create a guide to pests and pathogens

[teixeirak]

It would be good to have a student create an updated field guide to the pests & pathogens likely to appear in the plot. This could be based on existing guide(s) in this repo, review of VA dept of forestry reports, and literature/ web search.

[teixeirak]

Desired output

We want an .Rmd that produces a .pdf guide that can be used digitally or printed. It should be convenient for use in the field.

Outline

1. matrix of species x pests/pathogens for convenient reference as to which pests/pathogens may be affecting a certain tree species
2. table of contents for pests/pathogens, ordered by type (insect, fungus, etc.)
3. individual pages for each pests/pathogen, including info (see below) and photos
4. references

Desired info for each pest/pathogen

• pest_pathogen_common_name
• pest_pathogen_scientific_name
• tree_species_affected
• origin (native, exotic, cosmopolitan, undertermined)
• type and mechanism of damage (e.g., stem rot, xylem disruption, leaf herbivory)
• symptoms: specific symptoms that help ID the pest/pathogen. Include photos if available.
• status at SCBI: notes on any observations at SCBI, including year, how detected, etc.
• citations to info sources (with full list in references section)

Sources to reference

1. our list of insects & pathogens at SCBI. Includes many of the fields listed above.
2. https://github.com/SCBI-ForestGEO/SCBImortality/blob/main/doc/Protocols/Visual%20guides/Tree%20Mortality%20Guide_2020.pdf
3. https://github.com/SCBI-ForestGEO/SCBImortality/blob/main/doc/Protocols/Visual%20guides/Pest_pathogen%20watch.docx
4. Virginia Department of Forestry- Forest Health
   • https://dof.virginia.gov/wp-content/uploads/Tree-and-Forest-Health-Guide.pdf
   • other reports here: https://dof.virginia.gov/forest-management-health/forest-health/insects-and-diseases/

Process

1. start with list of tree species in our plot
2. based on this + the Virginia Department of Forestry (VDOF) Tree and Forest Health Guide, generate a matrix of species x pests/pathogens for convenient reference
3. compare with our list of insects & pathogens at SCBI - Most importantly, make sure there aren't any new/ emergent risks in the area that aren't in the DOF guide. It could also be helpful to update our list, but that might be more time consuming than we have time for.
4. look at our census data & results to identify the species with highest rates of disease and mortality. Use this list to prioritize additional research
5. Look at census data and photos (if time) to see how our results align with known causes of disease. For example, for a species commonly affected by an invasive fungal disease that causes cankers, are we recording cankers? Do photos match symptoms of the disease?
6. We may be able to get colleagues from the VDOF out for a site visit to help with our assessment

[teixeirak]

The Virginia Department of Forestry's Tree-and-Forest-Health-Guide (also loaded here, in this repo) provides a lot of the information outlined above. We don't want to re-invent the wheel.

What will be novel and useful is doing this assessment in the context of the data that we've been collecting. We'll want to look at mortality rates by species and proportions of unhealthy individuals in each species. Then, we'll want to look at FADs (factors associated with death) recorded for each species and compare these against common mortality agents, particularly for species with lots of disease/ decline. Are we detecting common agents of mortality? Or failing to detect because we don't know what to look for? Or is something else driving mortality? We can then produce a guide that will help field surveyors record appropriate info.

[teixeirak]

@irdangler , I'm responding to your questions here so that we preserve the record:

1. To find the species to focus on, will I be looking at the mortality data to find the trees with the highest mortalities and then finding any FADs associated with that and using those? I assume I should also compare with the VDoF guide and their pests/pathogens, but how do I pick which pests I'd like to focus on?

part 1: mortality rates (start here)

• Please use this file to describe mortality rates per species
• I've started a new file to list species of concern: https://github.com/SCBI-ForestGEO/SCBImortality/blob/main/doc/TreeDiseaseGuide/species_of_concern.md. I'll flesh this out with criteria, and then you can classify the species. To edit this, you click the pencil icon in the upper right corner. You can find a basic guide to this type of file here. It's pretty straightforward.

part 2: disease rates

• A second step would be to look at rates of disease in still-living trees (AU status), but let's come back to that.

3. When I do find the ones I'd like to focus on, should I highlight or bold them in the matrix so it's obvious? Or will there be another location where we can note this?

As above, let's note them here.

[teixeirak]

@irdangler , the criteria for identifying species of concern based on mortality is ready.

