short_course/kerasformula_diagnostic.md

In rdrr1990/kerasformula: A High-Level R Interface for Neural Nets

compatability check for kerasformula

Pete Mohanty 5/2/2019

This document attempts to fit a simple neural net using kerasformula. It also displays a number of version checks on kerasformula and its dependencies both in R and in Python. This document is intended to knit whether or not the model can be fit successfully. To run this code on your machine, click here.

if(!require(keras)) install.packages(keras)

## Loading required package: keras

if(!require(kerasformula)) install.packages(kerasformula)

## Loading required package: kerasformula

## Loading required package: dplyr

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

## Loading required package: Matrix

library(keras)
if(!is_keras_available()) install_keras()
keras_installed <- is_keras_available()

if(keras_installed){
  library(kerasformula)
  tried <- try(out <- kms(Species ~ ., iris, verbose=0))
  if(!inherits(tried, "try-error")) plot_confusion(out) else("Model failed to estimate.\n\n\n")
}else{
  message("keras did not install properly.\n")
}

system("which python > python_path.txt")
python_path <- readLines("python_path.txt")
python_path

## [1] "/Users/mohanty/.virtualenvs/r-tensorflow/bin/python"

If that path is correct, it should be set in two different ways. Making changing_settings=TRUE would accomplish that.

if(!require(reticulate)) install.packages(reticulate)

## Loading required package: reticulate

library(reticulate)

change_settings <- FALSE

if(change_settings){

  System.setenv(TENSORFLOW_PYTHON=python_path)
  use_python(python_path)

}

The Python path should appear for each of these key libraries...

py_discover_config("tensorflow")

## python:         /Users/mohanty/.virtualenvs/r-tensorflow/bin/python
## libpython:      /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/config/libpython2.7.dylib
## pythonhome:     /System/Library/Frameworks/Python.framework/Versions/2.7:/System/Library/Frameworks/Python.framework/Versions/2.7
## virtualenv:     /Users/mohanty/.virtualenvs/r-tensorflow/bin/activate_this.py
## version:        2.7.10 (default, Feb  7 2017, 00:08:15)  [GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.34)]
## numpy:          /Users/mohanty/.virtualenvs/r-tensorflow/lib/python2.7/site-packages/numpy
## numpy_version:  1.14.0
## tensorflow:     /Users/mohanty/.virtualenvs/r-tensorflow/lib/python2.7/site-packages/tensorflow
## 
## python versions found: 
##  /Users/mohanty/.virtualenvs/r-tensorflow/bin/python
##  /usr/bin/python
##  /usr/local/bin/python3
##  /Users/mohanty/env3/bin/python

py_discover_config("numpy")

## python:         /Users/mohanty/.virtualenvs/r-tensorflow/bin/python
## libpython:      /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/config/libpython2.7.dylib
## pythonhome:     /System/Library/Frameworks/Python.framework/Versions/2.7:/System/Library/Frameworks/Python.framework/Versions/2.7
## virtualenv:     /Users/mohanty/.virtualenvs/r-tensorflow/bin/activate_this.py
## version:        2.7.10 (default, Feb  7 2017, 00:08:15)  [GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.34)]
## numpy:          /Users/mohanty/.virtualenvs/r-tensorflow/lib/python2.7/site-packages/numpy
## numpy_version:  1.14.0
## numpy:          /Users/mohanty/.virtualenvs/r-tensorflow/lib/python2.7/site-packages/numpy
## 
## python versions found: 
##  /Users/mohanty/.virtualenvs/r-tensorflow/bin/python
##  /usr/bin/python
##  /usr/local/bin/python3
##  /Users/mohanty/env3/bin/python

py_discover_config("keras")

## python:         /Users/mohanty/.virtualenvs/r-tensorflow/bin/python
## libpython:      /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/config/libpython2.7.dylib
## pythonhome:     /System/Library/Frameworks/Python.framework/Versions/2.7:/System/Library/Frameworks/Python.framework/Versions/2.7
## virtualenv:     /Users/mohanty/.virtualenvs/r-tensorflow/bin/activate_this.py
## version:        2.7.10 (default, Feb  7 2017, 00:08:15)  [GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.34)]
## numpy:          /Users/mohanty/.virtualenvs/r-tensorflow/lib/python2.7/site-packages/numpy
## numpy_version:  1.14.0
## keras:          /Users/mohanty/.virtualenvs/r-tensorflow/lib/python2.7/site-packages/keras
## 
## python versions found: 
##  /Users/mohanty/.virtualenvs/r-tensorflow/bin/python
##  /usr/bin/python
##  /usr/local/bin/python3
##  /Users/mohanty/env3/bin/python

sessionInfo()

## R version 3.5.0 (2018-04-23)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Sierra 10.12.6
## 
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] reticulate_1.7     kerasformula_1.5.1 Matrix_1.2-14     
## [4] dplyr_0.7.5        keras_2.1.6       
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.19     plyr_1.8.4       compiler_3.5.0   pillar_1.3.0    
##  [5] bindr_0.1.1      base64enc_0.1-3  tools_3.5.0      zeallot_0.1.0   
##  [9] digest_0.6.15    jsonlite_1.5     evaluate_0.11    tibble_1.4.2    
## [13] gtable_0.2.0     lattice_0.20-35  pkgconfig_2.0.2  rlang_0.3.1     
## [17] yaml_2.2.0       bindrcpp_0.2.2   stringr_1.3.1    knitr_1.20      
## [21] rprojroot_1.3-2  grid_3.5.0       tidyselect_0.2.4 glue_1.3.0      
## [25] R6_2.3.0         rmarkdown_1.10   purrr_0.2.5      ggplot2_2.2.1   
## [29] magrittr_1.5     whisker_0.3-2    backports_1.1.2  scales_0.5.0    
## [33] tfruns_1.3       htmltools_0.3.6  assertthat_0.2.0 colorspace_1.3-2
## [37] labeling_0.3     tensorflow_1.5   stringi_1.2.4    lazyeval_0.2.1  
## [41] munsell_0.4.3    crayon_1.3.4

rdrr1990/kerasformula documentation built on June 6, 2019, 8:02 a.m.