Daniel Padfield

NCBI taxids not matching

2

Hi Firstly I have found the documentation and usage of mmseqs2 for taxonomic assignment to be extremely good and easy to follow! However, just a quick point that some of...

Can TimeTree convert a non-ultrametric tree to an ultrametric tree?

3

Hi I have created a tree using RaxML of a bacterial dataset which has ~4000 tips. For downstream analysis I need this to be ultrametric, but am struggling to find...

Getting taxonomic information from a standard blast database

7

Hi Great package. I am trying to get taxonomic information out of the BLAST call. I have added a custom format argument of `'6 staxids'`. I am running blast 2.10.10....

R code not working when function call stacked across two lines with radian.

1

**Describe the bug** When I send ggplot2 code from a script to a radian terminal on VSCode (v1.70.2), if the specific command is over two lines, it errors. It appears...

tbe values when using a constraint tree

1

Hi everyone I am running raxml-ng with a constraint tree and it does everything I want for a single tree. I manually re-root the tree using figtree and all my...

Latest install of rstanarm stan_surv() fails with random effects.

9

#### Summary: I downloaded rstanarm in my usual way and tried to run a stan_surv model with random effects and it errors. #### Description: When I run the example from...

Any way to get full text from rcrossref anymore

2

Hi everyone Just wondering if there is anyway to get full text from rcrossref anymore. I am interested in trying to collate Data Accessibility statements and am conscious publishers probably...

hex_to_rgb() returns string not matrix

2

Hi! Super cool package. I used it to extract hex codes for transparent values of a whole palette to use as different layers of a ggplot2, as the colours represent...

Keeping model fits when using SummarizeGrowthByPlate

2

Hi growthcurver team Just like to say how useful the package is. The one problem I have had using it is that it is hard to evaluate model fits when...

I get this error when trying to run `gistfo:::gistfo()`. `Error: Failed to create local cache ('.httr-oauth')`. Have run `usethis::gh_token_help()` and everything seems ok. Token scopes include 'gist, repo, user, workflow'...