13 Fish Passage Office Work Guide

13.1 Data Management

  • All fish passage data is inputted into the appropriate provincial submission templates (make sure you have latest version). It is very important to use only copy+paste+special values (right click or control + command + V) as there are “standards” in the input spreadsheets that can be violated with regular copy paste leading to issues later on in the submssion process.

We are looking to minimize hand work as it is time consuming, leads to errors and does not lend itself to reproducibility. In addition, we are continually improving our digital input forms so issues that do not allow the data to be transferred simply between digital forms and provincial templates should be dealt with through issues to dff-2022. Examples of issues to be dealt with are default inputs for things such as beaver presence, backwatering and embeddedment. In a perfect world we spend very little time fixing errors over and over again. We use our time to modify the scripts that produce the data and move on to improving our reporting and software products with our time.

13.2 Data Cleaning

Before data is imported to the PSCIS submission forms all data including the comments should be QA’d for spelling, to look for issues and add information.

A good way to do that is to copy and paste text into a table in word so you can see it nicely and get an intuitive spell check. Spelling and typo can be changed in QGIS. But if there are any repetitive errors, using R tidyverse functions will save time.

Exporting the PSCIS data to a gpkg is a great way to view everything spatially (ADD LINK to EXAMPLE). It can help clear up issues of missing information or incorrect data such as modelled crossing ids.

To see the site photos, look in Mergin and/or Onedrive directories.

13.2.1 PSCIS phase 1 data QA

Here is a rough list of things to check at each site for phase 1 QA:

  • Correct spelling.
  • Clear concise comments.
  • Add any relevant info from climate change assessments comments or pictures to the main assessment_comments column.
  • Backwatered, is the box ticked, does it align with the photos?
  • Embeddedment, is the box ticked, does it align with the photos?
  • Correct number of moti_chris_culvert_id. Check photos and comments to see how many culverts there are. If it’s a major Moti structure than include the chris_hwy_structure_road_id instead. Beware that MoTi datasets are really bad and often incorrect.
  • Beaver activity, is the box ticked, does it align with the photos?
  • Fish observations during assessment, is the box ticked?
  • Is the crossing type correct, check photos.
  • Are the 6 photos correct? Barrel, inlet, outlet, upstream, downstream, and road.
  • Is there an important landowner nearby? If so, could we collaborate?
  • Has there been past restoration work at the site? Search stream name in EcoCat. If yes and there is a link to a report, add relevant info and url link to the assessment comments. Additionally, add the reference to Zotero/region/ and then add the citation key to the my_citation_key column.
  • Is the culvert relatively close to the modelled crossing? If it’s more than ~30m away then create an issue for the site with a reminder to make sure bcfishpass links once the data is in PSCIS and if not link with bcfishpass csv.
  • QA road tenures to ensure accuracy. Query theFTEN road layer to obtain the “active” tenure holder. Append the forest_file_id to the end. An example is shown below. The road tenure for the starred crossing would be Canfor R01860.

  • Move survey sites to their proper locations by comparing with tracks and waypoints and remove unnecessary features. This should be done during the data entry stage so that the reporting and mapping products are accurate from the start.
  • Check out an example of the data cleaning process here.

Here is list of things to consider when assigned a priority to a site:

  • Is the site a barrier to fish passage?
  • Is it valuable habitat? Or could be with some restoration work?
  • Are there fish observations upstream, check using bsfishobs layer. If so, what species? Upstream presence of BT, CH, CO, BB is more important than RB and much more than coarse species like CC, LSU and PCC. They all matter but we prioritize the more rare and generally more “valued”. Mention BT, CH or CO if they are known upstream or are very close downstream (same stream or downstream trib before major system).
  • Unassessed crossings downstream?
  • Valuable landowners nearby?
  • Should the site be added to the “follow up with a habitat confirmation” list?
  • If it’s a OBS (bridge, ford, etc) then you don’t need to assign a priority.

13.2.2 PSCIS phase 2 data QA

  • Ensure locations for habitat surveys are at the downstream end. Remove excessive features that do not seem significant. However, you can make a note of them in the comments column. This should be done during the data entry stage so that the reporting and mapping products are accurate from the start.

13.3 Reporting

13.3.1 Background

This section of the report is important to give the reader perspective about the watershed groups of interest. In addition, it is also important to acknowledge the traditional territories on which these watersheds lie on. Provide some background info on the First Nations group or groups in the study area.

13.3.2 Site Memos

A tutorial on how to start a reporting site memo from a basic template using scripting and text can be found on OneDrive here.