[teixeirak]

@ValentineHerr , the file that needs help is TreeDiseaseGuide.Rmd. (Warning: I did some very bad coding! :-) )

The problem is in the chunk starting on l.12, where I pull in various files to compile info about tree species, which ultimately goes in table 1 of TreeDiseaseGuide.pdf. Rather than properly merging different tables, I relied -- when I could -- on the fact that 3 of the files (https://raw.githubusercontent.com/SCBI-ForestGEO/SCBI-ForestGEO-Data/master/species_lists/Tree%20ecology/SCBI_ForestGEO_sp_ecology.csv, a file created by @irdangler that links tree species with diseases called matrix.csv, and our original version of tree_species_summary.csv table) all had the same species in the same order (this is bad, I know!). The problem came when I merged two tables (current line 42), which reordered tree_species_summary.csv. This reordered the table and somehow messed up which species were included (e.g., rops was lost, replaced with other). To try to save it, I set the code to read in a version of the table from before I made this mess (l. 36). Most fields in tree_species_summary.csv are modified by this code, but there are a couple manually filled by @irdangler (mortality.rates and AU.status-- these are codeable, and ultimately we'll want to switch over to that.)

This also messed up my color-coding of columns in table 2, which relies on TDconcernIndex (l. 127).

[teixeirak]

The easiest solution would be to make it so that the merge on l.42 retains the exact same set and order of species. The code will still have weaknesses from my coding shortcuts, but would produce the intended results.

Ultimately, I'd like to make this more robust, but for now we just need something that works for Isabella's presentation next week.

[ValentineHerr]

looking into this now. So ideally you'd like would recreate a correctly ordered version of tree_species_summary (using the older version of it for now) and then change the code so it pull the new master version of it on line 36?

[teixeirak]

That would work. The best practice would be to have all the info (l. 38-40) populated via proper merges, rather than just assuming same order.

And, ultimately, all the info in tree_species_summary could be coded, and the file generated fresh on each run.

[teixeirak]

That would work. The best practice would be to have all the info (l. 38-40) populated via proper merges, rather than just assuming same order.

If that were done, and the TDconcern_index on l.127 were also done this way, the order of the table wouldn't matter.

[ValentineHerr]

That would work. The best practice would be to have all the info (l. 38-40) populated via proper merges, rather than just assuming same order.

And, ultimately, all the info in tree_species_summary could be coded, and the file generated fresh on each run.

to be generated fresh on each run it might be best to create a file with just the IUCN status (in the species order you want). Then we pull that in l.36 and add the other columns to create tree_species_summary from scratch

[teixeirak]

IUCN status is in this file: https://raw.githubusercontent.com/SCBI-ForestGEO/SCBI-ForestGEO-Data/master/species_lists/Tree%20ecology/SCBI_ForestGEO_sp_ecology.csv (read in as "tree_sp_ecology" data frame). The species names are there too, of course. The only unique info in "tree_species_summary" is two fields filled manually by Isabella (mortality.rates and AU.status). Both are codeable, and ultimately we'll want to switch over to that, but not necessary right now unless its easier.

[teixeirak]

The criteria for mortality.rates and AU.status are in this doc.

[ValentineHerr]

How did you make the list of species in the first part of that document?

[teixeirak]

I used the list from tree_species_summary, which I had manually copied the list from this file: https://raw.githubusercontent.com/SCBI-ForestGEO/SCBI-ForestGEO-Data/master/species_lists/Tree%20ecology/SCBI_ForestGEO_sp_ecology.csv (read in as "tree_sp_ecology" data frame). Same goes for the matrix.csv file. I then relied on the fact that those lists were identical.

[ValentineHerr]

oh sorry I meant the species list in this document

[teixeirak]

@irdangler generated that manually be reviewing this file: https://raw.githubusercontent.com/SCBI-ForestGEO/SCBImortality/main/R_results/mortrates_and_agbmort_by_species.csv, and the similar file for AU.rates. For each species in the tree_species_summary list, she checked which met the various criteria.

[ValentineHerr]

Oh I understand now. thanks for explaining. I have almost the same list except I don't find qupr and quve to be H but M, based on mort rates.

[ValentineHerr]

ha never mind, I forgot I was also looking at biomass mortality

[teixeirak]

If you're coding this, we can replace the manual entry with code. I'd like to update this in future years.

[ValentineHerr]

Yeah I am trying to code it. I am not quite there yet... caco does not get classified... I need to figure out why

[ValentineHerr]

ha, got it. And I have the same list. Now to the "based on unhealthy one"

[teixeirak]

We now have a guide that will work! It could be improved/ made easier to use by providing info about each pest/pathogen in the guide itself, rather than having to refer to external materials. @emacmonigle, this is something you may be able to help with. After you see @irdangler's presentation tomorrow, we can discuss next steps.