Data and MatCont-files to reproduce the main analyses in Lindmark et al (2018).
- Update: Early view is now online in Ecology Letters! https://onlinelibrary.wiley.com/doi/10.1111/ele.13235#.XHzzJqZzqpk.twitter
Data: contains simulated data used for creating figures R: scripts for producing figures based on already simulated data MatLab_Mat_Cont_model_files: contains model files and text files for implementing the model in MatCont
If you want to:
reproduce the figures
... based on the simulated data, please see the folder "R" which uses already simulated and saved data, stored in folder "Data". The packages used are:
tidyverse 1.2.1 -- v ggplot2 2.2.1 v purrr 0.2.4 v tibble 1.4.2 v dplyr 0.7.4 v tidyr 0.8.0 v stringr 1.3.1 v readr 1.1.1 v forcats 0.3.0
see how the model is implemented in matcont
... see "MatLab_MatCont_model_files_revision" or "MatLab_MatCont_model_files_generic" for the original model formulation, see "msII_Paper_MatCont_implementation.txt" and "User_functions.txt" (which are needed to track non-state variables in MatCont, such as maturation or net biomass production. Note, only in the "empirical" model!)
open the model in MatCont GUI and re-export or check simulated curves
... follow the instructions below.
Navigate to folder MatLab_MatCont_model_files:
The zip-file "MatCont_files" contains files for opening the model in MatCont GUI to redo analysis or re-export data used for plotting (see Data and R folders if you want to reproduce the figures based on already saved data):
The zip-file "MatCont_files" contains the following:
- The computed curves (Diagrams)
- msII_Paper.m (This is the model generated by MatCont GUI)
Steps: Install MatLab and MatCont (https://sourceforge.net/projects/matcont/) You will need the student version or any version that contains the symbolic package. This is needed to use the heavyside function that is implementeted in the maturation function; see text file "msII_Paper_MatCont_implementation".
- To open the model, to view the computed equilibrium curves and to use the matlab code (file: msII_Paper_export_data_MATLAB) to export data as .csv do like this:
- Navigate to the "Systems" folder in your MATLAB directory (MATLAB -> "matcont" -> Systems)
- Unzip the file "MatCont_files"
- Drag the unzipped contents (1) "msII_Paper" folder, (2) the msII_Paper.mat and (3) the msII_Paper.m files to the "Systems" folder in your MatLab folder, see above
- Open MatCont by typing matcont in the MATLAB command window.
- Now you can open all the diagrams and view them in matlab or use the MatLab code in the file "MatLab_MatCont_model_files/msII_Paper_exporting_curves" to export the diagrams as .csv files locally (*Note, change file path!)
- *Note, the names are very abbreviated! Rather than writing the names out here, I suggest you check first identify which analysis (figure) you want to look at, and then check the data-folder here to find which curves in Matcont correspond to which figure (in cases where this is not obvious!)