Seascape Models – Seascapemodels

Chris Brown’s blog on ocean science, quantitative ecology and R programming. Find our R blogs on R-Bloggers.

Estimating harvest levels to reduce feral deer populations in Tasmania

research

Feral deer were introduced to Tasmania for hunting, but are becoming an increasing environmental, agricultural and road safety issue. They damage sensitive vegetation and…

Environmental impacts of large language models

research

Just want to quickly highlight a few investigative blogs on the environmental impacts of LLMs.

modelbased package for plotting interactions

rstats

I’ve been a big fan of the visreg package for a while, it makes it convenient to plot predictions from models. But recently I was struggling with a model that had many…

Forage fish fisheries and marine predators

research

Below are some links for my class on this topic

Resource for using Large Language Model tools in R

rstats

genAI

If you’re interested in using Large Language Models (LLMs) with R, you should check out Luis D. Verde Arregoitia’s new online resource: Large Language Model tools for R. Its…

New online book AI Assistants for Scientific Coding

rstats

genAI

I’ve released a new online book, AI Assistants for Scientific Coding. It’s a practical guide to using language models to support scientific computing and analysis.

Automating the Github Copilot Agent from the command line with Copilot CLI

rstats

genAI

Github Copilot CLI (Command Line Interface) recently became available. It is an AI agent, meaning it can use tools autonomously in a loop. It has two modes:

Planning an effective workshop

research-skills

This week in lab meeting we discussed planning a workshop. Here are a few notes of pointers that came up in the discussion.

Generative AI and R workshops in Hobart Australia

rstats

genAI

In person Hobart Australia 11th and 12th November 2025

AI generated scicomm games

genAI

research-skills

This week I ran a talk and workshop for the Tasmanian Student Science Communicators Network.

Projecting Uncertainty in Ecosystem Persistence Under Climate Change

research

modelling

coastal-wetlands

Rising seas and coastal development are pushing mangrove forests beyond their historical limits. Predicting how these critical ecosystems will respond is much harder when…

Paper in a prompt creating a first draft in one prompt

rstats

genAI

*It was a rather long prompt

AI aided note taking

research-skills

genAI

This is my favourite workflow for note taking at the moment:

Making the jump from PhD to Postdoc

research-skills

In our lab meeting today we talked about the transition from a PhD to a postdoc position. I’m sharing some of the advice from the lab and reflections here.

Create reports and tutorials with generative AI from R

rstats

genAI

research-skills

Several AI model providers have integrated web search capabilities into their large language models. I was attempting to use these features via the R ellmer package.…

Points to consider when framing a regional study for the international literature

research-skills

At lab meeting today we discussed how to take your regional study and frame it for the global literature. This framing is essential for engaging international audiences and…

Quick tips for facilitating a good meeting

research-skills

In roughly chronological order.

It’s getting harder to predict ecological change

research

modelling

The increasing pace of climate change and human impacts on ecosystems is pushing ecosystems beyond the envelope of past conditions. The pace of change makes predicting that…

Writing scientific papers with quarto and AI assistants

rstats

research-skills

Below is my suggested workflow for using quarto to write scientific papers. I’m currently switching to doing as many projects as possible with quarto rather than word for a…

Prompting large language models for quality ecological statistics

rstats

genAI

Announcing a new pre-print on prompt engineering for ecological statistics.. https://doi.org/10.32942/X2CS80

Why we are all naturally Bayesians not frequentists

rstats

research

I don’t see why its a thing to say “I’m a Bayesian”. Being a Bayesian is normal for any rational person as we will prove in a couple of sentences. Being a frequentist is…

Setting up VScode for R and generative AI tools

rstats

research-skills

genAI

VScode has many extensions that let you create and run entire workflows via using prompts to a large language model. Its not widely used in the R community yet, but I expect…

Open repo of ecological data for use in teaching

rstats

Just a quick announcement. I’ve organized and posted two ecological datasets that I find helpful for creating examples for teaching. The repo and instructions for use and…

Vibe coding with AI agents is not for scientists

rstats

genAI

Vibe coding is the idea of creating software with large language models (e.g. chat GPT, Claude), using only prompting and no, or very little human written code.

Why every peer review you write should be nice

research-skills

As academics, the best way we can combat ignorance and help the environment is to train and support good scientists.

Translating data and models into benefits for coastal ecosystems

research

If you attended the seminar here’s the links to all the papers and resources. Feel free to email me (c.j.brown@utas.edu.au) if you need access to any pdfs.

How to get your LLM model to run and interpret R code

rstats

genAI

Tools let AI models run code and access other applications. This can be a tool on your computer (like an R function), or access and API.

