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Final Project: Western Hemlock Dwarf Mistletoe Spatial Patterns and Drivers

Western Hemlock Dwarf Mistletoe

Western hemlock dwarf mistletoe is a hemi-parasite of primarily western hemlock trees. It absorbs water, nutrients, and carbohydrates from its host. Infected branches produce small structures called aerial shoots that have minor photosynthetic capabilities, but are primarily for pollination and seed production and require a certain amount of light to emerge from an infection site. Seeds are explosively discharged from aerial shoots when fully mature. Once landing on a susceptible host branch they being germination and mechanical penetration of the host branch.

Research Question

I wanted to explore the spatial patterns of dwarf mistletoe infections after a mixed severity fire and the roles post-fire, forest structure and fire refugia play.

How does the spatial pattern of post-fire stand structure and species composition affect spatial patterns of dwarf mistletoe distribution throughout the stand through physical barriers to susceptible hosts and seed dispersal?

Description of Dataset

I have a 2.2 ha rectangular study area (Wolf Rock), just northwest of the HJ Andrews Exp. Forest that was stem mapped in 1992. Each tree has an X and Y coordinates, as well as the tree species, height, diameter, and a variety of other tree inventory related data. I only have ages for a few western hemlocks, but many more for Douglas-fir. Only one western hemlock core was identified as being over 100 years old, at 170 years. I have a polygon layer for the fire refugia that are documented on the study area. For the western hemlocks I have a presence/absence of western hemlock dwarf mistletoe as well as a severity measure. However, I am unsure of the scale and ethod of rating, so I will not be using it. The infection presence and absence are from a single measurement season.

Hypotheses and Predictions

Western hemlock dwarf mistletoe spreads easily through moderate canopy densities, where distances between trees are close to the average dispersal distance of 2-4 meters. Disturbances that create patchy gaps increase likelihood of spread because of increased light reaching infected branches and increase the rate of infection abundance because of the lack of physical barriers such as high densities of branches and foliage.

Disturbances can also remove the disease from a forested stand by killing or knocking down infected western hemlocks. Post-disturbance regeneration can enable or inhibit the parasite’s reintroduction to the stand. Non-susceptible hosts such as Douglas-fir or western redcedar regenerate readily alongside western hemlock and will intercept seeds. Some gaps are only conducive to western hemlock regeneration which will be readily infected by any surviving infected western hemlocks post-disturbance.

The Wolf Rock stand experienced two fires that created a mosaic of ~110 year old regeneration and >110 year old remnant trees in fire refugia. Remnant, infected western hemlocks survived the most recent fire in those fire refugia. From this stand structure, I have several hypotheses and predictions:

  1. Remnant, infected western hemlocks form the center of new infection centers post disturbance so infections in the regenerating susceptible hosts, will be clustered around these remnant trees.
  2. Non-susceptible hosts regulate the rate of infection spread through physical barriers to dispersal, so infection cluster size will have an inverse relationship with non-host density.
  3. Western hemlock infection spreads from a central remnant tree, so uninfected western hemlocks will have a dispersed spatial pattern from the remnant western hemlock, regardless of non-host density.
  4. Post-fire regeneration with higher western hemlock composition will have more susceptible hosts and less physical barriers to spread so infection cluster size will have a positive relationship with western hemlock composition.

Analysis Approaches

For Exercise 1,  I wanted to know about the spatial pattern of western hemlock trees infected with western hemlock dwarf mistletoe. I used a hotspot analysis to determine where clusters of infected and uninfected trees were in my 2.2 ha study area. I discovered a hot spot and a cold spot, indicating two clusters, one of high values (infected) and one of low values (uninfected).

For Exercise 2, I wanted to know how the spatial pattern of these clustered infected and uninfected trees were related to the spatial pattern of fire refugia outlined in my study site. I used Geographically Weighted Regression to determine the significance of this relationship, however I did not find a significant relationship between a western hemlock, its intensity of clustering and infection status, and it’s distance to its nearest fire refugia polygon edge.

