update protocole for 2023

Removed EAB, dead crown position if dead, photos

doc/Protocols/Mortality Protocol.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "SCBI-ForestGEO Tree Health and Mortality Census Protocol 2022"
+title: "SCBI-ForestGEO Tree Health and Mortality Census Protocol 2023"
 output: pdf_document
 ---
 
@@ -51,42 +51,39 @@ Avoid giving a tree the DN status; you need to do a thorough search for all tree
 (1) Mark status
 (2) Record crown position
 (3) Record percentage of crown still intact (%)
-(4) Record percentage of crown living
+(4) Record percentage of crown living (%)
 
 *If the status is "AU"*:
 (1) Record FADs in order of importance* (at least 1 factor)- See FAD codes below.
 (2)	Record crown position. 
 (3)	Record percentage of crown still intact (%). 
-(4)	Record percentage of crown living
+(4)	Record percentage of crown living (%)
 (5)	Record lean angle (if leaning > 15$^\circ$)
 (6)	Record liana load. 
-(7)	Record wound, canker, or rot categories (if applicable) 
-(8)	Take pictures: Take a picture of alive unhealthy tree if picture appropriately captures FAD. For example, take picture of wounds to main bole, but not of leaf damage high in canopy. Take a picture of the tag first then make 2-3 pics of main FADS. Make nice close-ups if any insect or insect galleries are found. 
+(7)	Record wound, canker, or rot categories (if applicable), and their level
 
 *If the status is "DS" & previously "A":*
 (1)	Record FADs in order of importance (at least 1 factor)- See FAD codes below.
-(2)	Record crown position *and* "Dead crown position". 
+(2)	Record crown position. 
 (3) Measure and record DBH (mm)
 (4)	Record Percentage of crown still intact (%). 
 (5)	Record percentage of crown living (%)
 (6)	Record lean angle (if leaning > 15$^\circ$)
 (7)	Record liana load. 
-(8)	Record wound, canker, or rot categories (if applicable) 
-(9)	Take pictures: Take a picture of dead tree if picture appropriately captures FAD. Take a picture of the tag first then make 2-3 pics of main FADS. Make nice close-ups if any insect or insect galleries are found. 
+(8)	Record wound, canker, or rot categories (if applicable), and their level
 
 *If the status is “DC” & previously “A”:*
 (1)	Record FADs in order of importance (at least 1 factor)- See FAD codes below.
 (2) Record Percentage of crown still intact (%). 
 (3)	Record percentage of crown living (%)
 (4) Measure and record DBH (mm)
 (5)	Record liana load. 
-(6)	Record wound, canker, or rot categories (if applicable) 
-(7)	Take pictures: Take a picture of dead tree if picture appropriately captures FAD. Take a picture of the tag first then make 2-3 pics of main FADS. Make nice close-ups if any insect or insect galleries are found. 
+(6)	Record wound, canker, or rot categories (if applicable), and their level
 
 
 *If the status is “DS” & previously “DS”:*
 (1)	Mark status 
-(2)	Record crown position* *and* "Dead crown position". 
+(2)	Record crown position*. 
 (3)	Record percentage of crown still intact (%)*
 (4)	Record percentage of crown living (%)*
 (5)	Record lean angle (if leaning > 15^$\circ$)*
@@ -109,17 +106,12 @@ This refers to the tree's *current* position (as opposed to where it may have be
 
 ![*Crown Position (a.k.a., "Crown illumination"; taken from Arellano et al., 2020)*](figures_tables/Crown_illumination.png){ width=40% } 
 
-#### *Dead Crown Position (collected on dead trees only)*
-For broken/fallen trees, this is an estimate of position before it died.
-**Dominant (D)**: Crown extends above the general level of the canopy receiving full sunlight. 
-**Codominant (CD)**: Crown forms main level of canopy, tree receives full sunlight from above. 
-**Intermediate (I)**: Shorter trees with smaller crowns, receive little light from above and none from sides. 
-**Suppressed (S)**: Crown below canopy, small crown receives no direct light. 
-**Open grown (OG)**: Crown on open areas of the stand. 
-
 #### *Dead DBH (diameter breast height in mm; collected on dead trees only)* 
 If a tree is dead, you will be prompted for a DBH measurement. Measure DBH, being sure to report **units in mm**. If a stem has fallen and it's DBH can't be measured with a tape, measure it later using a big caliper (find one in Radiotracking lab - Office Annex building). 
 
+
+\newpage
+
 #### *Percentage of Crown Intact*
 This is the percent of the crown intact. 
 
@@ -204,39 +196,6 @@ Record any relevant info for which there's no place in the form:
 - Plot/previous data problems: incorrect coordinates, missing tree tags, suspected problems with previous data
 - Sometimes a tree recorded dead in a previous year is “back to life”. If a dead tree is alive in the current census (meaning you are 100% sure it is alive), mark the tree as **A** or **AU** and make a note in comments.
 
-#### *Take photos*
-Take a picture of every unhealthy or dead tree found. Include photos of all factors associated with death (FADs). Make nice close-ups if any insect or insect galleries are found. 
-
-
-### Emerald Ash Borer Add-ons
-
-#### *EAB crown thinning*
-**1** = no sign of defoliation/ leaf loss
-**2** = slight reduction in leaf density (thinning), yet all top branches exposed to sunlight have leaves
-**3** = thinning canopy and some top branches exposed to sunlight are defoliated (<50% dieback)
-**4** = >50% defoliation/dieback
-**5** = No leaves in canopy other than epicormic sprouting
-
-![Guide to estimating EAB crown thinning via visual assessment per Smith/Flower 2013:](figures_tables/Ash_crown_assessment.png)
-
-
-#### *EAB Epicormic growth*
-Evaluate using 6-class rating system (see figure).
-
-![6-class dwarf mistletoe rating system (Hawksworth 1977) to evaluate epicormic growth](figures_tables/epicormics_assessment.png)
-
-#### EABF (Emerald Ash Borer Factors)
-**VB** = Vertical bark splitting,
-**SS** = Stump sprouts,
-**AS** = Ash snap of the branches/limbs,
-**W** = Bark blonding from woodpecker predation. In comment section, write percentage estimate.
-**DE** = D-shaped exit hole presence.
-
-#### *D-shaped exit hole count*
-Count all visible D-shaped holes around the circumference of the tree in an area 50 cm high at breast height and record this number. At SCBI almost all tags are located at 1.3 m, so use the tag as reference to visually define the 50 cm area. That is, search for DE all the way around the tree between 1.05 and 1.55m height.
-
-
-\newpage
 
 ## Coring of Dead Trees 
 If time allows, cores will be taken at the end of survey and saved for future analyses.
@@ -247,6 +206,3 @@ Follow steps in document “Coring_instructions_SCBI” located in ‘Protocol
 
 *We will need to take data on trees cored (instructions to be determined later).*
 
-
-## Changes from previous years
-- PD (previously dead) is no longer an option in FastField (was not in 2021 protocol)