The ellmer package for using LLMs with R is a game changer for scientists

rstats

genAI

In this tutorial we’ll look at how we can access LLM agents through API calls. We’ll use this skill for created structued data from documents.

How to use large language models to assist in systematic literature reviews

rstats

genAI

research-skills

In the near future, we will all be doing systematic lit reviews by getting LLMs to gather data from papers. Below is an example of how to extract text data from a study.…

Setting up VScode for R and Cline

rstats

Cline lets you create and run entire workflows via using prompts to a large language model. Its not widely used in the R community yet, but I expect it will be soon. You can…

How your research paper can have impact on environmental management

research

research-skills

If you ask someone who the intended audience for their paper is they will often say ‘managers’.

Speeding up the recovery and restoration of coastal habitats

research

modelling

coastal-wetlands

In our new study we predict the timescales of recovery for seagrass meadows after a disturbance. We found that recovery times are often longer and more variable than might…

PhD opportunity Integrated assessment of marine ecosystems

research

I’m looking to recruit a new PhD student (international or domestic) to work on integrating ecological and social dynamics for the assessment of marine ecosystems. The…

Stock assessment models overstate sustainability of the world’s fisheries

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modelling

fisheries

A deep dive into stock assessments of fisheries around the world has revealed their sustainability is overstated – and it has implications for fisheries management and…

Chris’ secret recipe to writing papers quickly

research-skills

Work with good collaborators that you know well and who you can rely on.

Making an ocean science video game

research-skills

genAI

I programmed my own video game. Its called ‘otter vs. urchins’. It’s a space invaders style game, where sea urchins rain down on a kelp forest. The player is an otter and…

Probability intervals with GAMs

rstats

modelling

A neat trick with GAMs (generalized additive models) fit using the mgcv package is that you can use simulation to get Bayesian credible intervals. This is handy because it…

Tips for providing written feedback to students

research-skills

If you are a supervisor or teacher you will need to provide written feedback to students. This is a skill that takes time to develop. Here are some tips I’ve developed over…

New PhD opportunities in fisheries

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phd-projects

Associate Professor Chris Brown has two new opportunities for PhD projects in fisheries. We place an emphasis on the application of science to real-world management…

Introduction to structural causal modelling

rstats

A primary goal of science is to understand causes. Structural causal modelling is a framework for developing causal hypotheses to test with data.

What does generative AI mean for literature reviews?

research-skills

genAI

Literature reviews are about to change in a big way thanks to artificial intelligence that can generate text, like chatGPT. This technology can be used to define search…

What do Australian marine scientists like about their jobs?

research

I caught up with some marine scientists (and a couple of other marine professionals) to ask them what they love about their jobs, what they find hard and for their advice to…

PhD projects on marine conservation and ecosystem modelling available

research

phd-projects

Current June 2023

Bayesian structural equation model tutorial

rstats

Structural equation modelling (SEM) is a tool for exploring relationships among multiple variables. lavaan and piecewiseSEM are two of the most widely used and accessible…

University education as social media

research-skills

What social media has that much online teaching lacks is its highly engaging while being cheap to produce.

Why GLMs should be a priority when teaching statistics

rstats

research-skills

There is often debate over the best place to start when teaching students inferential statistics. The teaching of statistics should start with basic understanding of what…

Tips for using chatGPT to learn R

rstats

genAI

ChatGPT can help you learn R code. Here are some tips my team and I have worked out for ways to use the model to help with learning R.

Making predictions from GAMs in R explained by an 18th century author

rstats

As explained by ChatGPT with some minor edits by me. This post is an example for my post “Tips for using chatGPT to learn R”

Organising R scripts

rstats

Here’s some key points for how I organise my R projects.

Moving to University of Tasmania

research

I’m pleased to announce I’ve accepted a new role as Associate Professor of Fisheries Science at the University of Tasmania. I’ll be joining the team at the Institute for…

Coaching your supervisor

research-skills

When we think of coaching we usually think of someone more experienced, like a supervisor, coaching someone less experienced, like their junior staff or students. But staff…

R workshops Brisbane February 2023

rstats

Hands-on R training!

New vlogs on conservation mapping

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Chris recently headed to Heron Island for a research workshop and field visit to work with a team of national and international experts on mapping and restoration.

New vlog Conservation Hackers

research

I haven’t been writing blog posts for a while because I have been spending my time on a new project: the Conservation Hackers vlog.

How to work with non-governmental organisations

research-skills

I attended a symposium for scientists and non-governmental organisations at the Centre for Biodiversity and Conservation Science at the University of Queensland recently.