Info/details to include in site memos:

  • Start by including a detailed description of where the site is located. Use QGIS to understand the context of where our site is, how large the watershed is, where it flows too etc. Check out fwapg and fwapgr for functions to help with calculating watershed areas.

  • If there is a waterfall or other relevant feature somewhere upstream or downstream of the subject culvert then include a photo, describe the height and distance to the barrier in the caption of the photo (ex. 6m high vertical falls located 800m upstream of PSCIS crossing 12345 on Thompson Creek).

  • Dewatering, beaver activity, past remediation work (baffles or Newbury riffles), etc. should be clearly identified in the text of the memo and often mentioned again in the conclusion.

  • Gather background info to include in reporting text by researching the web with simple searches using the stream name (or parent stream name), talking to locals and project collaborators, and using QGIS to investigate spatial site details. EcoCat and Skeena Salmon Data Catalogue are good online resources. Do your homework to determine if the site was prioritized in past reports (search background reports using the search function in the pdf) then include this information in the text along with a citation to the reference document.

  • Be sure to mention additional crossings and/or fish points that are located on the same stream or system as the subject site. Use QGIS to find info on past PSCIS crossings, FISS sites, fish observations, etc. These addition points can sometimes include links to old reports that contain helpful info.

  • Transcribe field notes from both upstream and downstream sites in a clean and concise way. Include the habitat value and justify its ranking by referencing info on available spawning and rearing habita data. Be specific and mention fish species and their habitat requirements.

  • If there is Lidar data available for a site - make a minimal figure for the site at the road with singleband pseudocolor (turbo color ramp) overlaid on a hillshade with the multiply layer rendering blending mode applied. Figure should be simple and made on 7” x 5” page size to show up best inline in report. Lidar can be linked to online data in LidarBC portal in QGIS through raster/https connection vs download.

  • In most cases, include 2 photos of the downstream survey and 4 photos of the upstream survey. The upstream section is more important, as this is the habitat that will be gained after remediation.

  • If fish sampling was conducted, include a photo of a fish or two. If there were salmon captured then definitely include a photo of each salmon species.

13.4 Data Submission Process

13.4.1 PSCIS Phase 1

A link to the BC Government PSCIS User Guide containing submission procedures can be found at the link here (Province of British Columbia 2017).

Other details/tips that are important in the workflow of Phase 1 submission are listed below:

  • Ensure you have the 6 required photos for submission in a folder with the crossing number on it

  • Make folders and move over photos to the correct directory using a script. An example can be found in the 2022 peace reporting repo here. Ensure that the repo and folder names match the project you’re working on. NOTE: The macros do not allow you to submit the spreadsheet from onedrive so the submission folder needs to be transferred to a directory on your local machine.

  • The submission process needs to be done in the Microsoft Edge browser

  • Go to Edge browser settings and find the Internet Explorer mode pages section and add the following three links (NOTE: These links will expire in 30 days so this step needs to be repeated every so often):

  • Before submitting, add a word doc to the submission folder titled dummy_report.docx. In this doc, record the following details:

    • a link where the gitbook report can be found (NOTE: ensure this is the github.io link, ex: newgraphenvironment.github.io/repo_name)
    • a link where the pdf report can be found, mention that the pdf report can go on ecocat but it’s versioned so they can grab the latest version from the url when it is time to post
    • a link where the associated archived map directories and zipped versions can be found
    • a link where the raw report data can be found

  • When submitting your folder to PSCIS, input a meaningful user reference and make note of it to make tracking easier

13.4.2 Fish Data and Habitat Confirmations

NOTE before beginning: The way to document all changes in habitat_confirmations.xls so that we can go back if something get really mangled (easy for that to happen with copy paste values in those spreadsheets) is to use the fpr_import_hab_con(row_empty_remove = T) function between steps and commit the resulting csv files that get generated in the data/backup directory. Run fpr_import_hab_con(row_empty_remove = T) AND COMMIT with really informative commit message after each step that involves moving rows and other moves that you think have potential to result in mangled files.

Steps to QA and submit habitat confirmation data contained in habitat_confirmations.xls :

  • If not done yet, ensure the UTM coordinates for each site are at the downstream starting point of the survey. Use basecamp to see GPS tracks and copy and paste coordinates to spreadsheet. Remove excessive features that aren’t significant

  • Make a lightweight current bcfishpass project on mergin in the Projects/gis/ directory using the qlr from the up to date bcfishpass repo.

  • Update the mapping objects (gpkg and geojson) in the report repo to confirm the locations are correct. Link to the geojsons directly in mergin project.

  • Add the 1:50,000 watershed codes to the spreadsheet. These can be found programmatically using a script. An example can be found in the skeena 2022 repo here.

