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RESOURCES & TIPS

My go-to's for advice in academia

CommKit

General tips for fellowship applications, CV/Resume, figure & poster design, manuscripts etc.

Gaston Sanchez 

List of R books, stats courses, coding tutorials (Version control, Git, data visualisation, R, makefile), softwares, talks, experiments from Gaston Sanchez.

Successful “skype” interview

Tips for a successful “skype” interview. Bill Currie (Dec 2018)

Manage large research project

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)

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)

5 common writing mistakes

Five common writing mistakes new scientists make. Jacquelyn Gill (Aug 2018)

Academic phasebank

Provides examples of some of the phraseological ‘nuts and bolts’ of writing organised according to the main sections of a research paper.

Replying to student emails

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)

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)

Which graph to use?

List of different data visualisations and descriptions. 

Presenting stat results

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)

Top Ten Slide Tips

Tips for better presentation slides. Garr Reynolds

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.

Caveats in data visualization

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)

My go-to's for statistical advice

Choosing statistical analysis

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.

GLMM F&Q

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. 

Estimated marginal means

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.

Interpreting lm outputs in R

Explains what formula call, residuals, coefficients, residual s.e.  r-squares, f-statistics means. 

Solving problems with GAMs

Provide solutions to some common problems when fitting GAMs with mgcv and ways to solve them. 

My go-to's for ggplot2 

ggplot2 essentials

EVERYTHING to do with ggplot2.

ggplot2 tutorial

Tutorial for creating plots in ggplot2.​

R tutorials

An introduction to R

Beginners guide to programming in R.

The Coding Club

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).

Meta-analysis

Tutorial using R package 'metafor'.

Fitting a quadratic model

Fitting polynomial models in R. 

ggpmisc functions

Various model fits on plots and more complex model fits.

jtools for regression models

Generate flexible table outputs, plotting predicted data from models, and regression coefficients

Plotting interactions

The interactions package provides several functions that can help analysis interaction effects more deeply.

AquaticLifeHistory

Length-at-age modelling using a multi-model approach, estimating age-at-maturity and length-at-maturity.

 

Resources

PR statistics

Provides training courses and workshops in a broad range of statistical methods quintessential to the analysis of many different types of ecological data.

WorldClim

Set of global climate layers with a spatial resolution of about 1 km2. These data can be used for mapping and spatial modeling.

Climate data Australia

Latest set of national climate projections for Australia.

Bio-ORACLE marine data

Set of GIS rasters providing geophysical, biotic and environmental data for surface and benthic marine realms.

SeaAroundUs

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.

Open Traits Network (OTN)

A global, decentralised dataset of biological traits across a range of taxa e.g. metabolic rate, lifespan, trophic level. 

RStudio cheatsheets

List of RStudio cheat sheets for favorite packages.

Markdown cheatsheet

Quick reference to write syntax in markdown. Adam Pritchard (May 2017) [Github]

Tracker video analysis

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

tidybayes is an R package that aims to make it easy to integrate popular Bayesian modeling methods into a tidy data + ggplot workflow.

Lab-based cheats

Solution dilution calculator

The calculator uses the formula M1xV1 = M2xV2.

ENDMEMO - molarity conversion 

Molarity calculator to and from mass. 

Open-source Lab

How to build Your own hardware and reduce research costs.

RRID portal

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. 

Respiratory calculator

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. 

ADInstruments - Labchart

Essentials of Data Quality: Optimizing your range, sampling and filtering settings.

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.

Grant applications

How to get a postdoc mobility fellowship

Tips for applying for independent postdoc fellowships (Oct 2019)

Gantt chart in R

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.

Graphic Design

Colour Wheel

Calculates complementary, monochromatic, analogous, triadic etc. 

ColorHexa

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). 

Academicons

Specialist icon font for academics.

Google Fonts

Font styles from Google.

BBC visual and data journalism style

Cookbook for producing BBC style visuals in R. 

Free images - no copyright

Free photos for uses in graphic design.

htmlwidgets for R - gallery

List of R widgets for data visualisation.

References and Infographics

Resource of image references and infographics e.g. colour theory, figure & anatomy, hands, perspectives.

Descience

A blog on the confluence of science communication and design.

Tabletop Whale

Updated occasionally with science-themed infographic, charts & animations. Eleanor Lutz 

Graph visualisation gallery D3

Gallery of graph examples sorted by graph types. 

Cool infographics

Compilation of infographics. 

Heuristics for better figure

Advice on making better figures. Jesse Silverberg (2018)

Tints and shades generator

Display tints and shades of a given hex color in 10% increments.  

drawdata.xyz

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)

ggplot2

ggplot 2 references

Explains ggplot2 functions.

ggplot2 extension gallery

extensions for ggplot e.g. animation, interactive graph, statsplot etc.

Visualising multivariate data

Multidimensional scaling, PCA, cluster analysis in R.

Colourblind-friendly palette

Colourblind-friendly palettes available in ggplot (also see viridis in R packages).

R colour palette list

List of compiled R colour palette packages by EmiHvitfeldt.

viridis

ggplot colour palette including colour-blind friendly styles. 

PNWColors

Some beautiful colour palettes inspired by Pacific North West photos. Jake Lawlor.  

Data transparency and reproducibility

Project directory layout example

Basic structure for project layouts to increase reproducibility

Intro to R Markdown

R Markdown is a file format for making dynamic documents with R. Garrett Grolemund (July 2014)

Drake example

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.

Diego Drake example

This is the example from Kirill Müller's drake pitch slides, and it is the most accessible example for beginners.

R packages

datapasta

Copying and pasting Excel data to and from R. [GitHub]

rphylopic

Add phylopic silhouettes to R plots.

pheatmap

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].

factoextra

Principal Component Analysis (PCA), Correspondence Analysis (CA)Multiple Correspondence Analysis (MCA)Multiple Factor Analysis (MFA), etc.

colortools

Generate colour schemes in R based on analogous, complementary, tetradic, sequential etc.

ggstatsplot

Extension of ggplot2 for creating graphics with details from statistical tests. 

ggridges

Ridgeline plots are partially overlapping line plots that create the impression of a mountain range.

ggpointdensity

Introduces geom_pointdensity(): A cross between a scatter plot and a 2D density plot. Lukas PM Kremer.

ggpubr

ggplot based publication-ready plots.

cowplot

Aligning plots in R.

patchwork

Aligning plots in R.

Model output as HTML table

Output statistical models (regression models) as HTML tables. Daniel Ludecke (Aug 2019)

rotl

Interface to Open Tree of Life API.

reactable

Interactive data tables for R.

workloopR

Analysis of work loops and other data from muscle physiology experiments in R.

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