createSimulation2 | R Documentation |
Changes: only an additional input with conditional if/else statements wherever an igraph object is generated. Will allow for user-supplied graph object as well, this functionality requires an igraph object specifically for now.
createSimulation2(
num.samples = 100,
num.variables = 100,
pct.imbalance = 0.5,
pct.signals = 0.1,
main.bias = 0.4,
interaction.bias = 0.4,
hi.cor = 0.8,
lo.cor = 0.2,
label = "class",
sim.type = "mainEffect",
pct.train = 0.5,
pct.holdout = 0.5,
pct.validation = 0,
save.file = NULL,
mix.type = NULL,
pct.mixed = 0.5,
verbose = FALSE,
plot.graph = FALSE,
use.Rcpp = FALSE,
prob.connected = NULL,
out.degree = NULL,
data.type = "continuous",
avg.maf = 0.2,
graph.structure = NULL
)
num.samples |
number of samples |
num.variables |
number of variables (features) |
pct.imbalance |
fraction of num.samples that are cases |
pct.signals |
fraction of num.variables that are functional |
main.bias |
approximate effect size for main effect simulations |
interaction.bias |
approximate effect size for interaction effects |
hi.cor |
parameter to use for network-connected pairwise correlations |
lo.cor |
parameter to use for network-non-connected pairwise correlations |
label |
should just be "class" for binary response |
sim.type |
a character that determines the type of simulation: mainEffect/mainEffect_Erdos-Renyi/mainEffect_Scalefree/interactionErdos/interactionScalefree/mixed |
pct.train |
fraction of num.samples used for training |
pct.holdout |
fraction of num.samples used for holdout |
pct.validation |
fraction of num.samples used for validation |
save.file |
logical but not currently being used |
mix.type |
character that determines the type of mixed effects simulation: main-interactionErdos/main-interactionScalefree |
pct.mixed |
percent of functional variables that are main effects (1 - pct_interaction). Use with sim.type="mixed" and specify mix.type. |
verbose |
logical indicating whether to display time required to generate simulation |
plot.graph |
logical indicating whether to plot networks |
use.Rcpp |
if true use Rcpp to correct negative eigenvalues |
prob.connected |
probability of drawing an edge between two arbitrary vertices in Erdos-Renyi graph |
out.degree |
out-degree of vertices in Scale-free graph |
data.type |
character indicating if data is from a "continuous" or "discrete" distribution |
avg.maf |
numeric in (0,1) indicating the desired average MAF for GWAS main effect simulations |
graph.structure |
(igraph) graph structure generated from igraph, NULL default |
New Parameter:
graph.structure - (igraph) graph structure generated from igraph. If NULL, then createSimulation2() typically generates one on its own. However, this will be handled by createfMRIsimulation() and the user will not be using createSimulation2() directly. This input is used to circumvent automatic simulation of graphs by the previous iteration of createSimulation2().
A list with:
traing data set
holdout data set
validation data set
the class label/column name
the variable names with simulated signals
total elapsed time
adjacency matrix for random network (for interaction/mixed/main plus correlation)
indices of main effect variables (for mixed simulations)
indices of interaction effect variables (for mixed simulations)
# main effects with correlation from Erdos-Renyi network (continuous)
num.samples <- 100
num.variables <- 10
dataset <- createSimulation2(
num.samples = num.samples,
num.variables = num.variables,
pct.imbalance = 0.5,
pct.signals = 0.2,
main.bias = 0.4,
interaction.bias = 1,
hi.cor = 0.8,
lo.cor = 0.2,
mix.type = "main-interactionErdos",
label = "class",
sim.type = "mainEffect_Erdos-Renyi",
pct.mixed = 0.5,
pct.train = 0.5,
pct.holdout = 0.5,
pct.validation = 0,
plot.graph = FALSE,
verbose = TRUE,
data.type = "continuous"
)
# main effects with correlation from Erdos-Renyi network
num.samples <- 100
num.variables <- 10
dataset <- createSimulation2(
num.samples = num.samples,
num.variables = num.variables,
pct.imbalance = 0.5,
pct.signals = 0.2,
main.bias = 0.4,
interaction.bias = 1,
hi.cor = 0.8,
lo.cor = 0.2,
mix.type = "main-interactionErdos",
label = "class",
sim.type = "mainEffect_Erdos-Renyi",
pct.mixed = 0.5,
pct.train = 0.5,
pct.holdout = 0.5,
pct.validation = 0,
plot.graph = FALSE,
verbose = TRUE,
data.type = "discrete"
)
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