PhD projects on marine conservation and ecosystem modelling available

research

phd-projects

Current until March 2023

Science Meets Parliament

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By Dr Mischa Turschwell, Research Fellow

How to ask more questions and be a better scientist

research-skills

As the world opens up we get to reconnect with our peers in person and make new connections. Much effort is put into training graduates to ‘make the pitch’ for their…

Climate smart mangrove restoration

research

coastal-wetlands

The extent of loss of coastal ecosystems means that to recover what we’ve lost we need to restore coastal habitats like mangroves. But coastal restoration is risky in a…

Reading for new quantitative ecology PhD students updated

research

phd-projects

Here is my recommended reading list for students just starting a PhD in some aspect of quantitative ecology (updated from the list published Feb 2020). I’ve written this…

Ambitious conservation action sees a brighter future for mangroves and seagrass

research

coastal-wetlands

Ambitious restoration of mangroves and seagrasses could lead to substantial recovery of these ecosystems new research has found.

Tips for the design of ecological experiments

rstats

research-skills

Are you planning an experiment in the lab or field, or an observational study? Its a good idea to talk to a statistician before you start.

Asking and answering questions at seminars

research-skills

In our lab meeting this week we practise asking and answering questions or seminars. Asking well framed questions at seminars takes practise so after a discussion of…

Electronic monitoring offers insights into catch of western Pacific tuna longline fisheries

research

fisheries

By Max Campbell

Time for grants: grant writing strategies

research-skills

Writing major grant applications (like ARC grants) takes time, this requires planning. In a previous post I looked at how much time it takes me. Here I’ll discuss some of…

Are lengthy grant applications fair?

research-skills

In a previous post I looked at how long it takes to write for a major national grant and the strategies I use to get the application done to a decent standard.

How much time does it take to write a grant?

research-skills

Writing grants takes time and effort, but how much time? In this post I’ll show data from my time tracking app that quantifies exactly how much time it took me to write…

Running R code for all combinations of some parameters with lapply karate

rstats

Sometimes we want to run the same bit of code many times for different parameters. Then if we have multiple parameters, we may want to run the code for all combinations of…

Current approaches to Species Distribution Modelling in R

rstats

My course notes for “Current approaches to Species Distribution Modelling in R” for World Fisheries Congress 2021 are now free online.

What’s the deal with global biodiversity maps

research

A recent article “Conservation needs to break free from global priority mapping” argues we have too many global conservation priority maps. This has stirred up controversy…

New fellowship on predicting coastal ecological futures in an era of unprecedented change

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We are entering a new era of science where ecosystem change is uncharted by historical observations. Observations are the foundation of predictive science, so how can we…

Predicting global emissions from mangrove deforestation

research

coastal-wetlands

In a new study we predict global carbon emissions from different drives of mangrove deforestation. Our predictions can help nations value mangrove conservation, identify…

Combining local knowledge and scientific surveys to estimate declines in threatened species

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coastal-wetlands

In the study “Community-based management fails to halt declines of bumphead parrotfish and humphead wrasse in Roviana Lagoon, Solomon Islands” we report on declines in two…

PhD projects on marine conservation and ecosystem modelling available

research

Current until March 2023

Predicting interactive effects of multiple stressors on marine ecosystems

research

coastal-wetlands

We are working towards models to predict the impacts of multiple stressors on coastal habitats, like seagrass and mangroves, funded by an Australian Research Council…

A comparison of terra and stars packages

rstats

The other day I wrote a comparison of raster and terra packages. The other newish raster package on the block is stars. So I go through the same code here.

A comparison of terra and raster packages

rstats

The terra package looks designed to replace an old favourite raster. It is made by a similar team. The terra documentation states “can do more, is simpler to use, and it is…

Filling gaps in global assessments of ecosystems to benefit coastal wetland conservation

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coastal-wetlands

The conservation of coastal wetland ecosystems, seagrass, saltmarsh and mangroves, receives less attention than other higher profile coastal ecosystems, like coral reefs. In…

Seaspiracy talking points for discussions with general public

research

The Netflix film ‘Seaspiracy’ has stirred up controversy for among scientists for good reason. BUT the film is creating lots of opportunities to talk about ocean…

How will heatwaves and coral loss affect reef fisheries?

research

fisheries

There has been a lot of focus on the challenge of managing overfishing with the controversial new documentary Seaspiracy on Netflix. But the overfishing issue isn’t as…

How to solve common problems with GAMs

rstats

Here I’ll provide solutions to some common problems I run into when fitting GAMs with mgcv and ways to solve them. The four problems are:

When interpolation doesn’t work with GAMs

rstats

GAMs shouldn’t be used for extrapolation, and they can give strange results for interpolation too. Here I’ll explain why and we’ll look at a solution that involves changing…

How do you forecast whether your next research project will be successful?

research-skills

Making reliable forecasts the outcomes of a project is important for project planning. A typical example for a researcher is planning a collaborative new research paper. You…

Basic math biologist should know by heart

research-skills

Here’s my list of basic math biologists that will help a biologist understand fundamental biological principles and be able to broadly read the literature. If you are…

Fast functions with pipes

rstats

Pipes are becoming popular R syntax, because they help make code more readable and can speed up coding. You can even use pipes to create functions. This is handy if you want…

Encouragement not praise

research-skills

An important goal for me as supervisor of PhD students is to build their confidence. Building confidence in a scientific topic comes through growing a student’s knowledge in…

R workshops in Brisbane 2021

rstats

Our annual series of popular R workshops is on again between 22nd and 25th June 2021, in person at the University of Queensland. Over the past 5 years we’ve successfully…

New course on preparation and graphing of biological data in R

rstats

We’re running a short online introduction to data preparation and graphing. The course will cover the basics of pre-processing data, including common data wrangling…

Correcting for confounded variables with GLMs

rstats

General (and generalized) linear models can be useful for analyzing field data, where sampling is often distributed unevenly across different environmental gradients or…

Universal inference in R

rstats

When we perform a statistical test we’d like to have confidence what the Type I error rate is what we say it is (rate of false positive findings). Often scientists choose a…

Research update, addressing trends emerging in 2020

research

An excerpt from our lab meeting 7th July 2020.

PhD projects on marine conservation and ecosystem modelling available

research

Current June 2020 until January 2021

Time sinks for data wrangling

rstats

Estimating the time it will take to complete a project is an important part of being a successful PhD student, researcher or consultant. A major time sink on many analytical…

How much has the data informed your isotope mixing model

rstats

The contributions of different food sources to animal diets is often a mystery. Isotopes provide a means to estimate those contributions, because different food sources…

Are trees greener near salmon spawning streams?

research

We usually think of nutrients moving down rivers to the ocean, not the other way around. But in many temperate rivers of the northern hemisphere migration of salmon brings…

A case against pipes in R and what to do instead

rstats

Pipes (%>%) are great for improving readibility of lengthy data processing scripts, but I’m beggining to learn they have some weaknesses when it comes to large and complex…

Home isolation work success plan

research-skills

So Australia is entering into a COVID lockdown and I have my two young kids home with me full time. That means every weekday I have roles as a Dad, a husband, a primary…

Adding desktop based work to your PhD? Here’s some things to think about

research-skills

The current pandemic is causing widespread disruptions to research, as travel, universities, labs and field stations shut-down. As a PhD student your timeline for submission…

Facing uncertainty with a growth mindset

research-skills

Facing uncertainty

research-skills

Here follows a recent email I posted to my research team. Someone said I should share it here.

Spatial predictions with GAMs and rasters

rstats

One powerful use of GAMs is for interpolating to unsampled locations. We can combine GAMs with raster package to conveniently predict a GAM model to places we have not got…

Reading for new quantitative ecology PhD students

research-skills

Here is my recommended reading list for students just starting a PhD in some aspect of quantitative ecology. I’ve written this reading list to keep in mind that many new…

Three ways to calculate distances in R

rstats

Calculating a distance on a map sounds straightforward, but it can be confusing how many different ways there are to do this in R.

Using R and power analysis to inform experimental design

rstats

A collaborator once asked me: “can you do that thing where you take a little bit of data and model it up to make lots more data?”

Seagrass habitats lack protection at a global scale

research

coastal-wetlands

This blog was written by PhD student Laura Griffiths.

Make a map of your study site with tmap

rstats

I’m loving the tmap package right now. Here’s why. And we’ll look at how to make a clean map of a study site as we go.

Informing priors for a time-series models to detect declines in tiger sharks

rstats

fisheries

research

Our new research has revealed a 71% decline in tiger sharks across Queensland’s coastline (open-access version).

Three myths youve probably heard about scicomm

research-skills

The idea of an ivory tower is far from my experience. I trained in a lab of conservation biologists who were working with NGOs and government regularly to inform on…

GLM tip getting non-linear with splines

rstats

This tip is great for a quick non-linear test, before you go all the way with a GAM or parametric non-linear model.

R courses February 2020

rstats

Our next series of R courses for professionals and graduate students is now open for registration. The courses include 1-day for absolute beginners, 3 days for intermediate…

Should I do more study or start a PhD?

research-skills

Finishing your undergraduate studies is a time to make big decisions about your career. Several people have asked me recently if they should pursue more study in graduate…

We’re hiring a quantitative ecologist

research

Applications to this position closed, July 2019. Here’s the original posts, for record purposes.

