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First release of software for the article: Searching for Low-Mass Exoplanets Amid Stellar Variability with a Fixed Effects Linear Model of Line-by-Line Shape Changes. This repository includes code and summaries corresponding to the paper "Searching for Low-Mass Exoplanets Amid Stellar Variability with a Fixed Effects Linear Model of Line-by-Line Shape Changes". The code uses R (https://www.r-project.org/) and assumes you have installed the following packages: tidyverse, rhdf5, Matrix, patchwork, collapse, parallel, pbmcapply Data used for this paper can be found at: https://doi.org/10.5281/zenodo.14841436 If you come across any issues or bugs, please contact Joseph Salzer at jsalzer@wisc.edu. 

The following repository contains the data used for the manuscript: "Searching for Low-Mass Exoplanets Amid Stellar Variability with a Fixed Effects Linear Model of Line-by-Line Shape Changes". Within line_property_files.zip there is file "line_property_files_README.md" that contains a description of each column of completeLines.csv. The important columns of this csv are date: time of observation line_order: unique identifier of a line, a combination of that line's central wavelength and order ID rv_template_0.5: the RV measure for a given line on a given day fit_gauss_a,fit_gauss_b,fit_gauss_depth,fit_gauss_sigmasq,proj_hg_coeff_0,proj_hg_coeff_2,proj_hg_coeff_3,proj_hg_coeff_4,proj_hg_coeff_5,proj_hg_coeff_6,proj_hg_coeff_7,proj_hg_coeff_8,proj_hg_coeff_9,proj_hg_coeff_10: the shape-change covariates that we use to control for stellar activity Below is a description of each of the data files completeLines.csv: this csv file contains the time series of every line's shape measurements and RVs, it is used throughout the analysis. line_property_files.zip: this directory contains .h5 files that contain all line-shape information and contaminated RVs for each line used in our analysis. The script clean_data.Rmd uses these as input and combines them all into a single csv file called completeLines.csv. project_template_deriv_onto_gh.h5: this contains the projection vector described in the paper to produce the orthogonal HG coefficients. The script clean_data.Rmd uses this as input and combines them all into a single csv file called completeLines.csv. models.zip: this directory contains the results from each model that was fit for our paper.