Creating A Vector Layer By Hand

I had been given some PDF maps with outlines to digitize, but with enough land features in the map to be able to geo-reference them. I screen-grabbed the maps from the PDFs and saved the screenshots as TIFF. Then, opened QGIS, added the Open Street Maps base layer and zoomed into my area of interest. From there, I used the QGIS georeferencer tool on the first image: https://docs.qgis.org/3.40/en/docs/user_manual/managing_data_source/georeferencer.html

Once I had the image georeferenced onto the map as a layer, I increased the transparency to be able to see through to see how well it lined up with the features on the base map. I then selected “New GeoPackage Layer…” and entered names for the file, layer, field(s) and defined the type (polygon). From there, I traced the boundaries I needed to create polygons that corresponded with the PDF map. In my case, I was going to need to clean up the outer edges with waterway and state boundaries in the end, so I made the edges of my polygons wide past where they would eventually be differenced out.

As I referenced more images, some did not line up great on the first try, so given that this exercise is a bit “interpretive” anyway with hand digitizing (and can be edited) I tried my best to trace a line where it should be. Each time I did that, I was glad my next image lined up with it, or I adjusted the boundary between the zones as needed. Thus, I had a polygon layer with edge boundaries that needed to be clipped down.

For my purpose, I needed…

I used those layers to either clip (DE river) or difference (DE, NJ land shapefiles) to keep only the areas of interest. From there, I had to do some cleanup…

  • delete holes from a feature I merged
  • split polygons and delete parts to do some finer manual work on getting rid of areas not in the map
  • vertex tool to change the shape of a polygon to include a water body that was clipped out

12 hr Pelagic

I was thrilled to get out on the water on the nicest November trip (weather-wise) I have enjoyed yet! Land temps ranged from the 40s into the 50s during the day. The day served as possibly the only Nov trip I have not been cold, once the sun was sufficiently high in the sky. This is what I wore, and quite comfortably at that…

  • shin-length down parka
  • heavy Smartwool base layer
  • wool sweater mid layer
  • fleece-lined leggings
  • Comrad wool compression socks
  • Arctic muck boots
  • faux fur lined trapper hat
  • waterproof lined gloves (my “winterproof” gloves that still allow for some dexterity)

So, make no mistake, I was still decked out in winter gear, but not feeling cold without my down vest under it this time of year was notable for me!

Acadia National Park

Happy Labor Day Weekend! We did a trip to Maine to celebrate my mom’s birthday. Today we crossed a NP off the bucket list! We drove the park loop most of the way, but turned off at Bar Harbor, so I’d still like to “close the loop” from there and drive back from Bar Harbor to the visitor’s center. But, we also did drive to the summit of Cadillac mountain and walk around the trails there a bit, and it was spectacular!

Landscaping: The Tree Edition

This year, I finally figured out how to get plants from the tree farm I’d kept meaning to visit: I was delighted to find they went to native plant fairs, and one was in my birth city! So I went home for the weekend and was able to get the species I’d been planning for years.

Behind the fence is more of a mix of transplants. Walking through the gate: there’s the other crab apple I bought, and a sweet gum I transplanted.

Last year, I transplanted red maples, a red cedar and a black cherry that have thrived. The species that most drove me to this particular native plant farm though was red mulberry. Unfortunately, something happened to one of the saplings, perhaps a casualty of my lawn care service. The other one took off though where it was planted.


I had a personal emergency this week so I was unable to see if the backyard flooded during the hurricane. But unfortunately, since these photos were taken, the back tree line that has looked so healthy all summer now looks wilted. Let’s hope the trees recover.

Flower Walk

Again, it’s summer, so allow me to share some re-wilding (well, sorta…) that I’ve been up to in my yard. I do enjoy varietals, so excuse the not strict wild-typing here. Otherwise, I have several natives to at least the state level, if not county. (Probably my next project is going to be separating that out.) I have species/varietal info in the photo captions, and also a list from the end of the walkway to the steps in order.

