simplerspec

The simplerspec package aims to facilitate spectra and additional data handling and model development for spectroscopy applications such as FT-IR soil spectroscopy. Different helper functions are designed to create a data and modeling workflow. Data inputs and outputs are stored in R objects with specific data structures. The following steps are covered in the current version of the package:

1. Read spectral data from text files (.csv) and Bruker OPUS binary files
2. Average spectra for replicate scans
3. Detect and remove outlier spectra based on robust PCA
4. Resample spectra to new wavenumber intervals
5. Perform pre-processing of spectra
6. Join chemial and spectral data sets
7. Perform calibration sampling and Partial Least Squares (PLS) regression modeling
8. Predict chemical properties from a list of calibrated models and new soil spectra

Installation

The newest version of the package is available on this GitHub repository. Note that the package is still under development. If you find bugs you are highly welcome to report your issues (write me an email or create an issue). You can install simplerspec using the devtools package.

# Uncomment and run the below line if you have not yet installed
# the devtools package
# install.packages("devtools")
# Install the simplerspec package from the github repository
# (https://github.com/philipp-baumann/simplerspec)
devtools::install_github("philipp-baumann/simplerspec")

Special installation note for Windows 8 and R version 3.3 and 3.4

For some Windows versions with recent R versions (3.3 and 3.4), there might be an error message that the Rcpp package can not be installed because there is no precompiled binary (packaging up) of the Rcpp package available on CRAN. Because the Rcpp package contains C++ code, the package needs compilation. The compiler is supplied in the R tools (contains GCC 4.9.3 and Mingw-W64 V3). First, you need to download and install the latest R tools version from here. Then, you need to install Rcpp from source provided on CRAN by

install.packages("Rcpp", type = "source")

After successful compilation and installation, you can install simplerspec and by:

devtools::install_github("philipp-baumann/simplerspec")

Key concepts and data analysis workflow

The functions are built to work in a pipeline and cover commonly used procedures for spectral model development. Many R packages are available to do tasks in spectral modeling such as pre-processing of spectral data. The motivation to create this package was:

1. Avoid repetition of code in model developement (common source of errors)
2. Provide a reproducible data analysis workflow for FT-IR spectroscopy
3. R packges are an ideal way to organize and share R code
4. Make soil FT-IR spectroscopy modeling accessible to people that have basic R knowledge
5. Provide a package interface that keeps data with various structures for spectral modeling related in R objects

This package builds mainly upon functions from the following R packages:

• prospectr : Various utilities for pre-processing and sample selection based on spectroscopic data. An introduction to the package with examples can be found here.
• plyr and dplyr : Fast data manipulation tools with an unified interface. See here for details.
• ggplot2 : Alternative plotting system for R, based on the grammar of graphics. See here.
• caret : Classification and regression training. A set of functions that attempt to streamline the process for creating predictive models. See here for details.

Consistent and reproducible data and metadata management is an important prerequisite for spectral model development. Therefore, different outputs should be stored as R objects in a consistent way using R data structures. Simplerspec functions uses tibble data frames as principal data structures because they allow to store lists within the well-known data frame structures. Lists are flexible and can e.g. contain other lists, vectors, data.frames, or matrices.

Example workflow

In a fist step, the spectra (one file per spectrum and replicate scan) are read from the text (.txt) files. Currently, an export macro within the Bruker OPUS software is used to convert OPUS binary files to spectra in the form of a text file. The argument path specifies the the folder where all spectral files to be loaded into R are located. The files contain two columns that are comma-separated. The first is the wavenumber and the second is the absorbance value.

# Load simplerspec package for spectral model development wrapper functions
require(simplerspec)
# Load tidyverse package: loads packages frequently used for data manipulation,
# data tidying, import, and plotting
require(tidyverse)

################################################################################
## Part 1: Read and pre-process spectra, Read chemical data, and join
## spectral and chemical data sets
################################################################################

## Read spectra in list ========================================================

# List of OPUS binary spectra files
lf <- list.files("data/spectra/soilspec_eth_bin/", full.names = TRUE)

# Read spectra from files into R list
spc_list <- read_opus_univ(fnames = lf, extract = c("spc"))

Pipes can make R code more readable and fit to the stepwise data processing in the context of developing spectral models. The pipe operator (%>%, called "then") is a new operator in R that was introduced with the magrittr package. It facilitates readability of code and avoids to type intermediate objects. The basic behaviour of the pipe operator is that the object on the left hand side is passed as the first argument to the function on the right hand side. When loading the tidyverse package, the pipe operator is attached to the current R session More details can be found here.

The model development process can be quickly coded as the example below illustrates:

## Spectral data processing pipe ===============================================

soilspec_tbl <- spc_list %>%
  # Gather list of spectra data into tibble data frame
  gather_spc() %>% 
  # Resample spectra to new wavenumber interval
  resample_spc(wn_lower = 500, wn_upper = 3996, wn_interval = 2) %>%
  # Average replicate scans per sample_id
  average_spc() %>%
  # Preprocess spectra using Savitzky-Golay first derivative with a window size
  # of 21 points
  preprocess_spc(select = "sg_1_w21")
  
## Read chemical reference data and join with spectral data ====================

# Read chemical reference analysis data
soilchem_tbl <- read_csv(file = "data/soilchem/soilchem_yamsys.csv")

# Join spectra tibble and chemical reference analysis tibble
spec_chem <- join_spc_chem(
  spc_tbl = soilspec_tbl_eth , chem_tbl = soilchem_tbl, by = "sample_id")


################################################################################
## Part 2: Run PLS regression models for different soil variables
################################################################################

# Example Partial Least Squares (PLS) Regression model for total Carbon (C)
# Use repeated k-fold cross-validation to tune the model (choose optimal 
# number of PLS components) and estimat model performance on hold-out 
# predictions of the finally chosen model (model assessment).
# This allows to use the entire set for both model building and evaluation;
# recommended for small data sets
pls_C <- fit_pls(
  # remove rows with NA in the data
  spec_chem = spec_chem[!is.na(spec_chem$C), ],
  response = C,
  evaluation_method = "resampling",
  tuning_method = "resampling",
  resampling_method = "rep_kfold_cv",
  pls_ncomp_max = 7 # maximum number of PLS components tested during tuning
) 

Details on functions, arguments, and input and output data structures

read_opus() function

Credits

I would like to thank the following people for the inspiration by concepts, code and packages:

• Antoine Stevens and Leonardo Ramirez-Lopez for their contributions to the prospectr package and the Guide to Diffuse Reflectance Spectroscopy & Multivariate Calibration
• Andrew Sila, Tomislav Hengl, and Thomas Terhoeven-Urselmans for the read.opus() function from the soil.spec package developed at ICRAF.
• Hadley Wickham for his work and concepts on data science within R