var_sel argument to lekprofile

fawda123 · Jul 7, 2015 · 137e71d · 137e71d
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: NeuralNetTools
 Type: Package
 Title: Visualization and Analysis Tools for Neural Networks
-Version: 1.3.7
-Date: 2015-06-29
+Version: 1.3.8
+Date: 2015-07-07
 Author: Marcus W. Beck [aut, cre]
 Maintainer: Marcus W. Beck <[email protected]>
 Description: Visualization and analysis tools to aid in the interpretation of

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.1.0): do not edit by hand
+# Generated by roxygen2 (4.1.1): do not edit by hand
 
 S3method(garson,mlp)
 S3method(garson,nn)

diff --git a/R/NeuralNetTools_lek.R b/R/NeuralNetTools_lek.R
@@ -4,6 +4,7 @@
 #' 
 #' @param mod_in input object for which an organized model list is desired.  The input can be an object of class \code{nnet} or \code{mlp}
 #' @param steps numeric value indicating number of observations to evaluate for each explanatory variable from minimum to maximum value, default 100
+#' @param var_sel optional chr string of explanatory variables to evaluate, defaults to all
 #' @param split_vals numeric vector indicating quantile values at which to hold other explanatory variables constant
 #' @param val_out logical value indicating if actual sensitivity values are returned rather than a plot, default \code{FALSE}
 #' @param ... arguments passed to other methods
@@ -93,8 +94,8 @@ lekprofile <- function(mod_in, ...) UseMethod('lekprofile')
 #' @export
 #' 
 #' @method lekprofile default
-lekprofile.default <- function(mod_in, steps = 100, split_vals = seq(0, 1, by = 0.2), val_out = FALSE, ...){
-
+lekprofile.default <- function(mod_in, steps = 100, var_sel = NULL, split_vals = seq(0, 1, by = 0.2), val_out = FALSE, ...){
+      
   ##
   #sort out exp and resp names based on object type of call to mod_in
   #get matrix for exp vars
@@ -115,6 +116,9 @@ lekprofile.default <- function(mod_in, steps = 100, split_vals = seq(0, 1, by =
     }
   }
 
+  # subset var_sens if var_sel is not empy
+  if(!is.null(var_sel)) var_sens <- var_sens[var_sens %in% var_sel]
+
   # stop if only one input variable
   if(ncol(mat_in) == 1) stop('Lek profile requires greater than one input variable')
 
@@ -168,9 +172,9 @@ lekprofile.default <- function(mod_in, steps = 100, split_vals = seq(0, 1, by =
 #' @export
 #' 
 #' @method lekprofile nnet
-lekprofile.nnet <- function(mod_in,steps = 100, split_vals = seq(0, 1, by = 0.2), val_out = FALSE, ...){
+lekprofile.nnet <- function(mod_in, steps = 100, var_sel = NULL, split_vals = seq(0, 1, by = 0.2), val_out = FALSE, ...){
 
-  lekprofile.default(mod_in, steps, split_vals, val_out)
+  lekprofile.default(mod_in, steps, var_sel, split_vals, val_out)
 
 }
 
@@ -183,7 +187,7 @@ lekprofile.nnet <- function(mod_in,steps = 100, split_vals = seq(0, 1, by = 0.2)
 #' @export
 #' 
 #' @method lekprofile mlp
-lekprofile.mlp <- function(mod_in, exp_in, steps = 100, split_vals = seq(0, 1, by = 0.2), val_out = FALSE, ...){
+lekprofile.mlp <- function(mod_in, exp_in, var_sel = NULL, steps = 100, split_vals = seq(0, 1, by = 0.2), val_out = FALSE, ...){
 
   ##
   #sort out exp and resp names based on object type of call to mod_in
@@ -193,6 +197,9 @@ lekprofile.mlp <- function(mod_in, exp_in, steps = 100, split_vals = seq(0, 1, b
   names(mat_in) <- paste0('X', seq(1, mod_in$nInputs))
   var_sens <- names(mat_in)
 
+  # subset var_sens if var_sel is not empy
+  if(!is.null(var_sel)) var_sens <- var_sens[var_sens %in% var_sel]
+
   #use 'pred_fun' to get pred vals of response across range of vals for an exp vars
   #loops over all explanatory variables of interest and all split values
   lek_vals <- sapply(
@@ -242,7 +249,7 @@ lekprofile.mlp <- function(mod_in, exp_in, steps = 100, split_vals = seq(0, 1, b
 #' @export
 #' 
 #' @method lekprofile train
-lekprofile.train <- function(mod_in, steps = 100, split_vals = seq(0, 1, by = 0.2), val_out = FALSE, ...){
+lekprofile.train <- function(mod_in, steps = 100, var_sel = NULL, split_vals = seq(0, 1, by = 0.2), val_out = FALSE, ...){
 
   # input data, x_names, and y_names
   mat_in <- mod_in$trainingData
@@ -261,6 +268,9 @@ lekprofile.train <- function(mod_in, steps = 100, split_vals = seq(0, 1, by = 0.
   resp_name <- y_names
   var_sens <- names(mat_in)
 
+  # subset var_sens if var_sel is not empy
+  if(!is.null(var_sel)) var_sens <- var_sens[var_sens %in% var_sel]
+
   #use 'pred_fun' to get pred vals of response across range of vals for an exp vars
   #loops over all explanatory variables of interest and all split values
   lek_vals <- sapply(
@@ -310,7 +320,7 @@ lekprofile.train <- function(mod_in, steps = 100, split_vals = seq(0, 1, by = 0.
 #' @export
 #' 
 #' @method lekprofile nn
-lekprofile.nn <- function(mod_in, steps = 100, split_vals = seq(0, 1, by = 0.2), val_out = FALSE, ...){
+lekprofile.nn <- function(mod_in, steps = 100, var_sel = NULL, split_vals = seq(0, 1, by = 0.2), val_out = FALSE, ...){
 
   # recreate the model using nnet (no predict method for nn)
   moddat <- mod_in$data
@@ -338,7 +348,7 @@ lekprofile.nn <- function(mod_in, steps = 100, split_vals = seq(0, 1, by = 0.2),
   mod_in <- eval(mod_in)
 
   # pass to lekprofile.nnet
-  lekprofile(mod_in, steps = steps, split_vals = split_vals, val_out = val_out, ...)
+  lekprofile(mod_in, steps = steps, var_sel = var_sel, split_vals = split_vals, val_out = val_out, ...)
 
