StatsGen Lab Code of Conduct - erynmcfarlane/StatsGenLabProtocols GitHub Wiki

Expectations you can have of me

To work to keep you safe. This means that I will work to foster a safe environment which celebrates folks from all backgrounds, races, ethnicities, religions, sexual orientations, gender expressions and abilities.
To support your development as a researcher - this means that I will help you to ask good questions, and work out how best to answer them
To support your development as a statistical geneticist - this means that I will help you to learn field, lab and statistical skills, which you will be able to take to your future positions
Frequent, constructive feedback on writing (English and code)
Financial support for project expenses, and a stipend (grad students) or salary (postdocs, technicians etc).
Career development support, including for your next steps in industry, academic or government careers
advice, support and some funding (or help finding funding) for conferences
kindness, grace and good humour - this means that I will expect you to make mistakes, help you to fix them, and make fewer in the future, and reassure you that they happen to everyone. And I will bring cake (or coffee, or fudge, or art supplies, or whatever we need to dust ourselves off after our mistakes and keep going).

Expectations I have of you

Treat research as your job - this means that I expect you to work hard, be engaged and be professional
Take responsibility for your project. Drive your research forward and be proactive. This includes working with me to write your proposal, timelines, and editing your timelines as needed.
Ask questions, including of me, of your labmates, and of the scientific literature. There are no bad or silly questions, as long as we are respectful to each other.
Work to improve your writing and computational skills
Publish peer reviewed papers (with my help)
Ask for help when you need it, or are stuck. Grad school is time limited - it is better to ask for help (or ask to be pointed toward help) than to spend a lot of time on a problem that could be quickly solved with some more expertise.
Come to me promptly with mistakes. Mistakes are expected and are easier to solve together.
Some more kindness and grace, both towards me (I am brand new at my job too, and will certainly make mistakes!), towards your labmates and your other colleagues. We're all in this together.

Expectations labmates can have of each other

A collaborative attitude. Research is a team sport, and the more we help each other, the more we will all get done. For example, reading each other's drafts before sending them to me will make them stronger when I get to see (and edit them). Brainstorming ideas, or methods, will lead to better research. This can be done formally, such as in our lab meetings, or informally, such as at your desks.
Help with fieldwork. Fieldwork can never be done alone (see Safety) which means that sometimes you will be expected to help with fieldwork that isn't directly related to your project. Authorship is often compensation for fieldwork, but there is also a reciprocal nature to it. Finally, fieldwork is fun, and helping each other with field work is one way to build skills that you might not get with your own project.
Help with lab work: You will quickly realize that lab work is not my forte. While I will do some lab work, and will certainly help with large batches, it is more likely that you learn from your lab mates (who are likely to have more experience than I do).
Help with code. This might include sharing scripts, helping to proofread code, or answering quick questions on slack if you happen to know the answer. We all start with an empty script at some point, never be afraid to ask for help!

Safety

Well Being

Academia, from undergrad to faculty, is a marathon not a race. We will do our best work when we take care of ourselves, and can come to work energized and engaged.

sick days. I don't work when I'm sick. I stay in bed, watch terrible tv and focus on recovering. This is for two reasons - 1) my brain is not at it's best when I'm ill and 2) because I have a little kid, I know that the only time I will have to recover is when she's (healthy and) at school. This means that I need to recover quickly for the rest of my responsibilities.
I will never expect you to work while you're sick. Please take time to recover so you can work as your best self.
If you need more than 2-3 sick days, please let me know so we can make arrangements if needed, and so that I'm not worried about you.

Field Safety

As PI, I have a responsibility to make my research group both safe and accessible. Together, will develop a 'field safety manual', developed as described by Rudzki et al. (2022). Prior to all field work, we will ensure all training is up to date, and identify and brainstorm solutions for risks in the field.