    • Look up the referenced stream layer in QGIS and QA sample sites to make sure the codes are correct before submission. NOTE if there is no 1:50,000 watershed code available for a site, enter the code of the nearest parent stream in the alias_local_name field.

  • Run the QA tool that ships with the submission template. The link to the tool within the spreadsheet is broken. The tool can be downloaded on this page here

  • Run code at the end of the extract_wsc_move_alias script so you can extract the local names of our sites and burn to csv. Erase the local names from the submission sheet AFTER copying and moving the file ready for submission. Move the file to a folder on OneDrive and ensure the name of the permit number is included in the file name (ex: SM21-626611_data.xls)

  • Visit the BC Fish Data Submission Page and login to the sharepoint submission site (link at the bottom of the page) to complete a project submission form. See old submissions on this page for guidelines and examples.

13.4.3 PSCIS Phase 2

The project is set up within the submission interface which can be found at the link below:

https://logon7.gov.bc.ca/clp-cgi/capBceid/logon.cgi?flags=1101:1,8&TARGET=$SM$https%3a%2f%2fa100%2egov%2ebc%2eca%2fext%2fpscis-ui

A link to the BC Government PSCIS User Guide containing habitat confirmation submission procedures can be found at the link here (BC Government 2017).

+ MAPS DOWNOAD FROM https://hillcrestgeo.ca/outgoing/fishpassage/projects/

Copy and paste the key information from the associated online report into the each of the Crossing ID reporting interfaces. A KEY area to get info from are the tables in the Results and Discussion section of the online reports (amount of habitat, species and comments). This information comes from the custom csv file habitat_confirmations_priorities.csv located in the data directory of each repo.

  • Almost always the surveyed crossings are connected to downstream habitat so you will almost always click this box - unless there are barriers downstream and we know somehow (background info or sampling) that there is no fish presence at all upstream (non-fish bearing).

  • Recommendation - proceed to design unless there is some reason its not worth it at all (priority - no fix or potentially low with complications of some sort)

  • Amount of habitat upstream (NOT THE MODELLING data but a more conservative estimate found in text - in the Conclusion and Stream Characteristics Upstream section of the individual site memo appendices of the online report).

  • Habitat Value - see Conclusion and Stream Characteristics Upstream sections of individual memos for the low, medium and high rating.

  • Habitat Value Rationale - see Conclusion and Stream Characteristics Upstream sections of individual memos for some brief details of why the habitat was rated as it was. See Table 3.3 of main report for some guideline criteria.

  • PLEASE NOTE that the online version of the PDF maps from this project are archived within https://hillcrestgeo.ca/outgoing/fishpassage/projects/bulkley/archive/2021-04-21/ . The links in the online report memo appendices will take you to the latest versions of the maps and it will not be easy to find the sites. You should look at the context for each site within the PDF maps because sometimes there are relevant things to see and potentially note. For example - for Site 123794 (example completed) there is a DV (dolly varden) fish observation upstream of the crossing that can be noted. Usually the species are described in the Background section of each memo (check there first) but if not - to see what the codes are you can search in the Fisheries Inventory Data Queries Fish Species Codes Query or you can view a lookup within the Species by Common Name page of the Fish Data Submission Template

  • Photos are in the data/photo/<site_id> directories. The upstream, downstream, inlet, outlet andbarrel photos are already loaded to the provincial system so upload five others (pick the ones with a _k_ in the filename FIRST as those are the ones from the report. If there is a _d_ in the filename it is from downstream and if there is a _u_ it is upstream. If there are not enough photos, pick extra photos from the habitat survey and label them with a _k_nm_. This is important as this filters out these photos from our interactive map so we don’t clutter it. Put very brief note in mandatory Description box (ex. habitat downstream).

  • Upload the correct PDF map from your locally unzipped https://hillcrestgeo.ca/outgoing/fishpassage/projects/bulkley/archive/2021-04-21/bulkley_2021-04-21.zip . Copy the filename from the map to populate the mandatory Description box. You can tell which is the right map from the name of the MAPGRID listed in the end of the Background section of each memo. See example completed site.

13.4.4 PSCIS Phase 3 - Design

Read instructions in PSCIS User Guide section titled : Initiating a Design Project.

  • Responsible Party is SERN BC (input their client number)
  • Responsible Party contact info is Al Irvine
  • Consultant Information section is the engineering company that carried out the design
  • Expiry Date can be 5 years from the proposal date (include note in comments “Remediation proposal expiry date estimated at submission and may not be accurate. Signing engineer should be consulted.” )
  • In Designer's Comments field, include info on who completed submission and links to site assessment appendixes in reports.

