PAST RESEARCH
NICHOLAS WU
Ecological Physiologist at Western Sydney University, Australia
0000-0002-7130-1279
RESOURCES & TIPS
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My go-to's for advice in academia
General tips for fellowship applications, CV/Resume, figure & poster design, manuscripts etc.
List of R books, stats courses, coding tutorials (Version control, Git, data visualisation, R, makefile), softwares, talks, experiments from Gaston Sanchez.
Tips for a successful “skype” interview. Bill Currie (Dec 2018)
Tips for managing large research projects. Eva Lantsoght (Jan 2013)
Questions asked during academic interviews
Common questions and tips for answering them. Mike Lee (Mar 2021)
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Writing tips
Writing your first scientific paper
Five minutre guide to writing your first scientific paper. Michael S. Y. Lee (Mar 2021)
How to write scientific abstract
Tips for writing scientific abstracts (Jan 2010)
The 5 pivotal paragraphs in a paper
Brian McGill (Feb 2016)
Five common writing mistakes new scientists make. Jacquelyn Gill (Aug 2018)
Provides examples of some of the phraseological ‘nuts and bolts’ of writing organised according to the main sections of a research paper.
Types of student emails and tips for replying back. Steffen Wilson and Dan Florell (Apr 2012)
Writing recommendation letters for undergrads
Advice for writing recommendation letters for undergrads. Prosanta Chakrabarty (Mar 2015)
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For PhD students
Choosing an appropriate PhD supervisor
Types of supervisors and approaches.
Twenty things I wish I’d known when I started my PhD
Lucy A. Taylor (Nov 2018)
How to write a PhD in Biological Sciences
An excellent, detailed guide for any PhD candidate in Biological Sciences. John Measey (Sept 2021)
Responding to reviewer comments
Suggestions for responding to reviewer comments. Alex Bond (Nov 2018)
List of different data visualisations and descriptions.
Presenting stat results in the result section of a scientific paper. Stephen Heard (Oct 2018)
Collegiality as a Graduate Student
How graduate students should behave towards other graduate students or academics they don’t know. Melissa R. Elmes (Mar 2014)
Tips for better presentation slides. Garr Reynolds
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My go-to's for Graphic design principles
How to Design an Award-Winning Conference Poster
Guide for designing a conference poster.
How to Make your First Scientific Poster
A well-thorough guide for designing conference posters. Melisa Morales (May 2022)
Fundamentals of Data Visualisation
A detailed guide on the theory and principles of visualising data in R.
A Scientist's guide to making presentations
A visual guide to making nice-looking presentations for scientist's.
A collection of common caveats in data presentation like spaghetti graphs, clutter, dual-axis, overplotting etc.
Why scientists need to be better at data visualization
Avoiding design missteps can improve understanding of research. Betsy Mason (Dec 2019)
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My go-to's for statistical advice
Tables with general guidelines for choosing a statistical analysis. Includes R codes.
Common linear model stat tests
List and guides of different linear models.
Principal Component Methods in R
To summarise and visualise information contained in large multivariate data sets. Provides practical examples and course videos to compute and interpret principal component methods (PCA, CA, MCA, MFA, etc).
Tools for summarising regression models
Summarising regression models in R.
F&Q for commonly used functions in mixed models like linear mixed models, generalized linear mixed models, nonlinear mixed models.
Partial Least Squares Regression in R
Example codes to build PLS model.
Example tutorial for estimating marginal means via emmeans R package.
Visual Introduction to Hierarchical Modeling
This visual explanation introduces the statistical concept of Hierarchical Modeling, also known as Mixed Effects Modeling or by these other terms. This is an approach for modeling nested data.
Meta-analysis tips for metafor package in R
Various tips and tricks with links to produce plots using the metafor package.
Explains what formula call, residuals, coefficients, residual s.e. r-squares, f-statistics means.
Provide solutions to some common problems when fitting GAMs with mgcv and ways to solve them.
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My go-to's for ggplot2
EVERYTHING to do with ggplot2.
Tutorial for creating plots in ggplot2.​
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R tutorials
Beginners guide to programming in R.
R tutorials ranging from MCMCglmm, spatial data and maps, time series, coding etiquette, data manipulation, dplyr etc.
Ancestral state reconstruction & visualizing ancestral states on a phylogeny
Liam J. Revell (Aug 2015).
Tutorial using R package 'metafor'.
Fitting polynomial models in R.
Various model fits on plots and more complex model fits.
Generate flexible table outputs, plotting predicted data from models, and regression coefficients
The interactions package provides several functions that can help analysis interaction effects more deeply.
Length-at-age modelling using a multi-model approach, estimating age-at-maturity and length-at-maturity.
Resources
Provides training courses and workshops in a broad range of statistical methods quintessential to the analysis of many different types of ecological data.
Set of global climate layers with a spatial resolution of about 1 km2. These data can be used for mapping and spatial modeling.
Latest set of national climate projections for Australia.
Set of GIS rasters providing geophysical, biotic and environmental data for surface and benthic marine realms.
Fisheries and fisheries-related data at spatial scales that have ecological and policy relevance, such as by Exclusive Economic Zones, High Seas, or Large Marine Ecosystems.