Working within your lab group to create a more equitable and diverse scientific workforce

research-skills

It is well recognized that science has an equity and diversity issue, including under-representation of women in the scientific workforce and lack of cultural diversity. But…

Dodging negativity bias in a critical work culture

research-skills

Academic culture is critical. Criticizing each other’s work is how scientists improve hypotheses and theories. Criticism is an important part of advancing knowledge.

Diary of becoming a Bayesian

rstats

research-skills

Here’s my timeline of going from frequentist stats to becoming a fully fledged Bayesian eco-statistician.

R course in data wrangling and spatial analysis notes are online

rstats

I have posted the notes to our new R course in data wrangling and spatial analysis notes on this webpage.

Hiring research assistant in spatial ecology

research

We are seeking a research assistant to assist with various projects in coastal marine science at Griffith University, Queensland. The person will support our work on the Glob…

How to get leadership experience in your PhD

research-skills

Many modern PhD students expect to learn leadership skills in their PhD studies. In a previous post I discussed why leadership skills are important for successful careers.…

What type of leaders should a PhD program produce

research-skills

I read a curious quote today. It comes from a Careers article in Nature Magazine (22 Nov 2018), where they talked to several PhD students:

Finding confidence in your PhD and overcoming imposter syndrome

research-skills

2018 has been a big year for me, at work and home. I started several major grants, including starting new PhD students and hiring my first ever postdoc. Then very quickly I…

Decline in large shark species on Queensland’s coastline

research

fisheries

In work just published we report extensive declines in large shark species on Queensland’s coastline.

Generalized Linear Models understanding the link function

rstats

Generalized Linear Models (‘GLMs’) are one of the most useful modern statistical tools, because they can be applied to many different types of data. Count, binary ‘yes/no’…

How I became a science communicator without realizing it

research-skills

Would you consider yourself to be a science communicator, that is not just writing papers but doing other activities like doing interviews on radio?

Beginner Intermediate and Advanced R courses February 2019

rstats

This is an announcement of our next set of R courses. There are 4 separate courses taught over 5th-8th February 2019.

Enforcing marine protected areas to reach ecological targets for recovery

research

fisheries

Marine protected areas are often implemented without sufficient ongoing funding to ensure their objectives are not compromised by poaching.

Improving fisheries means saving their habitats

research

fisheries

coastal-wetlands

Our new research published in Fish and Fisheries argues that protecting fish habitats is critical to recovering the world’s fisheries (here’s an open access version).

Five key skills to learn in your PhD and demonstrate in job interviews

research-skills

Our PhD student Laura Griffiths, who has worked in government and as a consultant prior to her PhD led a discussion in our lab meeting on skills to demonstrate for job…

Guide to posting pre-prints for ecologists

research-skills

I just posted my fourth pre-print to bioRXiv (pronounced bio-archive), a pre-print server. On doing so I realised that the whole process is pretty opaque, so I wanted to…

New PhD opportunities to work on conserving the health of coastal wetlands

research

We are seeking PhD students to conduct research with the new Global Wetlands (GLoW) program at Griffith University.

Survey your audience and visualise the results with R and Google forms

rstats

I wanted to make my presentation on dataviz at the UQ School of Bioinformatics more interactive.

A brief guide to data visuals in R in 2018

rstats

Here are the notes from my talk on dataviz at the 2018 UQ Winterschool in Bioinformatics.

Postdoctoral job in Aquatic Ecology

research

We are seeking a postdoctoral fellow in Aquatic Ecology to work on wetlands science and environmental accounting. The person will be supervised by Dr Chris Brown and work…

Keeping up your publication track record when you change jobs

research-skills

It is exciting to start a new job, but getting those old publications finished can be difficult to manage. You might have a lot of new work to do, so finding time can be…

Ecologists are misusing isotope mixing models

research

The study of animal movement, animal diets and more generally nutrient and carbon flows in ecosystems has been transformed by stable isotope ecology. However, in a new paper …

How do I interpret the AIC

rstats

My student asked today how to interpret the AIC (Akaike’s Information Criteria) statistic for model selection. We ended up bashing out some R code to demonstrate how to…

Growing your international scientific career as a parent

research-skills

An international reputation is considered by many to be an important part of having a successful scientific career.