Methods for engineering standards are found in Province of British Columbia (2013)

13.4.5 PSCIS Phase 4 - Remediation

Read instructions in PSCIS User Guide section titled : Initiating a Remediation Project.

13.5 Planning

In preparation for field work, we screen bcfishpass modelling outputs for sites that are likely to have high value habitat. These steps can be found in the field planning scripts extract_planning.R, check them out in the Fraser 2023 repo for a starting point. Preliminary workflows are described below.:

  • Add columns for comments and a priority ranking for follow up (no fix, low, mod, high)

  • Add column called my_citation_key1 through my_citation_key3 so that we can add zotero citation keys, use pull them out and use these citation keys to populate the references in the year end report.

  • We want to keep the entire bcfishpass.crossings table (with our new columns) vs make a new object without some of the sites. We can just query them out.

  • Look at sites that have no crossings downstream so that we don’t review the same tributary system over and over again.

  • Filter the crossings to select ones that meet some or all of the following criteria. These crossings will undergo a detailed review to facilitate prioritization for Phase 1 Fish Passage Assessments and Phase 2 Habitat Confirmations:

    • Confirmed fish presence upstream of the structure.
    • Stream width documented as > 2.0m.
    • Linear lengths of modelled upstream habitat <8% gradient for ≥1km.
    • Crossings located on streams classified as 3rd order or higher.
    • Crossings located on streams with >5 ha of modeled wetland and/or lake habitat upstream.
    • Habitat value rated as “medium” or “high” in PSCIS.

  • Export the sites to a geopackage. Queries for review can be done in QGIS query builder and should be saved in a corresponding repo, see info in next steps.

  • Through the process of review we update the bcfishpass repo. There are lots of opportunities to increase the state of knowledge for all including the modelling through the csvs at https://github.com/smnorris/bcfishpass/tree/main/data . It is important to understand what all of them do and use them all when appropriate.

  • Scoping for field sites is an opportunity to review background info and add references to zotero.

After executing the preliminary workflows described above you can view the sites in QGIS by following these steps:

  1. Sync with mergin first - this makes a huge difference because other team members may be working on the same QGIS project. Do this from another project to avoid conflicting .qgs files
  2. Open your new layer in the Q project, import it as a layer (don’t rename anything)
  3. Put it somewhere in the menu you consider rational
  4. Symbolize it so you can see it really nicely. Double click the layer to get to its properties
  5. Use the query builder to filter so you only see the layers that have a my_review = TRUE created the in its properties (Source window in properties)
  6. Add it to the reporting theme (be sure to 1. refresh that theme, 2. add only that layer, then 3. “Replace theme”

  1. Find out how to “dock” your attribute table in the bottom of your screen so you can work on editing the table while still looking at the map. Right-click layer to see attribute table.
  2. Sort by CO rearing habitat descending (just click in attribute table) and have a look at the first 3 sites. Review all the columns and learn what they do. Remember that we have access to all the column comments (that have them) by a move scripted in tables.R and some of them we put in our report methods tables.
  3. Be aware that we visited many sites this summer and you should see that data beside or on top of some of the sites. You should click into the field data of already assessed sites and see what it says. Photos for those sites are in the file too so you can look at those.
  4. If there is no associated field site you can fill in the custom columns as follows. For priority it is one of the following no_fix, low,mod and high. The my_priority_comments should include a justification for why it was given that ranking. For example, “stream appears to have good flow and tons of gravel in PSCIS photos” (accessible through image_view_url if it has a phase 1 completed already) or “known Chinook spawning location just downstream and target stream for restoration by Nechako streamkeepers.” no_fix are often ones that need adjustments in bcfishpass csvs.
  5. When you can tell a site is not a bridge or removed and it seems like a decent candidate to look at you can search its stream name (or parent stream name in EcoCat). We don’t really want excel files of fish data (usually accessible through the fiss layers in QGIS) but if there are relevant reports they go in Zotero/region/ or Zotero/region/watershed_group_code/ dependent on their context. They can then be referenced in the my_citation_key* columns, for example, my_citation_key1 = properly formated Zotero citation key.

Finally, the following are guidelines for planning workflows done shortly before field work days:

  • Research the watershed of interest and try to identify major tributaries of interest
  • Even if they did not appear in preliminary prioritization, investigate crossings that could be valuable
  • Regularly check satellite imagery for clues and evidence that a crossing does or doesn’t exist, this can save time in the field (ex: deactivated roads or fords). Add fords and bridges that aren’t modelled as open bottom structures to the bcfishpass repo.
  • Look out for streams that have fish points upstream, especially salmonids.
  • Gather helpful information on crossings by reading past survey comments (if available).