Part of what we will discuss is that risks in the field are not equally felt by everyone and that you must leave the field if you (or anyone you're working with) feels unsafe. This also means that we will never do field work alone, and I will always know when you are in the field and approximately where you are so that I can get help if needed.

Finally, part of what I will do to keep everyone safe in the field is to develop a field 'library' of gear. This means that I have a budget for high quality hiking boots and rain gear, I have sleeping bags available, and I will ensure all other field gear (i.e. tents and stoves) are in good working order prior to trips. Part of your responsibility is to 1) treat gear well when you're in the field and using it, and 2) let me know if anything has worn down and needs to be replaced.

Ticks

Ticks are part of doing lab work in Ontario. You can expect that if you're in the field, even if you're in a park in Toronto, that you will be exposed to ticks. There are ways to keep ourselves safe:

Long pants and long socks, with socks tucked into pants
Tick checks after field work. This means changing into street clothes, checking places on your body that ticks like (e.g. armpits, behind knees, hair lines and intimate areas). If you have long hair, consider shaking out your hair.
Ticks can transmit Lyme disease. This means that if you have one attached to your skin, you need to carefully remove it, and ensure that the head is not left in.
If you have a tick that has been attached to your body for more than 36 hours, consider consulting your doctor.
be aware of the symptoms of Lyme disease, and if you see these symptoms after having been bit by a tick, please consult your doctor.

More information from the Ontario Government on Ticks can be found here..

Lab Safety

TBD Will include

only working in the lab during regular work hours, so there are folks around if help is needed
keeping the biosafety permit in the lab up to date (this is an Eryn Responsibility)
feeling comfortable saying 'I don't know how to do this!'
feeling comfortable saying 'I think I messed up.'

Internal communication

meetings: Our lab will have regular, weekly lab meetings. In addition, I will have regular 1:1 meetings with each member, at the frequency (often once a week, possibly once every two weeks) that is appropriate for your success. For each meeting someone (decided on beforehand!) will bring an agenda.
phone: is the best way to get me in an emergency. If there is a dangerous incident in the lab or the field, please call me immediately at 519-830-2179, after calling 911 or performing first aid. Please call me in other emergency situations, such as if the freezer is broken, if you've been in a (even minor) car accident while doing fieldwork, or so on. 'We're out of buffer' on a Saturday is not an emergency, 'we're out of gas stuck on the highway north of Thunder Bay' is.
slack: is the absolute best way to ask me 'just a quick question'. If I'm at my desk, I nearly always have my slack on, and if I see that you've asked something, I will take the time to respond.
emails are the best way to send me material that you need feedback on, because then I have a record of it. That said, depending on where your drafts are, a slack ping might do the same thing. In general, I will aim to respond to emails within 24 hours, or the next working day in the case of weekends.
turn around timelines: your written work is one of my top priorities. That said, to give it the time it deserves, I need time to read it and comment on it. To reduce stress for everyone, please give me two weeks with any draft to return to you with comments, and two weeks advance notice to write references letters.

External Communication

Authorship

One of the goals of scientific research is to communicate it to the rest of the field. This means that we will often try to publish our work in scientific journals.

Unless we have discussed otherwise, expect that the first author of any paper is the student/post doc who's thesis is being written up (aka the person who has done the bulk of the writing). Other people who contribute to a paper (e.g. in the field, in the lab, in data analyses, in discussions etc) can become co-authors. A general rule to co-authorship is 'would this paper have happened without this person's contribution?'. If the answer is 'no' that person should probably be offered co-authorship.

Unless we have explicitly discussed otherwise, I will be the last author on all papers coming out of our lab. This is because I expect to contribute substantially to all papers that we write together, from conceiving the ideas to pushing the final product to publication. However, there could well be papers that are side projects (for example) that I am not involved in, on which I will not include myself as an author.

