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 match.arg(arg = arg, choices = choices, several.ok = several.ok) : 
  'arg' must be of length 1
Calls: best_fit_optim ... compare_Target -> <Anonymous> -> igraph.match.arg -> match.arg
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'tutorial.Rmd' using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: Matrix

Attaching package: 'expm'

The following object is masked from 'package:Matrix':

    expm


Attaching package: 'igraph'

The following objects are masked from 'package:dplyr':

    as_data_frame, groups, union

The following object is masked from 'package:tibble':

    as_data_frame

The following object is masked from 'package:netcom':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Quitting from lines 200-215 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
'arg' must be of length 1
--- 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 match.arg(arg = arg, choices = choices, several.ok = several.ok) : 
  'arg' must be of length 1
Calls: best_fit_optim ... compare_Target -> <Anonymous> -> igraph.match.arg -> match.arg
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: Matrix

Attaching package: 'expm'

The following object is masked from 'package:Matrix':

    expm


Attaching package: 'igraph'

The following objects are masked from 'package:dplyr':

    as_data_frame, groups, union

The following object is masked from 'package:tibble':

    as_data_frame

The following object is masked from 'package:netcom':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Quitting from lines 200-215 (tutorial.Rmd) 
Error: processing vignette ‘tutorial.Rmd’ failed with diagnostics:
‘arg’ must be of length 1
--- 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 match.arg(arg = arg, choices = choices, several.ok = several.ok) : 
  'arg' must be of length 1
Calls: best_fit_optim ... compare_Target -> <Anonymous> -> igraph.match.arg -> match.arg
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘tutorial.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: Matrix

Attaching package: 'expm'

The following object is masked from 'package:Matrix':

    expm


Attaching package: 'igraph'

The following objects are masked from 'package:dplyr':

    as_data_frame, groups, union

The following object is masked from 'package:tibble':

    as_data_frame

The following object is masked from 'package:netcom':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Quitting from lines 200-215 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
'arg' must be of length 1
--- 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 match.arg(arg = arg, choices = choices, several.ok = several.ok) : 
  'arg' must be of length 1
Calls: best_fit_optim ... compare_Target -> <Anonymous> -> igraph.match.arg -> match.arg
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘tutorial.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: Matrix

Attaching package: 'expm'

The following object is masked from 'package:Matrix':

    expm


Attaching package: 'igraph'

The following objects are masked from 'package:dplyr':

    as_data_frame, groups, union

The following object is masked from 'package:tibble':

    as_data_frame

The following object is masked from 'package:netcom':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Quitting from lines 200-215 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
'arg' must be of length 1
--- 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 match.arg(arg = arg, choices = choices, several.ok = several.ok) : 
  'arg' must be of length 1
Calls: best_fit_optim ... compare_Target -> <Anonymous> -> igraph.match.arg -> match.arg
Execution halted
Error(s) in re-building vignettes:
--- re-building 'tutorial.Rmd' using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: Matrix

Attaching package: 'expm'

The following object is masked from 'package:Matrix':

    expm


Attaching package: 'igraph'

The following objects are masked from 'package:dplyr':

    as_data_frame, groups, union

The following object is masked from 'package:tibble':

    as_data_frame

The following object is masked from 'package:netcom':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Quitting from lines 200-215 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
'arg' must be of length 1
--- 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 match.arg(arg = arg, choices = choices, several.ok = several.ok) : 
  'arg' must be of length 1
Calls: best_fit_optim ... compare_Target -> <Anonymous> -> igraph.match.arg -> match.arg
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: Matrix

Attaching package: 'expm'

The following object is masked from 'package:Matrix':

    expm


Attaching package: 'igraph'

The following objects are masked from 'package:dplyr':

    as_data_frame, groups, union

The following object is masked from 'package:tibble':

    as_data_frame

The following object is masked from 'package:netcom':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Quitting from lines 200-215 (tutorial.Rmd) 
Error: processing vignette ‘tutorial.Rmd’ failed with diagnostics:
‘arg’ must be of length 1
--- 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 match.arg(arg = arg, choices = choices, several.ok = several.ok) : 
  'arg' must be of length 1
Calls: best_fit_optim ... compare_Target -> <Anonymous> -> igraph.match.arg -> match.arg
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: Matrix

Attaching package: 'expm'

The following object is masked from 'package:Matrix':

    expm


Attaching package: 'igraph'

The following objects are masked from 'package:dplyr':

    as_data_frame, groups, union

The following object is masked from 'package:tibble':

    as_data_frame

The following object is masked from 'package:netcom':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Quitting from lines 200-215 (tutorial.Rmd) 
Error: processing vignette ‘tutorial.Rmd’ failed with diagnostics:
‘arg’ must be of length 1
--- 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.
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 match.arg(arg = arg, choices = choices, several.ok = several.ok) : 
  'arg' must be of length 1
Calls: best_fit_optim ... compare_Target -> <Anonymous> -> igraph.match.arg -> match.arg
Execution halted
Error(s) in re-building vignettes:
--- re-building 'tutorial.Rmd' using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: Matrix

Attaching package: 'expm'

The following object is masked from 'package:Matrix':

    expm


Attaching package: 'igraph'

The following objects are masked from 'package:dplyr':

    as_data_frame, groups, union

The following object is masked from 'package:tibble':

    as_data_frame

The following object is masked from 'package:netcom':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Quitting from lines 200-215 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
'arg' must be of length 1
--- 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.
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 match.arg(arg = arg, choices = choices, several.ok = several.ok) : 
  'arg' must be of length 1
Calls: best_fit_optim ... compare_Target -> <Anonymous> -> igraph.match.arg -> match.arg
Execution halted
Error(s) in re-building vignettes:
--- re-building 'tutorial.Rmd' using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: Matrix

Attaching package: 'expm'

The following object is masked from 'package:Matrix':

    expm


Attaching package: 'igraph'

The following objects are masked from 'package:dplyr':

    as_data_frame, groups, union

The following object is masked from 'package:tibble':

    as_data_frame

The following object is masked from 'package:netcom':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Quitting from lines 200-215 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
'arg' must be of length 1
--- failed re-building 'tutorial.Rmd'

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

Error: Vignette re-building failed.
Execution halted