default method for plotnet, all other methods are now shortened to on…

…ly relevant differences

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: NeuralNetTools
 Type: Package
 Title: Visualization and Analysis Tools for Neural Networks
-Version: 1.3.9.9000
-Date: 2015-08-01
+Version: 1.3.10.9000
+Date: 2015-08-26
 Author: Marcus W. Beck [aut, cre]
 Maintainer: Marcus W. Beck <[email protected]>
 Description: Visualization and analysis tools to aid in the interpretation of

NAMESPACE

@@ -20,6 +20,7 @@ S3method(olden,nn)
 S3method(olden,nnet)
 S3method(olden,numeric)
 S3method(olden,train)
+S3method(plotnet,default)
 S3method(plotnet,mlp)
 S3method(plotnet,nn)
 S3method(plotnet,nnet)

R/NeuralNetTools_utils.R

@@ -564,7 +564,7 @@ layer_lines <- function(mod_in, h_layer, layer1 = 1, layer2 = 2, out_layer = FAL
 #' @param mod_in neural network model object
 #' @param nid logical value indicating if neural interpretation diagram is plotted, default \code{TRUE}
 #' @param rel_rsc numeric value indicating maximum to rescale weights for plotting in a neural interpretation diagram. Default is \code{NULL} for no rescaling.
-#' @param all_out chr string indicating names of input variables for which connections are plotted, default all
+#' @param all_out chr string indicating names of response variables for which connections are plotted, default all
 #' @param pos_col chr string indicating color of positive connection weights, default \code{'black'}
 #' @param neg_col chr string indicating color of negative connection weights, default \code{'grey'}
 #' @param struct numeric vector for network structure

README.Rmd

@@ -38,7 +38,7 @@ install.packages('NeuralNetTools')
 
 Please cite this package as follows:
 
-*Beck MW. 2015. NeuralNetTools: Visualization and Analysis Tools for Neural Networks. Version 1.3.9. http://cran.r-project.org/web/packages/NeuralNetTools/*
+*Beck MW. 2015. NeuralNetTools: Visualization and Analysis Tools for Neural Networks. Version 1.3.10. http://cran.r-project.org/web/packages/NeuralNetTools/*
 
 ### Bug reports
 

README.html

@@ -81,7 +81,7 @@ <h4><em>Marcus W. Beck, <a href="mailto:[email protected]">[email protected]
 <div id="citation" class="section level3">
 <h3>Citation</h3>
 <p>Please cite this package as follows:</p>
-<p><em>Beck MW. 2015. NeuralNetTools: Visualization and Analysis Tools for Neural Networks. Version 1.3.9. <a href="http://cran.r-project.org/web/packages/NeuralNetTools/" class="uri">http://cran.r-project.org/web/packages/NeuralNetTools/</a></em></p>
+<p><em>Beck MW. 2015. NeuralNetTools: Visualization and Analysis Tools for Neural Networks. Version 1.3.10. <a href="http://cran.r-project.org/web/packages/NeuralNetTools/" class="uri">http://cran.r-project.org/web/packages/NeuralNetTools/</a></em></p>
 </div>
 <div id="bug-reports" class="section level3">
 <h3>Bug reports</h3>

README.md

@@ -31,7 +31,7 @@ install.packages('NeuralNetTools')
 
 Please cite this package as follows:
 
-*Beck MW. 2015. NeuralNetTools: Visualization and Analysis Tools for Neural Networks. Version 1.3.9. http://cran.r-project.org/web/packages/NeuralNetTools/*
+*Beck MW. 2015. NeuralNetTools: Visualization and Analysis Tools for Neural Networks. Version 1.3.10. http://cran.r-project.org/web/packages/NeuralNetTools/*
 
 ### Bug reports
 

man/bias_lines.Rd

@@ -18,7 +18,7 @@ bias_lines(bias_x, bias_y, mod_in, nid, rel_rsc, all_out, pos_col, neg_col,
 
 \item{rel_rsc}{numeric value indicating maximum to rescale weights for plotting in a neural interpretation diagram. Default is \code{NULL} for no rescaling.}
 
-\item{all_out}{chr string indicating names of input variables for which connections are plotted, default all}
+\item{all_out}{chr string indicating names of response variables for which connections are plotted, default all}
 
 \item{pos_col}{chr string indicating color of positive connection weights, default \code{'black'}}
 

man/plotnet.Rd

@@ -2,6 +2,7 @@
 % Please edit documentation in R/NeuralNetTools_plot.R
 \name{plotnet}
 \alias{plotnet}
+\alias{plotnet.default}
 \alias{plotnet.mlp}
 \alias{plotnet.nn}
 \alias{plotnet.nnet}
@@ -11,46 +12,36 @@
 \usage{
 plotnet(mod_in, ...)
 