Conferences

Conferences are important to get feedback on your ideas, network with your peers, and find new people you'd like to work with in the future. The two main conferences that folks in the lab will likely want to attend are CSEE (Canadian Society for Ecology and Evolution) or SSE (Society for the Study of Evolution), although there are many other more specialised conferences. For grad students, I will help to facilitate travel to one conference a year (this means working on your abstracts to apply, applying for grants with you, covering some costs).

Travel is not equally accessible for everyone (e.g. due to caring responsibilities, citizenship), so if travel is not possible or easy for you, for any reason, talk to me. Networking and training that can be attended virtually, there are local conferences, or we can work to find funding or care to make attendance possible (e.g. funding for additional hours of dependent care, or conferences with available childcare).

Work/Life balance (finding what works for you)

I commute - can expect me to be on campus 2-3 days a week, depending on my teaching
work from home, but I will make sure you have a desk, and everything you need to be able to work either at York or at home (i.e. a labtop, access to Compute Canada etc).
The hours I work are often not 9-5. Part of this is due to my commute (it's easier for me to leave later and stay later), part of this is because of how my brain works, part of this is because I have a small child who needs to be dropped at school at a particular time, but goes to bed earlier than I do (most evenings!). My best thinking often happens in the late afternoon/evenings, so that's when I prefer to write. Mornings are better for meetings for me, because I can be unfocused at my desk, but productive in person. Think about and find what times in the day work well for you, either because that's when you find your moments of brilliance, or because that's what your other commitments require. I am not particular about when you work, within the confines of safety (lab is done during the Uni's operating hours, field work is never done alone), and with a recognition that drop ins on me (or your lab colleagues) in my office or slack are more likely to be successful during weekdays. Finally, with the occasional exception of field work, I never work on weekends, and will never expect you to work on weekends. If fieldwork happens over a weekend, I will expect you to make sure to take some R&R during the week. Burn out is real, and insidious, and happens too often in academia.
in person meetings are awesome, especially if we can do it as a group - need to find a way to make the most cautious person comfortable. E.g. meeting outside, meeting with masks, meeting on zoom.
- If anyone needs a meeting on zoom (because they're recovering from illness, travelling to the department is not possible, caregiving responsibilities) we will switch to zoom
- that said, if you're sick, you're sick! Please don't work when you're sick, please focus on recovering (see above on well being!)
personal emergencies - if you have a personal emergency, and need time away, please just let me know. You needn't tell me more than you're comfortable with; this would just let me know not to expect you, for whatever time you need.

Liz's Laws on Data Management and Analyses (Liz is a beloved friend-of-the-lab that some of you know, and all of you will hear about)

Thou shalt:

Format data cleanly, in a flat format that can be saved as ASCII text in a .csv, .tsv, .txt or similar
Use conditional formatting for the initial data entry when possible to reduce formatting and data entry errors
Use a "Comments" or "Notes" field to express uncertainty - no question marks, "maybe"s, etc. in actual data entry columns
Use version control [e.g. github!], keep a master version up to date, always update the master version rather than creating your own special sub-version for each use
Subset reproducibly using R or Unix, not by point-and-click in Excel
Save original datasheets, both as paper copies and scanned to PDF
Save GPS points WITH original data at the time of original data entry
Use unique IDs for individuals
Use the same format for each individual ID
Enter "NA" when an entry has no information, rather than leaving it blank
Save dates as 3 columns, not 1: Month, day, year
Do QA/QC - plot histograms, scatter plots, or box plots, check for outlier values, check dimensions of data, check that data format is correct, use unique() to find typos in character fields, use length(unique()) to check that there are the right numbers of things (i.e., number of individuals)

Thou shalt not:

Use spaces in column headers
Use spaces in file or directory names - Use punctuation in column headers
Use colors, font, or bolding to convey any meaning whatsoever
Include question marks to indicate uncertainty - this should go in a "Notes" field
Use duplicate IDs for individuals, even in different projects or different years
Do any analysis whatsoever within Excel. Excel and Google Sheets are for data entry, not analysis.