annakrystalli / campsite Goto Github PK

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• Trait at Tips: Distribution of trait values of extant lineages at the tips of the simulated phylogenies

• Trait disparity through time:

• MMND through time: Mean Nearest Neighbour Distance of trait values of extant lineages through time

• Diversification rates: Not sure what the two lines are

Phylogeny Vis

• Example extant phylogeny
• Example full phylogeny
• Lineages through time
• Example trait evolution

Here, the supplied parameter m is being overwritten. Is that intentional?

Hello @alexsla!

I've begun working on the simulation app now and the first job is to turn the campsite code to a package. I've made a fork of your repository and will make a pull request back to it when I'm done so that the commit history remains intact and the package ends up in your account.

An important file in any package is the DESCRIPTION file. Here is the current draft https://github.com/annakrystalli/CAMPSITE/blob/main/DESCRIPTION.

I need a few details from you though to complete correctly:

• Title: a short title for your package
• Description: A longer description of what the package does. Can be a short paragraph
• Authors: List of all authors with details of:
  • First name
  • Surname
  • email address (I use my personal one rather than work one which may change)
  • role (for example, you would be author & creator). You can also add funder details if wanted). I initially put myself as contributor but by the time I'm done, according to the definition in ?person I reckon the contribution will be greater than just code patches. Have a look and let me knwo what you think.
  • ORCID ID (if available)
• License: I've just added a permissive MIT license for now. Are you happy with that or would prefer something more restrictive? Here's some info on licensing: https://r-pkgs.org/license.html

For details on all metadata contained in DESCRIPTION files, have a look here: https://r-pkgs.org/description.html

Let me know if you have any questions!

Am I correct in interpreting that each trait vector relates to one of the lineage vectors?

In which case I have a few questions:

• Just to confirm, the comparison will always on a single trait and be between two lineages, correct? Or do you want the code to be able to adjust to more comparisons?
• Is any information in the trait vector a reperition of information in an associated lineage vector? ie how does status value in trait vectors relate to status in lineage vectors?
• Also, just to confirm, parental node (lineage number) in the lineage vector (first element) refers to the same property as parental lineage number (third element) in the trait vector does and therefore should have the same values across associated trait & lineage vectors? If so, why do both lineage vectors have the same parent_node:

  CAMPSITE/R/sim_CAMPSITE.R

  Lines 46 to 47 in 560f8b5

  	lineages <- rbind(c(1, 0, 0, -1, 1, 0, 0),
  	c(1, 0, 0, -1, -1, 0, NA)) #matrix of extant lineages: for each lineage (element in list), a vector of seven values: parental node (lineage number), descendent node (0 if tip), starting time, ending time (-1 if still active), status (incipient=-1/good=1/extinct=-2), speciation completion or extinction time, speciation completion time (NA if still incipient)

  whereas the parent node values in the trait vectors are different?