Four new postdoc and science communicator positions to work on the global health of wetlands

research

coastal-wetlands

Applications for these jobs have now closed, but I have kept the post here for reference

Identifying conservation priorities for ridge to reef management in tropical catchments

research

The nascent field of Ridge to Reef management aims to help plan for the impacts of land-use change and pollutant runoff on coastal marine ecosystems. One way this planning…

Should I learn sf or sp for spatial R programming

rstats

I recently received an email about some of the short-courses on my webpage. The correspondant was asked whether my course on Maps and GIS in R was still relevant, it being…

The fallacy of the 90 hour work week

research

You might often hear senior academics say you need to work extreme hours to ‘make it’ in academia. Such comments often elicit considerable debate.

How do I calculate the R squared metric for a Bayesian model

rstats

A good friend I met on a field trip long ago, Dominique Roche, recently emailed me to ask about evaluation of Bayesian models.

General Linear Models The Basics

rstats

modelling

General linear models are one of the most widely used statistical tool in the biological sciences. This may be because they are so flexible and they can address many…

New postdoc and PhD positions on multiple stressors of ecosystems

research

Applications for the postdoc job and PhD position have now closed, but I have kept the post here for reference

In rememberance of the ecosystems I knew as a child

research

Sitting on narrow rock ledge, the cold Tasmanian ocean at my feet, I wondered if ten years of living in the sub-tropics was going to ruin my attempt to dive back into the…

e-media tools for the creation, publication and promotion of academic papers

research-skills

I recently signed up for a Slack channel, a kind of chat room for work projects that seems to be popular with programmers and that some academics are picking up for their…

Aiming for balance between recreational and commercial fisheries

research

fisheries

The Queensland State Election is on 25th November. Past elections have seen promises on new fisheries policy. In a recent article for the Machinery of Government blog I…

New grant to study impacts of interacting stressors on marine ecosystems

research

I was excited to learn today that Professor Rod Connolly, Professor Isabelle Côté and I had been awarded an Australian Research Council grant to start in 2018.

Checking residual distributions for non-normal GLMs

rstats

If you are fitting a linear regression with Gaussian (normally distributed) errors, then one of the standard checks is to make sure the residuals are approximately normally…

Managing for uncertain interactions among multiple stressors of marine populations

research

This blog supplements my talk for Marine Alliance for Science and Technology Scotland workshop on Cumulative Stressors. Some of it is published by myself and others and some…

Frustration and success when trying to make a difference

research-skills

Perhaps a stereotype is the young scientist who has graduated from university and is setting out in the world to make a difference. In our field they will be typically…

Queenland The Coal State

research

I’m over here in Scotland at their National marine science and technology conference (‘MASTS’). There are a lot of talks about the ecological issues associated with green…

Stay motivated with R programming by knowing your emotions

rstats

We don’t usually think of programming as an ‘emotional’ experience. It is all code and computer logic and if using R, probably statistics.

Some thoughts about Bayesian Kriging in INLA

rstats

I have been playing around with spatial modelling in the R INLA package. This blog just records a few thoughts I have had about using INLA for kriging (spatial…

Socially equitable recovery of fisheries

research

fisheries

Efforts to recover fisheries are often contentious. Recovering fisheries may cause economic hardship to fishers who have to reduce their catches in order to allow fish…

seascapemodels.org version 2

rstats

I just (8-8-2017) updated my webpage to version 2 styling. If something is missing that you use, please let me know.

Impact of the conservation optimism hashtag

rstats

The hashtag #conservationoptimism became popular during the recent International Congress for Conservation Biology symposium. Michael Burgass asked me what its twitter…

What analysis programs drive conservation science?

rstats

With the International Congress for Conservation Biology on at the end of July I was wondering, what analysis programs are supporting conservation science? And, what…

Memorable dataviz with the R program, talk awarded people’s choice prize

rstats

For the past two years Dr Nick Hamilton has invited me to give a talk on creating data visuals with the R program at the wonderful UQ Winterschool in Bioinformatics.

What are people saying about ICCB2017 on Twitter?

rstats

Here’s a brief analysis of tweets from the International Congress for Conservation Biology to date. The conference started on the starting 23rd July I was curious to see…

What analysis program do conservation scientists use?

rstats

With the International Congress for Conservation Biology starting 23rd July I was wondering, what analysis programs are most commonly used by conservation scientists? And…

Data visuals notes for my talks in 2017

rstats

Supplementary notes for CJ Brown’s talks on dataviz in 2017 for Griffith University’s honours students and the UQ Winterschool in Bioinformatics.

Data visuals notes for my talks in 2017

rstats

Supplementary notes for CJ Brown’s talks on dataviz in 2017 for Griffith University’s honours students and the UQ Winterschool in Bioinformatics.

