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followers: 49.0 following: 63.0 repos: 60.0 gists: 77.0

Name: Daniel Padfield

Type: User

Company: University of Exeter

Location: Cornwall

Blog: https://padpadpadpad.netlify.app/

I am a microbial ecologist at the University of Exeter with broad interests that span climate change, evolution, and community ecology. I have been using R for >10 years and authored and maintain the R packages nls.multstart and rTPC and specialise in the wrangling and manipulation of large datasets and statistical analyses. I am also a bioinformatician, processing and analysing everything from 16S sequencing to de novo genome assembly, the latter using bash. Basically a bit of jack-of-all-trades master of none!

All of my code and data from my publications should live on GitHub, so if you have any questions about my work, please contact me.

Daniel Padfield's Projects

2023_ecehh_openscience

addinslist

Discover and install useful RStudio addins

aimee_dose_response

Script for the analysis of some dose response data of communities

alex_biolog_sequencing

Cleaning, analysis and visualisation of biolog data and sequencing analysis

bact_comm_ab

bacterial-genome-assemblies-with-multiplex-minion-sequencing

bartlett_et_al_2022_human_pathogens

bayestraitsacrallnodes

Example of how to reconstruct all ancestral nodes using BayesTraits

blogdown_source_old

Repository to store blown source content

breweruoe

Use University of Exeter Colour Schemes Easily in R

castledine_2022_frontiers

castledine_et_al_2018_jeb

data, analyses and figures from Castledine et al. (2018) JEB

copper

get pictures of Copper (my dog) in your R console

cv

My CV/resume

dada2_pipeline_r

Pipeline for running sequencing analyses using dada2

dataviewer

An RStudio Addin for visualising data, exploratory analyses, and identifying outliers

docker-treepl

Dockerfile for treePL

edenmicrobes

Data and analysis of projects related to microbes at the Eden Project.

engsoccerdata

English and European soccer results 1871-2020

f1000_workflow

five_species_community

Processed data and scripts from the work describing a stable five species community.

five_species_community_paper

Processed data and code for paper describing 5-species microbial community

host_parasite_invasibility

Looking at how host-parasite coevolution influences invisibility in Pseudomonas fluorescens

lab_methods

instructions for simple lab methods

lear_et_al_2022_stoten

Code and analysis for: Lear et al. (2022) Bacterial colonisation dynamics of household plastics in a coastal environment. Science of the Total Environment

markdown-cv

Simple Markdown CV / Resume

mctoolsr

Microbial community analysis tools in R

microbiouoe

R package for Buckling and Westra labgroups

myxo_diversification

Processed data and code for the project exploring the macroevolution of Myxobacteria in natural environments.

nls.multstart

Non-linear regression in R allowing multiple start parameters

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