For Exercise 3, I wanted to know how the spatial patterns of remnant western hemlocks related to the spatial patterns of regeneration western hemlocks, uninfected western hemlocks, and non-western hemlock tree species. I used the Kcross and Jcross functions in spatstat in R and prepared the data in ArcMap to analyze spatial relationships between trees. I found clustering between regenerating western hemlocks and non-hosts to remnant western hemlocks but the uninfected western hemlock’s spatial pattern was independent of the remnant western hemlocks.

Results

I produced several maps that showed the spatial patterns in my study site which were helpful for understanding and investigating further relationships. I produced several charts from my exercise 3 analysis that were useful for visual representations of the relationships between trees. In Exercise 3 I also produced a map from raster addition that gave me the best visualization of where western hemlock and non-host trees were in the stand. Exercise 2 produced a map and statistical relationship but was not significant in explaining a hemlock’s infection and density status.

Significance

The biggest finding was that the fire refugia polygons are not significant for my analysis, the remnant infected hemlocks are more important explanatory variables in spatial patterns of infected trees. This supported hypothesis 1. Because refugia can be effectively defined using the “for what, from what” framework, western hemlock dwarf mistletoe refugia from fire could be delineated differently in the field focusing only on the remnant western hemlocks.

Data was not available to determine the rates of infection spread over time because I only had one season of measurements. I also could not evaluate the size of clusters because I did not have GPS points of infection center extent so I could not assess hypothesis 2 and 4 directly. However using Ripley’s K and the cross-variant I could see how the clusters changed over distance. I learned that infected, regenerating trees are going to be found closer to the remnant infected trees and that non-host trees may be blocking the spread of mistletoe into an uninfected patch because they were found clustered around remnant trees as well. This provides support for Hypothesis 1, 2, and 3.

Silvicultural prescriptions with the goal to preserve old growth forest structure, but that want to limit the amount of dwarf mistletoe in a forest can appropriately remove old infected hemlocks to preserve infection spread and extent. These prescriptions will also be able to predict future dwarf mistletoe spread. Forest operations that simulate disturbances that leave remnant hemlocks such as harvests, can incorporate spread predictions to limit regeneration being infected.

Learning From The Process

I learned a lot about the spatial analyst tools in ArcMap and how to produce easily interpretable maps and graphs. I also learned how to use several function in spatstat. I learned a lot about interpreting R outputs and spatial. Spatial autocorrelation can tell you a lot about what your data are doing but I thought it was most useful to be able to see on a map or chart what is specifically happening.

Comparing the Spatial Patterns of Remnant Infected Hemlocks, Regeneration Infected Hemlocks, and Non-Hosts of Western Hemlock Dwarf Mistletoe

Overview

For Exercise 1, I wanted to know about the spatial pattern of western hemlock trees infected with western hemlock dwarf mistletoe. I used a hotspot analysis to determine where clusters of infected and uninfected trees were in my 2.2 ha study area (Map 1). I discovered a hot spot and a cold spot, indicating two clusters, one of high values (infected) and one of low values (uninfected).

For Exercise 2, I wanted to know how the spatial pattern of these clustered infected and uninfected trees were related to the spatial pattern of fire refugia outlined in my study site. I used Geographically weighted Regression to determine the significance of this relationship, however I did not find a significant relationship between a western hemlock, its intensity of clustering and infection status, and it’s distance to its nearest fire refugia polygon.

This result led to the realization that the polygons as they were drawn on the map were not as relevant as the actual “functional refugia”. I hypothesized that, after the 1892 fire, the only way for western hemlock dwarf mistletoe to spread back into the stand would be from the trees that survived that fire, or “remnant” trees. These would then infect the “regeneration” tree that came after the 1892 fire. The functional refugia I am interested in are defined by the location of the remnant western hemlocks. I also hypothesized that the spatial pattern of non-susceptible host tree (trees that were not western hemlocks) would play a role in the distribution of the mistletoe.