What does under or over-dispersion look like?

rstats

One issue that often comes up in analysis with linear models is under or over dispersion.

Smoothing a time-series with a Bayesian model

rstats

Recently I looked at fitting a smoother to a time-series using Bayesian modelling. Now I will look at how you can control the smoothness by using more or less informative…

Quantifying the magnitude of a population decline with Bayesian time-series modelling

rstats

Population abundances tend to vary year to year. This variation can make it make it hard detect a change and hard to quantify exactly what that change is.

Enhancing your research network with social media

research-skills

What defines a (successful) scientist? Their collaborations, their Phd supervisor, their students, who they cite, conferences they attend and citations of their publications…

Networks of habitats increase the vulnerability of migratory species to climate change

research

Migratory species are important components of many ecosystems and human societies. Salmon are one of the most well known migratory fish, they move between freshwaters and…

Hacks for making time-effective and lower stress decisions

research-skills

Decisions are a fundamental currency of human life. Let me give you some examples.

Visualising uncertainty in time-series using animations

rstats

I was reading an example of visualising election outcome uncertainty using a wobbly needle and wondered, could animating uncertainty help communicate for the kind of work I…

Choosing R packages for mixed effects modelling based on the car you drive

rstats

There are many roads you can take to fit a mixed effects model (sometimes termed hierarchical models) in R. There are numerous packages that each deploy different engines to…

A fast method to add annotations to a plot

rstats

Making professional looking plots in R can be fiddly. One task that I often spend ages doing is manually finding coordinates to add labels. Wouldn’t it be nice if you could…

Mean trophic levels of a genera from FishBase

rstats

How would you selectively aggregate observations using R? For instance, say you have a table of trophic level estimates by fish species, but many species are missing values.…

Make your R simulation models 20 times faster

rstats

R can be frustratingly slow if you use its loops. However, you can speed it up significantly (e.g. 20 times!) using the Rcpp package. That could turn a day long simulation…

Part 3: Spatial analysis of geotagged data

rstats

See the other parts in this series of blog posts.

Good research papers build coherent stories, but what is a coherent story

research-skills

Good storytelling is essential to write a successful research paper. And I don’t mean making things up. Science stories need to rely on data. But we need to write up the…

The next advance in spatial R

The programming tools available for scientists to use for data analysis are becoming increasingly complex and sophisticated. This trend will continue, however I believe the…

Highlights of 2016

research

It’s not every day that someone discovers something as fundamental as a new type of causality. In 2012, Sugihara and colleagues did, well almost. They describe a new method…

Protecting forests in Fiji to give coral reefs a future

research

Many of us become scientists because we have witnessed the degradation of the environment and want to ‘make a difference’. I was therefore excited when the Wildlife…

Create an interactive web map with geotagged photos

rstats

See the other parts in this series of blog posts.

Google controls who you cite

research-skills

Do you use Google scholar to search for academic papers? Then beware, the search engine is controlling, or at least strongly influencing, who you will cite.

From geotagged photos to species distribution models

rstats

My camera comes with an inbuilt GPS allowing you to geotag photos. I was on a family holiday on the beautiful Hornby Island (near Vancouver) and started wondering why the…

Extracting exif data from photos using R

rstats

See the other parts in this series of blog posts.

A ‘tidyverse’ approach to simulation models

rstats

I am a big fan of Rstudio’s (mainly led by Hadley Wickham) series of R packages known as the ‘tidyverse’. The packages modernise much of R’s functionality to better deal…

Create an inset plot

rstats

The difficulty of plotting one plot over the top of another in R has always frustrated me. I often end up opening some photo editing software (like Gimp, which is free) and…

An Introduction to Spatial Analysis in R

rstats

It takes a lot of effort to learn to program and to use R. So why bother? Here are some very good reasons
1. R is free
2. R programs are repeatable. You can share them with…

Learning from failures

research-skills

“There is no winning and losing, only winning and learning”

A fast start to R scripts

I recently heard about the Atom text editor. It has been designed for coders by coders. The idea is to have a text editor that works on any OS and is hackable. That means…

Spurious doomsday scenarios?

research

This recent article in The Guardian caught my eye (thanks to Euan Ritchie for posting it on twitter).

