_norm = FALSE,
+      verbose = FALSE
+ )
Error in igraph::transitivity(igraph_graph, type = "weighted") : 
  At vendor/cigraph/src/properties/triangles.c:885 : Barrat's weighted transitivity measure works only if the graph has no multi-edges. Invalid value
Calls: best_fit_optim -> compare_Target -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building 'tutorial.Rmd' using rmarkdown

Quitting from lines 200-215 [Classify networks] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
At vendor/cigraph/src/properties/triangles.c:885 : Barrat's weighted transitivity measure works only if the graph has no multi-edges. Invalid value
--- failed re-building 'tutorial.Rmd'

SUMMARY: processing the following file failed:
  'tutorial.Rmd'

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘ggraph’ ‘reshape2’
  All declared Imports should be used.
Running examples in 'netcom-Ex.R' failed
The error most likely occurred in:

> ### Name: best_fit_optim
> ### Title: Empirical parameterization
> ### Aliases: best_fit_optim
> 
> ### ** Examples
> 
> # Import netcom
> library(netcom)
> 
> # Adjacency matrix
> size <- 10
> network <- matrix(sample(c(0,1), size = size^2, replace = TRUE), nrow = size, ncol = size)
> 
> # Calculate how similar the input network is to Small-World networks with 
> # a rewiring probability of 0.28.
> best_fit_optim(
+      parameter = 0.28, 
+      process = "SW", 
+      network = network, 
+      net_size = 12, 
+      net_kind = "matrix", 
+      mechanism_kind = "grow", 
+      resolution = 100, 
+      resolution_min = 0.01, 
+      resolution_max = 0.99, 
+      reps = 3, 
+      power_max = 5, 
+      connectance_max = 0.5, 
+      divergence_max = 0.5, 
+      mutation_max = 0.5, 
+      cores = 1, 
+      directed = TRUE, 
+      method = "DD", 
+      cause_orientation = "row", 
+      DD_kind = c(
+          "in", "out", "entropy_in", "entropy_out", 
+          "clustering_coefficient", "page_rank", "communities"
+      ), 
+      DD_weight = 1, 
+      max_norm = FALSE,
+      verbose = FALSE
+ )
Error in igraph::transitivity(igraph_graph, type = "weighted") : 
  At vendor/cigraph/src/properties/triangles.c:885 : Barrat's weighted transitivity measure works only if the graph has no multi-edges. Invalid value
Calls: best_fit_optim -> compare_Target -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building 'tutorial.Rmd' using rmarkdown

Quitting from lines 200-215 [Classify networks] (tutorial.Rmd)
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
At vendor/cigraph/src/properties/triangles.c:885 : Barrat's weighted transitivity measure works only if the graph has no multi-edges. Invalid value
--- failed re-building 'tutorial.Rmd'

SUMMARY: processing the following file failed:
  'tutorial.Rmd'

Error: Vignette re-building failed.
Execution halted