-\method{plotnet}{nnet}(mod_in, nid = TRUE, all_out = TRUE, all_in = TRUE,
-  bias = TRUE, wts_only = FALSE, rel_rsc = 5, circle_cex = 5,
-  node_labs = TRUE, var_labs = TRUE, x_lab = NULL, y_lab = NULL,
-  line_stag = NULL, cex_val = 1, alpha_val = 1,
-  circle_col = "lightblue", pos_col = "black", neg_col = "grey",
-  bord_col = "lightblue", max_sp = FALSE, ...)
-
-\method{plotnet}{numeric}(mod_in, struct, nid = TRUE, all_out = TRUE,
-  all_in = TRUE, bias = TRUE, wts_only = FALSE, rel_rsc = 5,
-  circle_cex = 5, node_labs = TRUE, var_labs = TRUE, x_lab = NULL,
-  y_lab = NULL, line_stag = NULL, cex_val = 1, alpha_val = 1,
-  circle_col = "lightblue", pos_col = "black", neg_col = "grey",
-  bord_col = "lightblue", max_sp = FALSE, ...)
-
-\method{plotnet}{mlp}(mod_in, nid = TRUE, all_out = TRUE, all_in = TRUE,
-  wts_only = FALSE, rel_rsc = 5, circle_cex = 5, node_labs = TRUE,
-  var_labs = TRUE, x_lab = NULL, y_lab = NULL, line_stag = NULL,
+\method{plotnet}{default}(mod_in, x_names, y_names, struct = NULL,
+  nid = TRUE, all_out = TRUE, all_in = TRUE, bias = TRUE, rel_rsc = 5,
+  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",
-  prune_col = NULL, prune_lty = "dashed", max_sp = FALSE, ...)
-
-\method{plotnet}{nn}(mod_in, nid = TRUE, all_out = TRUE, all_in = TRUE,
-  bias = TRUE, wts_only = FALSE, rel_rsc = 5, circle_cex = 5,
-  node_labs = TRUE, var_labs = TRUE, x_lab = NULL, y_lab = NULL,
-  line_stag = NULL, cex_val = 1, alpha_val = 1,
-  circle_col = "lightblue", pos_col = "black", neg_col = "grey",
-  bord_col = "lightblue", max_sp = FALSE, ...)
-
-\method{plotnet}{train}(mod_in, nid = TRUE, all_out = TRUE, all_in = TRUE,
-  bias = TRUE, wts_only = FALSE, rel_rsc = 5, circle_cex = 5,
-  node_labs = TRUE, var_labs = TRUE, x_lab = NULL, y_lab = NULL,
-  line_stag = NULL, cex_val = 1, alpha_val = 1,
-  circle_col = "lightblue", pos_col = "black", neg_col = "grey",
-  bord_col = "lightblue", max_sp = FALSE, ...)
+  max_sp = FALSE, prune_col = NULL, prune_lty = "dashed", ...)
+
+\method{plotnet}{nnet}(mod_in, x_names = NULL, y_names = NULL, ...)
+
+\method{plotnet}{numeric}(mod_in, struct, x_names = NULL, y_names = NULL,
+  ...)
+
+\method{plotnet}{mlp}(mod_in, x_names = NULL, y_names = NULL,
+  prune_col = NULL, prune_lty = "dashed", ...)
+
+\method{plotnet}{nn}(mod_in, x_names = NULL, y_names = NULL, ...)
+
+\method{plotnet}{train}(mod_in, x_names = NULL, y_names = NULL, ...)
 }
 \arguments{
 \item{mod_in}{neural network object or numeric vector of weights}
 
 \item{...}{additional arguments passed to plot}
 
+\item{x_names}{chr string indicating names for input variables, default from model object}
+
+\item{y_names}{chr string indicating names for output variables, default from model object}
+
+\item{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.}
+
 \item{nid}{logical value indicating if neural interpretation diagram is plotted, default \code{TRUE}}
 
 \item{all_out}{chr string indicating names of response variables for which connections are plotted, default all}
@@ -59,8 +50,6 @@ plotnet(mod_in, ...)
 
 \item{bias}{logical value indicating if bias nodes and connections are plotted, default \code{TRUE}}
 
-\item{wts_only}{logical value indicating if connections weights are returned rather than a plot, default \code{FALSE}}
-
 \item{rel_rsc}{numeric value indicating maximum width of connection lines, default 5}
 
 \item{circle_cex}{numeric value indicating size of nodes, default 5}
@@ -69,10 +58,6 @@ plotnet(mod_in, ...)
 
 \item{var_labs}{logical value indicating if variable names are plotted next to nodes, default \code{TRUE}}
 
-\item{x_lab}{chr string indicating names for input variables, default from model object}
-
-\item{y_lab}{chr string indicating names for output variables, default from model object}
-
 \item{line_stag}{numeric value that specifies distance of connection weights from nodes}
 
 \item{cex_val}{numeric value indicating size of text labels, default 1}
@@ -89,8 +74,6 @@ plotnet(mod_in, ...)
 
 \item{max_sp}{logical value indicating if space between nodes in each layer is maximized, default \code{FALSE}}
 
-\item{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.}
-
 \item{prune_col}{chr string indicating color of pruned connections, otherwise not shown}
 
 \item{prune_lty}{line type for pruned connections, passed to \code{\link[graphics]{segments}}}