plotnet
Plot a neural network model
Plot a neural interpretation diagram for a neural network object
Usage
plotnet(mod_in, ...)
"plotnet"(mod_in, x_names, y_names, struct = NULL, nid = TRUE, all_out = TRUE, all_in = TRUE, bias = TRUE, rel_rsc = c(1, 7), circle_cex = 5, node_labs = TRUE, var_labs = TRUE, line_stag = NULL, cex_val = 1, alpha_val = 1, circle_col = "lightblue", pos_col = "black", neg_col = "grey", bord_col = "lightblue", max_sp = FALSE, prune_col = NULL, prune_lty = "dashed", skip = NULL, ...)
"plotnet"(mod_in, x_names = NULL, y_names = NULL, skip = FALSE, ...)
"plotnet"(mod_in, struct, x_names = NULL, y_names = NULL, ...)
"plotnet"(mod_in, x_names = NULL, y_names = NULL, prune_col = NULL, prune_lty = "dashed", ...)
"plotnet"(mod_in, x_names = NULL, y_names = NULL, ...)
"plotnet"(mod_in, x_names = NULL, y_names = NULL, skip = FALSE, ...)
Arguments
 mod_in
 neural network object or numeric vector of weights
 ...
 additional arguments passed to or from other methods
 x_names
 chr string indicating names for input variables, default from model object
 y_names
 chr string indicating names for output variables, default from model object
 struct
 numeric vector equal in length to the number of layers in the network. Each number indicates the number of nodes in each layer starting with the input and ending with the output. An arbitrary number of hidden layers can be included.
 nid
 logical value indicating if neural interpretation diagram is plotted, default
TRUE
 all_out
 chr string indicating names of response variables for which connections are plotted, default all
 all_in
 chr string indicating names of input variables for which connections are plotted, default all
 bias
 logical value indicating if bias nodes and connections are plotted, default
TRUE
 rel_rsc
 numeric indicating the scaling range for the width of connection weights
 circle_cex
 numeric value indicating size of nodes, default 5
 node_labs
 logical value indicating if labels are plotted directly on nodes, default
TRUE
 var_labs
 logical value indicating if variable names are plotted next to nodes, default
TRUE
 line_stag
 numeric value that specifies distance of connection weights from nodes
 cex_val
 numeric value indicating size of text labels, default 1
 alpha_val
 numeric value (01) indicating transparency of connections, default 1
 circle_col
 chr string indicating color of nodes, default
'lightblue'
, or two element list with first element indicating color of input nodes and second indicating color of remaining nodes  pos_col
 chr string indicating color of positive connection weights, default
'black'
 neg_col
 chr string indicating color of negative connection weights, default
'grey'
 bord_col
 chr string indicating border color around nodes, default
'lightblue'
 max_sp
 logical value indicating if space between nodes in each layer is maximized, default
FALSE
 prune_col
 chr string indicating color of pruned connections, otherwise not shown
 prune_lty
 line type for pruned connections, passed to
segments
 skip
 logical if skip layer connections are plotted instead of the primary network
Details
This function plots a neural network as a neural interpretation diagram as in Ozesmi and Ozesmi (1999). Options to plot without colorcoding or shading of weights are also provided. The default settings plot positive weights between layers as black lines and negative weights as grey lines. Line thickness is in proportion to relative magnitude of each weight. The first layer includes only input variables with nodes labelled arbitrarily as I1 through In for n input variables. One through many hidden layers are plotted with each node in each layer labelled as H1 through Hn. The output layer is plotted last with nodes labeled as O1 through On. Bias nodes connected to the hidden and output layers are also shown. Neural networks created using mlp
do not show bias layers.
A primary network and a skip layer network can be plotted for nnet
models with a skip layer connection. The default is to plot the primary network, whereas the skip layer network can be viewed with skip = TRUE
. If nid = TRUE
, the line widths for both the primary and skip layer plots are relative to all weights. Viewing both plots is recommended to see which network has larger relative weights. Plotting a network with only a skip layer (i.e., no hidden layer, size = 0
) will include bias connections to the output layer, whereas these are not included in the plot of the skip layer if size
is greater than zero.
