topology_models: Milestone network models for generating toy examples

In dynverse/dyntoy: Generating simple toy data of cellular differentiation

Description

Milestone network models for generating toy examples

Usage

model_linear(num_milestones = function() rbinom(1, size = 10, 0.25) + 2)

model_cyclic(num_milestones = function() rbinom(1, size = 10, 0.25) + 3)

model_bifurcating()

model_multifurcating(num_branchpoints = function() rbinom(1, size = 10,
  0.25) + 1, max_degree = function() sample_discrete_uniform(1, 3, 6))

model_binary_tree(num_branchpoints = function()
  sample_discrete_uniform(1, 3, 6))

model_tree(num_branchpoints = function() sample_discrete_uniform(1, 3,
  6), max_degree = function() sample_discrete_uniform(1, 3, 6))

model_converging()

model_diverging_converging(num_modifications = function() rbinom(1, size
  = 10, 0.25) + 1, nodes_per_modification = function()
  sample_discrete_uniform(1, 3, 6))

model_diverging_with_loops(num_modifications = function() rbinom(1, size
  = 10, 0.25) + 1, nodes_per_modification = function()
  sample_discrete_uniform(1, 3, 6))

model_multiple_looping(num_modifications = function() rbinom(1, size =
  10, 0.25) + 1, nodes_per_modification = function()
  sample_discrete_uniform(1, 3, 6))

model_connected(num_modifications = function() rbinom(1, size = 10, 0.25)
  + 1, nodes_per_modification = function() sample_discrete_uniform(1, 3,
  6))

model_disconnected(num_trajectories = rbinom(1, size = 5, 0.25) + 2, ...)

topology_models

Arguments

num_milestones	The number of milestones in the trajectory (linear, cyclic)
num_branchpoints	The number of branchpoints in the trajectory (bifurcating, diverging, converging)
max_degree	The maximum degree of a branch node, must be at least 3 (diverging, converging)
num_modifications	Number of modifications made to the original trajectory (diverging_converging, diverging_with_loops, multiple_looping, connected)
nodes_per_modification	The number of nodes to use per modification (diverging_converging, diverging_with_loops, multiple_looping, connected)
num_trajectories	The number of disconnected trajectories to generate
...	Parameters to pass to other models. Can be in the form of 'linear = list(num_milestones = function() sample(2:8, 1)' or just 'num_milestones = 10'.

Format

An object of class list of length 12.

dynverse/dyntoy documentation built on May 25, 2019, 4:26 p.m.