R package: APRLmpf

APRL (multi-)peak fitting tool. Resolves overlapping bands according to procedure and values described by Takahama, Johnson, and Russell, Aerosol Sci. Tech., 2013.

More generally, the purpose of this package is to provide a framework for

locating peak positions
simultaneously fitting peaks and fixed profile shapes using different search algorithms and multiple conditions for fitting (e.g., initial values)
visualizing fits
converting fitted peaks to [micro]moles of a substance

Subject to substantial modification. Keep up-to-date with git pull.

General Instructions

First, please see installation instructions for APRLspec, on which APRLmpf depends.

Install for R (replace {username} and {password} with account for which access to private repository is granted):

> devtools::install_git('https://{username}:{password}@gitlab.com/aprl/APRLmpf.git')

After installation, get a copy of example files (templates). To copy them into a new folder called “mpf” in your working directory:

$ cd /path/to/workingdir/
$ R -e "APRLspec::CopyPkgFiles('APRLmpf', 'example_files', 'mpf')"
$ cd mpf/

To copy them into an existing working directory (“.” as third argument) - e.g., the current one where you have used baseline correction scripts - you can optionally pass a prefix as the fourth argument to the CopyPkgFiles function:

$ cd /path/to/workingdir/
$ R -e "APRLspec::CopyPkgFiles('APRLmpf', 'example_files', '.', 'mpf')"

This will add a prefix to all the example files in this directory to prevent naming conflicts with files from other packages.

To uninstall, run the command in R:

> remove.packages("APRLmpf")

Fit peaks

$ Rscript main_fits.R testcase/userinput.json

Key parameters in .json file:

specfile: sectra file
peaksequence: list of peaks or profiles to be fitted in sequence
limitcCOH: limit estimated moles[carboxylic COH] to be less than or equal to estimated moles[carboxylic CO]. carboxylic CO must appear before carboxylic COH in peaksequence

Outputs:

fitpars.csv
pkareas.csv

Plot fits

$ Rscript plot_fits.R testcase/userinput.json

Key parameters in .json file:

specfile: sectra file

Outputs:

specfits.pdf

Apply Beer-Lambert law

$ Rscript conv_areas.R testcase/userinput.json

Key parameters in .json file:

abscoef: (optional) json file of absorption coefficients

Outputs:

moles.csv: micromoles per collection surface area

Test cases

testcase: Use with main_fits.R. Most similar to Takahama et al. (2013).
testcase2: Use with main_fits.R. Experimental – fit everything together.
testcase3: Use with main_fits_constr_cCOH.R. Constrain moles of carboxylic COH <= moles of carboyl CO.

Future work

improve I/O
allow specification of numerical maskbounds
Lorentzian and Voigt lineshapes