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I wasn't sure where to start reproducing the analysis. Please clarify the order of execution of steps in all readme files.

It seems like the base file (https://github.com/lypluo/photocold_manuscript/tree/main/data/data_used/df_all_results) is not part of the github repo. We should find a solution for that so that everybody who wants (and definitely GECO group members) can reproduce the analysis.

Ideally, you start by stating in the top-level readme what the original data file is and where it was obtained from. In our case, this was a file (data frame) containing daily data for all sites with variables including meteorological drivers, observed GPP, modelled GPP (different model setups), and MODIS fAPAR. Clarify where that file is.

Different analysis steps then complement this data frame (smoothed GPP, SD of error w.r.t. normal distribution of errors fitted outside greenup) and produce derived data frames (e.g., one with SOS, POS, and EOS for each site and year). Where are these files? Please describe files read and produced, and respective scripts implementing each analysis step in the README.

Complement readme in https://github.com/lypluo/photocold_manuscript/tree/main/analysis to make the following analysis steps discoverable (describe which scripts implement which analysis step, data objects and files produced by each step/script). Most important analysis steps are:

• LME model fitting
• Steps described in manuscript section 2.3 Identifying environmental drivers of DSPR:
  • normalisation
  • smoothing spline
  • SOS, POS and EOS definition
  • normal distribution of errors and SD for each day's bias
  • classification into overestimation-affected days and years
• Analysis of aligned plots (Fig. 2); should be part of the analysis step because you transform a data object.
• Implementation of the cold acclimation modifier (where is that function?)
• Calibration of parameters in cold acclimation modifier