#rstudio #github missing command lines for mac setup @rstudio @github @swcarpentry

Every few months, I try to do a clean install on my machine. I know that OS X Sierra is due out in September, but I elected to do a wipe and clean install now for the remainder of summer.


Wipe, reinstall OSX from usb, brief minor hack/tweaks, then just a few apps including base-r and rstudio. I prefer to connect to github without desktop app and use rstudio directly.

Limitation, I forgot two little things that consumed forever to get rstudio and github to connect. So, if you are a mac user too, here is a synopsis.


Most steps well articulated online
#open terminal/shell.
git config –global user.name “your_username”
git config –global user.email “your_email@example.com”

#missing 1 for macs: tell osx keychain to store password
git config –global credential.helper osxkeychain

#generate SSH RSA key via command line
ssh-keygen -t rsa -C “your_email@example.com”

#alternatively, you can do via rstudio tools/global options/enable version control
#then create RSA key, save, copy, and paste over to your github account online.

#check authentication works
ssh -T git@github.com

#missing 2 for macsdo a command line push to get password into osxkeychain
#I tried clone/new repo, make changes, commit, then push, and failed because no password to push changes via version control to github was stored and rstudio does not talk to keychain #frustrating
#so make/clone a repo, generate a change, and then do push from command line

git push -u origin gh-pages


git push -u origin master

#depending on branch name

#I hope this note-to-self provides you with the missing lines you need to get your next level too!



The Wardle Test for a #socialmedia #selfie effect in science


‘And I am immortal’ (through social media).
Connor MacLeod (The Highlander).

A recent paper in the journal Ideas in Ecology and Evolution inspired me to rethink/temper my optimism in social media as a panacea for effective scientific communication. The running title of the paper, how to tweet your way to honour and glory, by David Wardle captures several primary concerns with altmetrics as a tool to estimate merit, value, or even global reach. We are discussing these ideas at NCEAS today, and as a heuristic, I prepared the following deckumentary (commentary + slide deck). The strengths and limitations of social media as a tool to communicate science are explored.  Several basic solutions are proposed. However, there is an incredible opportunity here to more throughly examine how we handle social media as a tool and evaluate its capacity for effective outreach.

One of the highlights proposed in the article that I really enjoyed but want to emphasize more directly here is the test of a particular potential limitation – non-independence of outreach from the social media stream of the producer.  I propose we should entitle the test developed The Wardle Test for a social-media selfie effect in science.

The social-media selfie effect workflow

  1. Select a set of products with different authors but from a similar outlet (i.e. a journal).
  2. Structure sampling of products to ensure reproducibility (i.e. regular, random, or random-stratified sampling from the outlet), and ensure author-identities are unique in each instance.
  3. Record altmetric scores reported for each product.
  4. Capture twitter-stream for each product.
  5. Assign tweets to product producer (rule: personal twitter account matches first author or organization such as lab) or other (potentially independent twitter account).
  6. Contrast altmetric scores between products tweeted by producers relative to others.

Fantastic idea as a proxy for the positive and negative ‘echo-chamber’ effect discussed widely online. We need an r-script to scrape a larger set of products and associated accounts!

Then, can can calculate not only this social-media selfie effect but also explore some of the contemporary analytical solutions produced online by many ‘influence’ indices including diversifying the signal analysis, weighting (often by audience), and normalization.

The ‘quickening’ of social media amplification is perhaps not immortal, but it is a challenge and thus opportunity for scientific communicators and critical citizens to better validate and use this effect appropriately.



A legal workaround idea for non #openaccess ecology articles – university library #openpaper #outreach days

The access paywall of many scientific journals is a significant barrier to a rapid, efficient process of securing many peer-reviewed ecology and science articles. Recently, I needed to assess the state-of-the-art for animal camera trapping in wildlife ecology. I used google scholar and web of science to populate a list of papers to read. I was ‘behind the paywall’ at a university IP address. Even with this barrier removed, it was a challenge.  I wanted to pull down a total of 20 papers, and only 60% of these were readily available because even with the exorbitant subscription fees the university library pays, some journals were not included. I realized that few wildlife ecologists and managers have even the limited level of access that I had to these very applied papers. This is a problem if we want evidence-based conservation and management of natural systems to prevail. There are numerous solutions of course including contacting the authors directly, searching for it online and hoping you get lucky to find it posted somewhere, checking researchgate, and joining a few other similar access author-based portals. There are two other simple solutions of course to engage managers – share with them directly when it is in print and encourage them to join a service like researchgate. Identifying managers interested in our work and sending it to them is a form of scientific communication and outreach. We need to do it. However, I had an even more broad public outreach idea – use university libraries as public access research portals.

University libraries pay subscription fees to many publishers. Leverage this access to run open science or open paper days.  In my experience, even with a temporary guest ID on wifi at most university campuses, one is able to access their full offerings of peer-reviewed publications. Universities could use this access and do even more – educate on peer review and show off all the incredible research that more often than not taxpayer dollars fund.

University-library solutions
1. DayUse Research-IDs. University libraries are increasingly digital repositories of information. Show this off to the public, the parents, and local applied researchers by offering guest-research IDs for a day at time for the public to browse holdings.
2. Notifications for digital research content. University libraries are increasing more like digital cafes than physical holdings of books. Advertise the resources that are available behind this paywall to all users, regularly, when they are online. Notifications/alerts, additional linking to primary research from courses and less on textbooks, and potential (non-obtrusive) pop-ups within the network for students on new research developments.
3. Open-paper public days. University libraries should run access days to teach the public about modern bibliometric search tools, explain the peer-review process, explain the publishing process, and show/allow folks to look up primary research that interests them. There will always be a topic someone needs to know about and a journal for it. Most importantly, these days will promote scientific literacy and also potentially provide fuel to new pay models or even better different profit models for academic publishers. If non-academics that pay taxes fully comprehended how much awesome research is out there in this academic stream that they never get to see, access, and pay for through tax dollars, it is hard not to imagine they would not want to see big changes.