 }
 

diff --git a/README.Rmd b/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 1.3.2. http://cran.r-project.org/web/packages/NeuralNetTools/*
+*Beck MW. 2015. NeuralNetTools: Visualization and Analysis Tools for Neural Networks. Version 1.3.8. http://cran.r-project.org/web/packages/NeuralNetTools/*
 
 ### Bug reports
 

diff --git a/README.html b/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 1.3.2. <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 1.3.8. <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>

diff --git a/README.md b/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 1.3.2. http://cran.r-project.org/web/packages/NeuralNetTools/*
+*Beck MW. 2015. NeuralNetTools: Visualization and Analysis Tools for Neural Networks. Version 1.3.8. http://cran.r-project.org/web/packages/NeuralNetTools/*
 
 ### Bug reports
 

diff --git a/README_files/figure-html/unnamed-chunk-6-1.png b/README_files/figure-html/unnamed-chunk-6-1.png
diff --git a/README_files/figure-html/unnamed-chunk-7-1.png b/README_files/figure-html/unnamed-chunk-7-1.png
diff --git a/README_files/figure-html/unnamed-chunk-8-1.png b/README_files/figure-html/unnamed-chunk-8-1.png
diff --git a/README_files/figure-html/unnamed-chunk-9-1.png b/README_files/figure-html/unnamed-chunk-9-1.png
diff --git a/man/garson.Rd b/man/garson.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/NeuralNetTools_gar.R
 \name{garson}
 \alias{garson}

diff --git a/man/lekprofile.Rd b/man/lekprofile.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/NeuralNetTools_lek.R
 \name{lekprofile}
 \alias{lekprofile}
@@ -11,20 +11,20 @@
 \usage{
 lekprofile(mod_in, ...)
 
-\method{lekprofile}{default}(mod_in, steps = 100, split_vals = seq(0, 1, by
-  = 0.2), val_out = FALSE, ...)
+\method{lekprofile}{default}(mod_in, steps = 100, var_sel = NULL,
+  split_vals = seq(0, 1, by = 0.2), val_out = FALSE, ...)
 
-\method{lekprofile}{nnet}(mod_in, steps = 100, split_vals = seq(0, 1, by =
-  0.2), val_out = FALSE, ...)
+\method{lekprofile}{nnet}(mod_in, steps = 100, var_sel = NULL,
+  split_vals = seq(0, 1, by = 0.2), val_out = FALSE, ...)
 
-\method{lekprofile}{mlp}(mod_in, exp_in, steps = 100, split_vals = seq(0, 1,
-  by = 0.2), val_out = FALSE, ...)
+\method{lekprofile}{mlp}(mod_in, exp_in, var_sel = NULL, steps = 100,
+  split_vals = seq(0, 1, by = 0.2), val_out = FALSE, ...)
 
-\method{lekprofile}{train}(mod_in, steps = 100, split_vals = seq(0, 1, by =
-  0.2), val_out = FALSE, ...)
+\method{lekprofile}{train}(mod_in, steps = 100, var_sel = NULL,
+  split_vals = seq(0, 1, by = 0.2), val_out = FALSE, ...)
 
-\method{lekprofile}{nn}(mod_in, steps = 100, split_vals = seq(0, 1, by =
-  0.2), val_out = FALSE, ...)
+\method{lekprofile}{nn}(mod_in, steps = 100, var_sel = NULL,
+  split_vals = seq(0, 1, by = 0.2), val_out = FALSE, ...)
 }
 \arguments{
 \item{mod_in}{input object for which an organized model list is desired.  The input can be an object of class \code{nnet} or \code{mlp}}
@@ -33,6 +33,8 @@ lekprofile(mod_in, ...)
 
 \item{steps}{numeric value indicating number of observations to evaluate for each explanatory variable from minimum to maximum value, default 100}
 
+\item{var_sel}{optional chr string of explanatory variables to evaluate, defaults to all}
+
 \item{split_vals}{numeric vector indicating quantile values at which to hold other explanatory variables constant}
 
 \item{val_out}{logical value indicating if actual sensitivity values are returned rather than a plot, default \code{FALSE}}

diff --git a/man/neuraldat.Rd b/man/neuraldat.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/NeuralNetTools_neuraldat.R
 \docType{data}
 \name{neuraldat}

diff --git a/man/neuralskips.Rd b/man/neuralskips.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/NeuralNetTools_utils.R
 \name{neuralskips}
 \alias{neuralskips}

diff --git a/man/neuralweights.Rd b/man/neuralweights.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/NeuralNetTools_utils.R
 \name{neuralweights}
 \alias{neuralweights}

diff --git a/man/olden.Rd b/man/olden.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/NeuralNetTools_old.R
 \name{olden}
 \alias{olden}

diff --git a/man/plotnet.Rd b/man/plotnet.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/NeuralNetTools_plot.R
 \name{plotnet}
 \alias{plotnet}

diff --git a/man/pred_sens.Rd b/man/pred_sens.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/NeuralNetTools_utils.R
 \name{pred_sens}
 \alias{pred_sens}