Here is the list of what’s planted, in order:

  • New Jersey tea
  • “prairie splendor” deep rose coneflower
  • “Pollynation magenta” coneflower
  • “green twister” coneflower
  • whorled milkweed
  • butterfly flower (Asclepias tuberosa)
  • “fireball” bee balm
  • “ice ballet” swamp milkweed
  • Hibiscus moscheutos
  • Jacob’s ladder
  • wild lupine
  • orange coneflower (Rudbeckia fulgida)
  • “pow wow white” coneflower
  • “Luna red” Hibiscus moscheutos
  • “sunstruck” false sunflower
  • purple coneflower
  • Asclepias syriaca
  • New England aster
  • “balmy pink” bee balm
  • “Goldsturm” Rudbeckia fulgida

ASAP Fish Model

As mentioned in my prior post, I intend to do some walk-throughs and take some notes on some fisheries analysis processes. Right now, I’m going to add some notes on where I’m at, which is not the beginning! Ideally, more tutorials to come, and more content to be presented in order 🙂

Currently, we’re working through the age-structured assessment program (ASAP). The leader of our subcommittee was kind enough to provide us a tutorial and commentary, so this is me transcribing some notes for myself (and hopefully that someone else might find helpful)…though plenty will be specific to me and this exercise/session/assessment (including video timestamp references).

Inputs

Any

  • For tog in our region, dead releases are lumped in with total catch (i.e. not handled separately in the “discards” tab)
  • selectivity blocks
    • don’t need to change (15:37)
    • if you wanted to add one… (16:16)
  • your data CAA (29:40) the scale of what’s entered on the catch-at-age tab doesn’t matter (e.g. if a prior year used 1000s of fish, you can use raw numbers because ASAP converts it to proportions immediately)
    • tog specific data considerations (32:06)
  • indices (41:52)
    • don’t add for an update
    • you can try dropping them for sensitivity runs (42:48)
    • data (46:43)
      • age structured (46:51)
      • sample size (47:09)
  • provided to us: time series of data for MRIP index and CAA (48:28 – 50:29)
  • lambdas (56:01)

Retrospective

for me: your last block starts 2018 so set there to not “overrun” the next block

  • 1:13:30 gets to running the model (below)

Interpreting results

  • can set option to keep terminal open to see more output
  • “scan …results” under “Run” allows you to read results back in

Diagnostic Results

  • stage 2 multipliers is where you find the ESS you can re-run with (1:15:41) for final run only, adjust effective sample sizes based on output
  • you can try to optimize RMSE…(you don’t have to)
    • increase CV where RMSE > 1, decrease where it’s < 1
    • if CV is too big, it won’t fit to the index
    • ideal: indices and catch RMSE = 1

ASAP Model Results

  • SSB: roughly 4321 is ok
  • MSY: roughly 933 is ok

Retrospective results (1:24:40)

R plots (1:30:12)

Yard Tree Candidates

From the list native to the county that would also produce some yummy fruits (for me and the birds) or add conservation value…

  • green ash – can tolerate poorly-drained (back yard)
    • https://entomologytoday.org/2016/03/07/heres-how-to-inspect-your-trees-for-emerald-ash-borer/
    • https://eab.russell.wisc.edu/signs-and-symptoms/
    • questionable native status in the county though: http://capemaywildlife.com/_templates/group_oleaceae.html
  • common serviceberry well drained (front yard)
  • sand hickory – front yard
  • common hackberry – not picky (back yard?)
    • native status in the county disputed: http://capemaywildlife.com/_templates/group_elms.html
  • common persimmon – loamy (front yard)
  • American holly – Berryland (backyard)
  • black walnut – sandy loam (front yard)
  • tulip tree – well-drained (front yard)
  • American plum not picky (back yard?)

My First Fisheries Post!

Disclaimer: anything published here on my blog is my own personal content, and does not necessarily reflect the views or positions of NJDEP.

One of my primary responsibilities of my still-new (i.e. as of this year) job is to work on stock assessments. As such, I’ve been on a steep learning curve of the assessment process! I intend to do some walk-throughs here (and maybe even a video walk-through at some point). I think publicly accessible documentation on this process is at times lacking, and given that this is a process that involves public comment, I think it’s important! So, I’d be thrilled as you learn along with me.

Today is more or less the kickoff for me to start working on the Atlantic States Marine Fisheries Council (ASMFC) tautog update.