The function of a university library
University libraries can still look like this.


More often that not university libraries instead look like massive digital cafes or computer labs.


The problem with all the information in the ether and behind these paywalls is that this intangibility hides the depth of the resource and extent that information could and should be available more broadly.  I love the ‘learnings common’ philosophy that is evolving in many university libraries. I am just concerned that it is not reaching far enough out – at least to the parents of the students that attend the university.

University library websites have improved dramatically and feel more contemporary. However, there is a limited signal of the extent of the digital research that are held and no indication of how the public might access even a tiny bit of this infrequently to learn. I recognize public libraries and university libraries are not quite the same thing, but why do they have to be so different. Can they partner, co-evolve, and reduce the paywall limitation to the research that matters for better decisions at least for health and the environment?


My best guess is that university libraries thus provide three significant functions in this domain.
1. Provide access to research.
2. Provide a space to access and do research.
3. Train and educate on how to do research.

As a researcher, the first is the most critical to me. As an educator, all three are important to my students.

I recognize all of this misses the point – research should be open. Primary researchers should strive to be OA all the time with our work, but I recognize that there are reasons why we can not necessarily achieve this goal quite yet. Journals can also work towards this end too.

In interim, much of research needed to make the best possible decisions is out there now – i.e. where and how to deploy animal cameras for conservation this field season for my team – and the natural now is changing rapidly.
I want science to help. To do so, we need to be able to see it. Now.

Break-up letter you can use with VW

Dear VW,
Our relationship is over. You lied to us. When we entered into this partnership, I agreed to look after you, and you agreed to look after me, my family, and the environment we share. All these years you were however silently, sneakily lying. I cleaned you, looked after you, bought you new things when you needed them, and cared for you. All you had to do was be honest and help me get where I needed to be. I do not even want to see you anymore. I am stuck with you now until your family decides what to do. Trust is earned not bought. I cannot stay in a relationship with someone who does not realize that we have only one chance to make the world a better place.


‘#Elementary’ ecology and the value of red herrings


At first, I resented the postmodernism of Elementary. However, I now enjoy the human dimension associated with character development and for its challenges to my thinking about the science of interactions and hypothesis testing. The most recent episode was a brilliant piece for me in terms of my struggles with a paper I am working on with a collaborator that includes contrasting predictions. The episode was entitled ‘Hemlock’, and it is a very apt metaphor (for me at least) for some of the challenges that modern ecologists face.

Here are the elements that inspired me to think about how we sometimes approach ecological interpretations to evidence.

1. Sherlock and Watson investigate the disappearance of a lawyer. Unlike most episodes in contemporary detective/police shows (and even this show), this episode does not begin with a macabre crime scene or body. We never do see the body. Sounds like ecology. Species disappear, and we need to know why. Dramatic global change is occurring, but frequently, the effects are evident only in the gradual loss of a species or process and not through a disaster with a grisly, photographic opportunity for collection of evidence or political leverage. There is no smoking gun. In ecology, we rarely happen upon outcomes that are not driven by complexity or sets of interactions with processes emergent from interdependence.  There can be a smoking gun, but sometimes, it is the indirect interactions with the gun/agent that are real driver of change and not the direct effects. Positive interactions can also have negative effects on ecosystems (i.e. no gun at all but smoke).

smoking gun

2. Sherlock generates both numerous hypotheses (explanations of how the system/phenomenon works) and associated predictions (testable, specific outcomes with evidence) that are refuted as mostly immaterial evidence accumulates in this episode. This is fascinating to me. There are many more failures to support predictions than the usual episode, and it is refreshing. I get the sense that many contemporary experimental community ecology studies certainly generate the hypothesis a priori but refine/adjust the predictions post hoc. I recognize that we have moved beyond strict Popperian falsification, but we are talking about single studies that have associated prediction sets within each paper reported as perfectly satisfied. This seems a bit convenient. My collaborator and I set up the particular experiment we are writing up now with a hypothesis to describe the system but with opposing predictions. Given that ecology embraces complexity, I realized that I have read few papers recently that have contrasting predictions sets that alternatively support or refute the hypothesis. I want that complexity back, and I want to include some of it my papers from now on to highlight the importance of judgment and fair evidence handling alongside appropriate statistics. I know there is a very real bias against non-statistically significant findings and failure to support dominant hypothesis within a subdiscipline, nonetheless, the red herrings we chase make the instances of support all the more robust, honest, and reproducible.

I propose there are at least conceptions of the red herring from the detective genre for ecology.

1. Red herring as distraction. RED HERRING

In the most reviled sense from a publication-bias perspective, failure to support is a distraction at best, a hindrance to scientific progress at worst.  I disagree. Distractions provide insight, illuminate errors, and highlight the importance of effective methods in detecting and reporting false positives.

2. Red herring as Bayesian calibration tool.


Our capacity to assess relative frequency, importance, and experience from a procedural/effective experimental design paradigm is enhanced and accelerated by a clear sense of the red-herring effect within sets of factors or within the manifestations of ecological processes of interest.

3. Red herring as a source of creative inquiry.


Ecology is both science and art. Explicitly seeking the red herring can provide information on processes that are difficult to measure directly, and in imagining and designing experiments wherein a factor does not apply, we better understand the context when it does. The red herring moments are also often synonymous with eureka moments – perhaps not even for you but for the reader in enjoying your narrative of how you solved the ecological mystery at hand.

Failure in science is not a crime, and false leads provide necessary scientific truths.