Category Archives: project

GLM study notes

1) what is the difference between a GLM and a GLMM?

GLM: only has fixed effects
GLMM: has fixed and random effects

both have: a set distribution and associated link function,  response variable not assumed to be linear or normal, response variable should be continuous, explanatory variables are categorical and can have continuous covariates

2)What is the difference between fixed and random effects? 

Fixed: this is the treatment in your experiment, should have an effect on your response (slope changes)
Ex: soil characteristics are the fixed effect when testing the influence of soil on plant growth of different species

Random: intercept changes but should not have an effect on your response (slope does not change)
Ex: species is a random effect when testing the influence of soil characteristics on plant growth of different species

3) Checklist of steps for running a GLM/GLMM (Box 4 Bolker)

  • specify model: define – fixed effects, random effects, covariates, response variable, a priori  decide on the number of factors to include in the model
  • choose distribution and appropriate link function
  • check assumptions: homogeniety of variances, outliers, does your distribution match the assumed distribution? (goodness of fit statistics). If variances are not homogeneous or the distribution does not match then change your model, adding effects or covariates, interactions etc
  • recheck assumptions of final model (see previous step)
  • check overdistribution (especially for poisson distributions)
  • can choose/compare models using AIC values (lower AIC = better)

4) Common errors that are made when performing a GLM/GLMM

Selecting the wrong distribution and/or the wrong link function
not checking the fit of the model to the distribution

 

Rubrics for assignments

Systematic review paper/workflow review /50

Title: informative, clear, useful. /2
Abstract: summarizes enture paper succinctly including implications /5
Introduction: Clear, appropriate length, introduces topic, states purpose and objective /10
Methods: Replicable, transparent /5
Results: Written description can stand alone /3
Discussion: Clear, does not repeat results, highlights novelty, relates to previous research, states implications /10
Lit cited & lit reviewed: appropriate and extensive (at least 40 citations and sufficient body reviewed)  /5
Figures & tables: sufficient, clear, stand alone capacity, summarizes salient findings /10

 

Open-science products /25

Options
datasets on figshare
presentation on slideshare
figures/infographics on figshare
interactive figure on plot.ly
video on camtasia

Information content sufficient to communicate main finding and include salient evidence/main findings /5
Visually captivating and attractive to appeal to a wide audience /5
Text associated with product well written and appropriately conveys details needed to understand product (i.e. meta-data, tags, text on slides, text on infographic, etc). /5
Science behind product sound, evidence-based, not too simplistic, and can be assessed by a scientific non-expert to your field /5

Related evidence also referenced (other workflows, reviews, statistical tests, products etc) very important to show how your work connects to other /5

 

Instructions for submitting paper

Here are the options associated with submitting the paper next week by 629pm (Oct 23rd).

1. Submit to peerj as a pre-print. The class & I will review and post feedback.
https://peerj.com/about/preprints/what-is-a-preprint/

2. Email to me directly as word doc and pdf.

3. Submit to google folder for class to download (folder I shared with you at beginning of the course).

If you would prefer for only me to see, use option 2. If you want more feedback, use option 1.

Remember: use appendices in the paper and include PRISMA report for systematic reviews.

Systematic review guidelines

hi team,  just a quick update.

1. I deleted all commenting on blog. Spam is so annoying. Those bots!
2. Remember, you have to publish the data you collect for your review on figshare as part of your grade. It must include meta-data etc.
3. I have had a request for guidelines.  If you are not afraid of getting scooped, I strongly recommend you publish paper on peerj as a pre-print.

Guideline
Copy for formatting style of this paper.

https://peerj.com/articles/265/

Summary – you must publish data, include a PRISMA report, have at least two figures, and write a paper like the peerj example.

We can discuss this all next week, Oct9th, in class. However, in the interim keep cranking on those papers, get the two-three figures ready, the PRISMA report, and maybe the methods & results too.

The more you have prepped for next week, the more I can help.

Research Topic- Jacob=)

Hey Guys! The overall objective of my research project is to create a lab-on-a-chip device platform for drug/chemical assays using fruit fly embryos. The first part of my project is to study Drosophila oviposition (specifically, its response to physical properties such as textures). From this, I plan to micro-fabricate a patterned device to collect embryos and to pass chemicals through them for developmental imaging. So, for this course, I think I’ll be looking at how statistics is used in presenting oviposition data and errors.

Research Topic-Amy

Hi all,

For my research I am focusing on how plant facilitation effects associated animal species.  For my systematic review I will look at the statistical tests used in studies that examine plant (specifically shrubs) facilitation that also incorporate another trophic level in some way.  My search terms are facilitat* AND shrub.

Water Levels and Climate Change

Generally, my topic is about water levels in inland lakes in Ontario and how they change during periods of climate change. I’ll be looking at lakes in the boreal zone in Canada and extending the concept to Europe, and possibly the Great Lakes. I’m still hashing out the details but I think I’ll be looking at abiotic factors in hydrology in the first chapter, then looking at how the changes I identify will affect productivity, water quality, and fish diversity in the second chapter.