The numeric method for plotting requires the input weights to be in a specific order given the structure of the network. An additional argument struct
(from neuralweights
is also required that lists the number of nodes in the input, hidden, and output layers. The example below for the numeric input shows the correct weight vector for a simple neural network model with two input variables, one output variable, and one hidden layer with two nodes. Bias nodes are also connected to the hidden and output layer. Using the plot syntax of I, H, O, and B for input, hidden, output, and bias to indicate weighted connections between layers, the correct weight order for the mod_in
vector is B1H1, I1H1, I2H1, B1H2, I1H2, I2H2, B2O1, H1O1, H2O1. For a generic network (three layers) with n input nodes, j hidden nodes, and k output nodes, the weights are ordered as the connections from B1, I1,...,In to H1,...,Hj, then B2, H1,..,Hj to O1,...,Ok.
Value

A graphics object unless
wts_only = TRUE
, then neural network weights from neuralweights
.
References
Ozesmi, S.L., Ozesmi, U. 1999. An artificial neural network approach to spatial habitat modeling with interspecific interaction. Ecological Modelling. 116:1531.
Examples
## using numeric input
# B1H1, I1H1, I2H1, B1H2, I1H2, I2H2, B2O1, H1O1, H2O1.
wts_in < c(13.12, 1.49, 0.16, 0.11, 0.19, 0.16, 0.56, 0.52, 0.81)
struct < c(2, 2, 1) #two inputs, two hidden, one output
plotnet(wts_in, struct = struct)
# numeric input, two hidden layers
# B1H11, I1H11, I2H11, B1H12, I1H12, I2H12, B2H21, H11H21, H12H21,
# B2H22, H11H22, H12H22, B3O1, H21O1, H22O1
wts_in < c(1.12, 1.49, 0.16, 0.11, 0.19, 0.16, 0.5, 0.2, 0.12, 0.1,
0.89, 0.9, 0.56, 0.52, 0.81)
struct < c(2, 2, 2, 1) # two inputs, two (two nodes each), one output
plotnet(wts_in, struct = struct)
## using nnet
library(nnet)
data(neuraldat)
set.seed(123)
mod < nnet(Y1 ~ X1 + X2 + X3, data = neuraldat, size = 5)
plotnet(mod)
## plot the skip layer from nnet model
mod < nnet(Y1 ~ X1 + X2 + X3, data = neuraldat, size = 5, skip = TRUE)
plotnet(mod, skip = TRUE)
## Not run:
# ## using RSNNS, no bias layers
#
# library(RSNNS)
#
# x < neuraldat[, c('X1', 'X2', 'X3')]
# y < neuraldat[, 'Y1']
# mod < mlp(x, y, size = 5)
#
# plotnet(mod)
#
# # pruned model using code from RSSNS pruning demo
# pruneFuncParams < list(max_pr_error_increase = 10.0, pr_accepted_error = 1.0,
# no_of_pr_retrain_cycles = 1000, min_error_to_stop = 0.01, init_matrix_value = 1e6,
# input_pruning = TRUE, hidden_pruning = TRUE)
# mod < mlp(x, y, size = 5, pruneFunc = "OptimalBrainSurgeon",
# pruneFuncParams = pruneFuncParams)
#
# plotnet(mod)
# plotnet(mod, prune_col = 'lightblue')
#
# ## using neuralnet
#
# library(neuralnet)
#
# mod < neuralnet(Y1 ~ X1 + X2 + X3, data = neuraldat, hidden = 5)
#
# plotnet(mod)
#
# ## using caret
#
# library(caret)
#
# mod < train(Y1 ~ X1 + X2 + X3, method = 'nnet', data = neuraldat, linout = TRUE)
#
# plotnet(mod)
#
# ## a more complicated network with categorical response
# AND < c(rep(0, 7), 1)
# OR < c(0, rep(1, 7))
#
# binary_data < data.frame(expand.grid(c(0, 1), c(0, 1), c(0, 1)), AND, OR)
#
# mod < neuralnet(AND + OR ~ Var1 + Var2 + Var3, binary_data,
# hidden = c(6, 12, 8), rep = 10, err.fct = 'ce', linear.output = FALSE)
#
# plotnet(mod)
#
# ## recreate the previous example with numeric inputs
#
# # get the weights and structure in the right format
# wts < neuralweights(mod)
# struct < wts$struct
# wts < unlist(wts$wts)
#
# # plot
# plotnet(wts, struct = struct)
#
# ## color input nodes by relative importance
# mod < nnet(Y1 ~ X1 + X2 + X3, data = neuraldat, size = 5)
#
# rel_imp < garson(mod, bar_plot = FALSE)$rel_imp
# cols < colorRampPalette(c('lightgreen', 'darkgreen'))(3)[rank(rel_imp)]
#
# plotnet(mod, circle_col = list(cols, 'lightblue'))
# ## End(Not run)