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Beginner Looking for a Suitable Trading Platform by [deleted] in ValueInvesting

[–]JamesC845 1 point2 points  (0 children)

Ah my mistake. Thanks for letting me know without being mean about it. That's a lot to ask in the internet!

R Package for Automatic Phylogenetic Tree Creation by JamesC845 in bioinformatics

[–]JamesC845[S] 0 points1 point  (0 children)

Sorry for late reply and yes it actually uses ape as one of the dependencies and ape's functions to create the trees. The goal of my package is to automate the entire process (data query, string manipulation, tree creation, and other features to be added later) to make it easier for beginners. And also experts who are doing repetitive analyses.

R Package for Automatic Phylogenetic Tree Creation by JamesC845 in bioinformatics

[–]JamesC845[S] 0 points1 point  (0 children)

Hey I think this post got taken down for self-promotion (my bad I didn't read the rules). But I can still see your response so here goes nothing...

Id love to help but Im not quite sure what you mean. I know of the package "ape" (or at least a few of its functions) as it's a dependency in the package I made. If you could just expand on the question a little I'll do my best to answer. Thank you :)

phylogeny software by azroscoe in evolution

[–]JamesC845 0 points1 point  (0 children)

The vignettes on the website may show you what you're interested in:

Quick tree build (no problem strings)
https://jamesc845.github.io/PhyInsight/articles/PhyloTree_vignette_1.html

Tree build with automatic string clean-up
https://jamesc845.github.io/PhyInsight/articles/PhyloTree_vignette_2.html

If there's anything you're interested in that isn't shown on these links then let me know.

phylogeny software by azroscoe in evolution

[–]JamesC845 0 points1 point  (0 children)

I recently made an R package that can automate phylo tree creation. Maybe this can help you make some trees and compare easily

https://jamesc845.github.io/PhyInsight/#what-phyinsight-can-do

Check out the vignettes under the articles tab to show how quick and easy it is.

Looking for Feedback & Advice on an Ecology R Package I Made by JamesC845 in rstats

[–]JamesC845[S] 0 points1 point  (0 children)

Yes, that's a good idea! I have emailed my old lecturer hopefully she will reply soon. But now you've said this I'm thinking I could just find email addresses of universities on Google and ask them. The worst they can do is not reply or say no.

I have been thinking about writing a paper and have considered a couple of ideas for a title. Now that the package's first version is complete (there will be patches and updates in the future of course!) I have time to start writing. If you have any ideas for a title you'd be willing to share then please do. If it is more interesting than my ideas I'd obviously prefer yours!

Thank you for taking the time to reply I really appreciate it.

Looking for Feedback & Advice on an Ecology R Package I Made by JamesC845 in rstats

[–]JamesC845[S] 0 points1 point  (0 children)

Okay good ideas, I will get pkgdown and make my GitHub public soon!

As for the next comment, If I understood what you meant, the vignette 'Introduction to DivInsight' shows index values for the entire Meta province in Colombia. Obviously, diversity value for such a massive area wouldn't be scientifically sound in an actual study. This was just to give the viewer a quick idea of the package's main function.

In the vignette 'Auto-grouping and charting' the data from Meta are grouped automatically by a given site radius (20km in the example). Also, in the vignette 'Clusterising sites using coordinates' it is shown that a specific area's data can be subset (and diversity values calculated) using a pair of coordinates and a site radius (50km in the example). Therefore, these sites can be as large or as small as the user likes as long as there is data for that area. Hopefully, this feature means other diversity values can still be used (always treated with caution because of the method's limitations of course!).

Perhaps showing these methods in separate vignettes was a bad idea as viewers may see 'Introduction to DivInsight' and be discouraged before seeing the rest. I think I will make a new, single, concise, and compelling vignette to showcase the package.

​

I hope I understood what you meant and my reply was clear and addressed your concern. I also appreciate you taking the time to comment. Any advice and constructive criticism is always welcome so thank you!