joelnitta

#' Write out a geography file in PHYLIP format for BioGeoBears
#'
#' @param data Dataframe; species distributions in regions, with one row per 
#' region per species. Must have columns 'species' and 'region'
#' @param output_file Path to write outputfile
#'
#' @author Joel Nitta
#' 
#' @return The the path to `output_file`.
#' 

joelnitta

library(tidyverse)

dat <- tibble(var = c("a_b", "c_d"))

split_vec_to_df <- function(x) {
  tibble(
  var_1 = str_split(x, "_")[[1]][[1]],
  var_2 = str_split(x, "_")[[1]][[2]]
  )
}

joelnitta

library(tidyverse)

path_to_csv_file <- "change/this/to/the/path/on/your/machine.csv"

# Load the participants responses
# The `#` column has a unique ID for each answer, but this is not the same
# as the user-entered unique ID (those are unfortunately NA in some cases as the
# participant didn't answer that question)
partic <- read_csv(path_to_csv_file) %>%
  rename(num = `#`)

joelnitta

# Filter a list of references in YAML format to those cited in an RMD file
#
# The YAML list should be exported from Zotero
# like this: file -> "export library" -> "Better CSL YAML"
#
# Exporting YAML from Zotero requires the Better Bibtex for Zotero extension
# to be installed https://retorque.re/zotero-better-bibtex/

library(tidyverse)
library(yaml)

joelnitta

#' force_ultrametric
#'
#' Force the branch lengths of a tree to be ultrametric. Most useful in cases
#' when a time-tree is imported into R but the branch lengths are not exactly
#' ultrametric due to rounding error. Uses a different (faster) method from
#' phytools::force.ultrametric()
#'
#' @param tree Input tree; list of class "phylo". Should already be ultrametric 
#' within rounding error.
#' @param force.positive Logical; should the branch lengths be forced to be

joelnitta

---
title: "`posterdown`: Generate Reproducible & Live HTML and PDF Conference Posters Using RMarkdown"
author:
  - name: Brent Thorne
    affil: 1
    orcid: '0000-0002-1099-3857'
  - name: Another G. Author
    affil: 2
affiliation:
  - num: 1

joelnitta

<?xml version="1.0" encoding="UTF-8" standalone="no"?><beast beautitemplate='Standard' beautistatus='' namespace="beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood" required="" version="2.6">


    <data
id="primates"
spec="Alignment"
name="alignment">
                    <sequence id="seq_Gorilla" spec="Sequence" taxon="Gorilla" totalcount="4" value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAAC

joelnitta

library(tidyverse)

# Specify directory with files to get checksums
dir <- "my_folder"

# Get checksums
list.files(dir, full.names = TRUE) %>%
  tools::md5sum() %>%
  tibble(file = names(.), checksum = .) %>%
  filter(!is.na(checksum)) %>%

joelnitta

# This function can be called inside of other functions to check
# if the names of the input match the names of the arguments
check_args <- function(call_match) {
	call_names <- as.character(call_match)
	arg_names <- names(as.list(call_match))
	stopifnot(
		"Names of input must match names of arguments" = isTRUE(all.equal(call_names[-1], arg_names[-1]))
	)
}

joelnitta