Write like a runner trains

research-skills

Whenever I complain about about having to edit some writing, my wife likes to remind me that my skill at writing has improved a lot in the past few years. Not that I am…

R programming tools for conservation scientists

research-skills

rstats

More info on my talk at SCBO 2016

research

Making continuous colour palettes with RColorBrewer

The RColorBrewer package makes choosing colours for your graphs easy. If you follow the link on the help page for the handy brewer.pal function, you can get to a web app…

Twitter stats from ICRS2016

research

rstats

A few people have asked me about statistics on tweets at the International Coral Reef Symposium. You can actually download all tweets that match a certain search term and…

R programming tools for coral reef scientists

research

rstats

What is the future of coral reefs? - ICRS summary

research

Coral reef ecosystems face unprecedented threats, but stories of people give me hope for the future

International Coral Reef Symposium Day 2

research

21 June 2016, Honolulu Hawaii

International Coral Reef Symposium Day 1

research

20 June 2016, Honolulu Hawaii

Wind predicts connectivity for coral reef fish

research

Connectivity of organisms among habitats is fundamental to population dynamics, the evolution of species and their conservation. Two paradigms of connectivity dominate…

PhD position on fisheries dependence on marine habitats

research

Sustaining fisheries is important for economies, livelihoods and human health, but globally numerous fisheries are threatened by rapid loss of aquatic habitat. The role of…

Sensitivity analysis in R the easy way

rstats

Is the tedious process of running sensitivity analyses on your numerical model getting you down? Have you got loops inside of loops inside of loops in an attempt to iterate…

Costing the impact of cyclone Winston on Fiji’s ecosystem services

research

Tropical cyclone Winston hit Fiji in February 2016 leaving 43 people dead, 120,000 without shelter and devastating infrastructure . As Fiji recovers, Fiji’s government is…

Impact of recreational fishing areas

research

fisheries

Recently the Queensland Government has declared several net fishing free zones in bays and estuaries of central and North Queensland. The aim of these zones is to enhance…

How to create a culture of using R programming at your institution

research-skills

rstats

Promoting the use of the R programming language at your institution can bring many benefits. Your colleagues will be able to access cutting edge statistical analyses that…

Tall Young Poppy Award

research

I am honoured to receive a Young Tall Poppy Award for Scientific Research and Communication.

Welcome to my new webpage

Welcome to my new webpage. I got tired of the limitations imposed by my old google sites page. I was looking for a new alternative, that would allow me to post my own html…

How long does it take to write major national grant?

research

During “grant season” (~Dec - March in Aus) you might find your colleagues bemoan all the work they have to do writing grants, or turning down meetings because they are too…

Automate adding labels to figures in R

rstats

The other day I was resubmitting a paper to a new journal for the fourth time and I decided I had had enough with reformatting of figure labels each time I resubmitted to a…

Species on the Move - Day 3 synopsis

research

12 February 2016, Hobart Tasmania

Species on the Move - Day 2 synopsis

research

11 February 2016, Hobart Tasmania

Species on the Move -some things I learned

research

10-12 February 2016, Hobart Tasmania

Species on the Move - Day 1 synopsis

research

10 February 2016, Hobart Tasmania

Measuring range shifts

research

It is well established that species are moving their ranges towards the poles to keep up with global warming. We would like to know how fast species are likely to move, so…

Are more marine protected areas needed to protect ocean biodiversity?

research

Marine protected areas are a primary tool for conserving marine ecosystems, habitats and species. For instance, the Convention on Biological Diversity, has 193 signatory…

Commandments for entering data to use in R

rstats

Meta-data should include location and time information, the short-hand names of the variables matched to a description that includes their units, and a description of the…

New fellowship on fisheries and their habitats

research

I am pleased to announce I was awarded a national fellowship from the Australian Research Council recently. I will be funded through to 2018 to pursue a new research…

Quickly load many files into R

rstats

I had the pleasure of attending the Earth to Ocean group’s (at Simon Fraser University) ‘StatsBeers’ yesterday. One question that came up was how to quickly summarise data…

How statistics help us get causation right

research-skills

Statistics are often maligned. People can play with numbers to bias the way we interpret reality. Or we can find reasons why two events happened at the same time without any…

Digitising graphs with R

rstats

I recent had reason to digitise some graphs from published papers. You could buy a program to help you do this, but it is actually also possible with R. Here is how to do it.

How to think like an economist

research

If you are a conservation biologist at some point you will probably find yourself writing about $. Conservation often requires restricting people’s use of natural resources…

Marine reserves without the short-term losses in harvest

research

fisheries

Marine reserves are a popular management tool for recovering depleted fish stocks. However, before fishers receive the long-term benefits of spillover from the reserve, they…

What are conservation priorities?

Maps of ‘priorities’ for conservation are popular product of conservation research. One approach is to make ‘hotspots’ maps of species richness, or rare species, or rare…

Data Wrangling using R

What is data wrangling?
Wikipedia defines it as “Data wrangling or data wrangling is loosely the process of manually converting or mapping data from one ‘raw’ form into…