A global, decentralised dataset of biological traits across a range of taxa e.g. metabolic rate, lifespan, trophic level.
List of RStudio cheat sheets for favorite packages.
Quick reference to write syntax in markdown. Adam Pritchard (May 2017) [Github]
A free video analysis and modeling tool for kinematic and biomechanics analysis.
Bayesian Data Analysis course material
This repository has course material for Bayesian Data Analysis course at Aalto (CS-E5710).
tidybayes is an R package that aims to make it easy to integrate popular Bayesian modeling methods into a tidy data + ggplot workflow.
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Lab-based cheats
The calculator uses the formula M1xV1 = M2xV2.
Molarity calculator to and from mass.
How to build Your own hardware and reduce research costs.
Resource Identification Portal to authenticate key biological resources: Antibodies, Model Organisms, and Tools (software, databases, services).
Electrophoresis – Protein Staining Reagents
Reagents detection and compatibility table for Western blotting.
Calculators to estimate metabolic rate of various taxa, pressure, STP, rate and volume correction, temperature, water vapor.
Vaisala Humidity Calculator 5.0
Calculate humidity from temperature and atmosphere pressure.
Essentials of Data Quality: Optimizing your range, sampling and filtering settings.
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Publishing
How to publish in Biological Sciences
Detailed guide on publishing in peer-reviewed journals. John Measey (Sept 2021).
JANE - Journal/Author Name Estimator
Not sure to which journal you should submit to? Or maybe you want to find relevant articles to cite in your paper? Or are you an editor, and do you need to find reviewers for a particular paper? Just enter the title and/or abstract and JANE will then compare your document to millions of documents in PubMed to find the best matching journals, authors or articles.
10 most- common mistakes when choosing a paper title
Anna Clemens.
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Grant applications
How to get a postdoc mobility fellowship
Tips for applying for independent postdoc fellowships (Oct 2019)
Create project timetable in ggplot2. Jeremy Yoder (Jan 2019)
Output publications from ORCID
Converts authors OCRID publications and output's the papers in alternative formats to suit what the funder wants.
Sample Size Calculations with {pwr}
A way to estimate sample size for study designs and timelines.
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Graphic Design
Calculates complementary, monochromatic, analogous, triadic etc.
Free color tool providing information about any color and generating matching color palettes for your designs (such as complementary, analogous, triadic, tetradic or monochromatic colors schemes).
Specialist icon font for academics.
Font styles from Google.
BBC visual and data journalism style
Cookbook for producing BBC style visuals in R.
Free photos for uses in graphic design.
List of R widgets for data visualisation.
Resource of image references and infographics e.g. colour theory, figure & anatomy, hands, perspectives.
A blog on the confluence of science communication and design.
Updated occasionally with science-themed infographic, charts & animations. Eleanor Lutz
Graph visualisation gallery D3
Gallery of graph examples sorted by graph types.
Compilation of infographics.
Advice on making better figures. Jesse Silverberg (2018)
Display tints and shades of a given hex color in 10% increments.
Draw your line or scatter data points and download into R to plot.
Guide to designing infographics
10 things to know before designing an infographic. Ryan Hammill (2020)
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ggplot2
Explains ggplot2 functions.
extensions for ggplot e.g. animation, interactive graph, statsplot etc.
Multidimensional scaling, PCA, cluster analysis in R.
Colourblind-friendly palettes available in ggplot (also see viridis in R packages).
List of compiled R colour palette packages by EmiHvitfeldt.
ggplot colour palette including colour-blind friendly styles.
Some beautiful colour palettes inspired by Pacific North West photos. Jake Lawlor.
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Data transparency and reproducibility
Project directory layout example
Basic structure for project layouts to increase reproducibility
R Markdown is a file format for making dynamic documents with R. Garrett Grolemund (July 2014)
This repository is part of a community effort to collect, curate, and share publicly available examples of data analysis projects powered by the drake R package.
This is the example from Kirill Müller's drake pitch slides, and it is the most accessible example for beginners.
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R packages
Copying and pasting Excel data to and from R. [GitHub]
Add phylopic silhouettes to R plots.
Implementation of heatmaps that offers more control over dimensions and appearance.
dabestr: Data Analysis using Bootstrap-Coupled Estimation
Estimation statistics is a simple framework that avoids the pitfalls of significance testing. It uses familiar statistical concepts: means, mean differences, and error bars. More importantly, it focuses on the effect size of one's experiment/intervention, as opposed to a false dichotomy engendered by P values [Github].
Principal Component Analysis (PCA), Correspondence Analysis (CA), Multiple Correspondence Analysis (MCA), Multiple Factor Analysis (MFA), etc.
Generate colour schemes in R based on analogous, complementary, tetradic, sequential etc.
Extension of ggplot2 for creating graphics with details from statistical tests.
Ridgeline plots are partially overlapping line plots that create the impression of a mountain range.
Introduces geom_pointdensity(): A cross between a scatter plot and a 2D density plot. Lukas PM Kremer.
ggplot based publication-ready plots.
Aligning plots in R.
Aligning plots in R.
Output statistical models (regression models) as HTML tables. Daniel Ludecke (Aug 2019)
Interface to Open Tree of Life API.
Interactive data tables for R.
Analysis of work loops and other data from muscle physiology experiments in R.
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