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Daniel Padfield padpadpadpad

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padpadpadpad / mutate_at_base_R_example.R

Last active September 4, 2017 13:29

example using mutate_at() and base R to edit multiple columns indexed from another data frame

	# load in packages
	library(dplyr)

	# create two random dataframes
	random <- data.frame(y = rnorm(30, 10), x = rnorm(30, 100), z = rnorm(30, -15))
	fixed <- data.frame(y = rnorm(30, 10), x = rnorm(30, 10), z = rnorm(30, 10), a = rnorm(30, 10))

	# find columns to change the values of
	cols_change <- colnames(fixed)[colnames(fixed) %in% colnames(random)]

padpadpadpad / RStudio__brms_play.R

Created October 5, 2017 16:25

	# testing non-linear regression methods

	# devtools::install_github('padpadpadpad/nlsLoop')

	library(nlsLoop)
	library(dplyr)
	library(tidyr)
	library(ggplot2)
	library(brms)
	library(ggridges)

padpadpadpad / RStudio__2017-10-08-using-blast-on-sanger-sequences-in-r.R

Created October 8, 2017 14:27

	## ---- setup, echo = FALSE------------------------------------------------
	knitr::opts_knit$set(root.dir = normalizePath('../..'))

	## ---- load_packages, message = FALSE, warning = FALSE--------------------
	# load packages into R
	library(rBLAST)
	library(taxize)
	library(dplyr)
	library(tidyr)
	library(purrr)

padpadpadpad / get_guardian_crossword.R

Last active November 14, 2017 16:13

code to get Guardian quick crossword

	# load packages
	library(dplyr)
	library(tidyr)

	# get today's date and base url in the dataframe
	dat <- data.frame(date = as.character(Sys.Date()),
	url = 'https://crosswords-static.guim.co.uk/gdn.quick.pdf')

	# replace '-' with ''
	dat <- mutate(dat, date = gsub('-', '', date))

padpadpadpad / Testing_ips_raxml.R

Last active December 7, 2017 11:13

A rough and ready test of ips::raxml()

padpadpadpad / phylo_tree_with_FastTree.R

Last active December 11, 2017 10:27

padpadpadpad / mothur_PCoA.R

Last active December 17, 2017 12:02

	# Mothur PCoA Dirk sequencing

	library(ggplot2)
	library(dplyr)
	library(tidyr)

	# replace metadata with new metadata
	meta_new <- read.csv('~/Desktop/Work/dirk_sequencing/data/metadata.csv', stringsAsFactors = FALSE) %>%
	mutate(., time = as.character(time))

padpadpadpad / nls_bootstrap.R

Last active December 19, 2017 23:32

Quick bootstrap of a nls model using dplyr and broom

	# quick bootstrap of a TPC model

	# load packages
	library(ggplot2)
	library(dplyr)
	library(tidyr)
	library(nls.multstart) # devtools::install_github('padpadpadpad/nls.multstart')
	library(broom)
	library(purrr)
	library(patchwork) # devtools::install_github('thomasp85/patchwork')

padpadpadpad / plot_league_tables.R

Last active December 27, 2017 10:36

Use engsoccerdata to plot league tables through time

	# Get league tables from engsoccerdata
	# Daniel Padfield

	# load in packages
	library(engsoccerdata)
	library(dplyr)
	library(tidyr)
	library(ggplot2)

	# load in data

padpadpadpad / fct_reorder_example.R

Created February 5, 2018 16:08