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carbonatestratpalevo's Issues

Make figure S2

As figure 6, but for the tests that cover the time interval of scenario B

Make supplementary figures

Preservation of stasis, Brownian motion, and weak & strong Brownian drift at different distances from shore in scenario A and B. See supplementary materials folder in onedrive for captions

Rewrite results for scenario B & adjust figure.

Rewrite section "Carbonate Platform B" in results section after adjustment of sea level curve.

  • Redo figures 1 & 2 based on captions in manuscript. Raw figures are on GH under figs/matlab

Minor Adjustments Figures

  • Make capitalization consistent (Trait value -> Trait Value, Time domain -> Time Domain etc.)
  • Make axis labels consistent (e.g. in fig. 4 parts are "Stratigraphic Height [m]", others just "Height [m]")
  • Reduce font size of titles to avoid cut-off of titles (e.g. fig. 4 bottom right)
  • Shift letters indicating sub-plots a bit to the right to reduce ambiguity
  • fig 6 & related figures:
    • move km from ticks labels to axis labels
    • reduce line width on box plots
    • make y axis consistent from 0 to 1
    • move legend out of plot windows on the right
    • adjust capitalization of titles

Make figure of time elapsed between successive samples

Make a figure with 2 rows (one for each scenario) and 5 rows (one for each distance from shore)
Each subfigure is a histogram of the time elapsed between successive samples taken in the stratigraphic domain. The y axis is number (dimensionless), the x axis is time difference (myr). Make sure the x axis limits are the same for each subplot and start at 0

Adjust Figures

  1. Name figures according to their name in the manuscript _raw (e.g. Fig1_raw.pdf, FigS2_raw.pdf)
  2. Redo Figs. 4-7. Specifically 6 & 7 based on new data
  3. Adjust figure size to Journal requirements (https://bmcecolevol.biomedcentral.com/submission-guidelines/preparing-your-manuscript#preparing+figures)
  4. Reduce temporal resolution for plots of trait evo in time domain, (maybe 200 sampling points, distributed over the 2 / 2.56 Myr)
  5. Check if for stasis, figures become more clear with only one lineage. If yes, plot only one lineage for stasis
  6. Make axis labels smaller & titles larger
  7. Rearrange order of subfigures in Fig. 5 & similar figures (ADM & time domain 1st row, dist. from shore in 2nd & 3rd row) - Maybe there is a better/more aesthetic arrangement?
  8. Automate labeling of subfigures (A, B, C, ...)

Make plot of strat completeness & hiatus duration

Make a fists sketch of the figure with stratigraphic completeness and hiatus duration vs. basin position.
Make one plot for each scenario, name it scenarioX_strat_info.pdf
The plot should contain:

  • x axis: ranging from 0.1 to 15, distance from shore [km]
  • left y axis: stratigraphic completeness as percent
  • right y axis: hiatus duration in myr. Start with plotting median, max, and 1st and 3rd quartile of the hiatus distribution. Use a log scale if if necessary

Beautify figure completeness_and_hiat_duration_raw.pdf

  • Reduce whitespace at the bottom
  • x axis labels consistent "Distance from shore [km]"
  • left y axis labels "Stratigraphic completeness [%]"
  • right y axis labels "Hiatus duration [Myr]"
  • Change header to "scenario X"
  • Make letter same size as header
  • cut off x axis at 13 km
  • Add legend to top left corner, listing
    • Completeness
    • maximum hiatus dur.
    • 1st quartile hiatus dur.
    • Median hiatus dur.
    • 3rd quartile hiatus dur.

Deposit raw data on OSF

When ms is in final stage

  • Deposit large data files on osf, specifically .mat, .Rdata files
  • Add code to automate data download

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