Question Asked

How are the spatial patterns of remnant western hemlocks related to the spatial patterns of regeneration western hemlocks, uninfected western hemlocks, and non-western hemlock tree species, and how are these relationships related to the spread of western hemlock dwarf mistletoe in the stand?

The Kcross and Jcross Functions

The cross-type functions (also referred to as multi-type functions) are tools capable of comparing the spatial patterns of two different type events (type i and j) in a similar spatial window, of some point process, X. It does this by assigning labels to the events differentiating the type and summarizing the number or distance, of and between events, at differing spatial scales, or radius circles (r).

The statistic Kij (r) , summarizes the number of type j events, around a type i event at a distance of r, or a point process X. Deviations of the observed Kij(r) curve from the the Poisson curve, or if type j events are truly randomly distributed, indicates dependence of type j events on type i events. Similar results can be obtained from the regular Ripley’s K: deviations above the curve indicate clustering and deviations below indicate dispersal.

(Incredibly helpful and interactive explanation link: https://blog.jlevente.com/understanding-the-cross-k-function/)

The statistic Jij(r) = (1 – Gij(r))/(1-Fj(r)) summarizes the shortest distance between a type i and j event and compares it to the empty space function of type j event. This is another test for inferring independence or dependence of type j events to type i. Deviations of the Jij(r) curve the value of 1, indicate levels of dependence of the events to each-other. Specific deviations from 1 can be hard to interpret without an understanding of the Fj(r) function so imagining it stationary in the ratio makes it easier. As Gij(r) increases, the numerator shrinks, creating a smaller Jij(r) statistic. Deviations below 1 indicate that type i and j events are dependent and that as r increases, the shortest distance between points of type i and j increases. As Gij(r) decreases, the numerator grows, creating a larger Jij(r) statistic. Deviations above 1 indicate that type i and j events are dependent and that as r increases, the shortest distance between points of type i and j decreases.

Methods Overview

In R, the package “spatstat” provides a suite of spatial statistic functions including the cross-type functions. In order to use these you need to create a “point pattern process” object. These objects incorporate X and Y coordinates, and a frame of reference, or a “window,” and give spatial context top a list of values. Then marks are applied to these points that create the necessary multi-type point pattern process object. These marks serve to distinguish the type i and type j events described earlier in your analysis. Then running the “Kcross()” or “Jcross()” functions with the specified type events produces a graph that you can interpret, very similar to producing the normal Ripley’s K plot.

  • I took my X – Y coordinates of all trees on the stand and added a column called “Status” to serve as my mark for the point pattern analysis.
    1. The four statuses were “Remnant,” “Regen,” “Uninfected,” and “NonHost” to identify my populations of interest.
      1. I had access to tree cores, so I identified trees that were older than 170 yrs old and these trees’ diameters served as my cutoff for the “Remnant” diameter class.
      2. All trees DBH > 39.8 cm.
    2. Doing this in ArcMap removed steps I would have to have taken when I migrated the dataset to R.
    3. I removed all the dead trees because I wasn’t concerned with them for my analysis.
  • I exported this attribute table to a csv and loaded it into R Studio.
  • I created the boundary window of my study site using the “owin()” function, and the corner points from my study site polygon.
  • The function “ppp()” creates the point pattern object and I assigned the marks to the data set using the “Status” column I created in ArcMap
    1. It’s important your marks are factors otherwise it is not converted into a multi-type point pattern object.
  • The last step is running the “Kcross()” and “Jcross” to compare the “Remnant” population to the “Regen,” “Uninfected,” and “NonHost” populations.
    1. This produced 6 plots, 3 of each type of cross-type analysis.
    2. Compare these easily using the “par()” function, for example:

par(mfrow = c(1,3))

plot(Ex3.Kcross1)

plot(Ex3.Kcross2)

plot(Ex3.Kcross3)

This produces the three plots in a single row and three columns.

Results

Because I am assuming the remnant, infected western hemlock trees are one of the main factors for the spread of western hemlock dwarf mistletoe and that they are the center of  new infection centers on the study site, I did all my analysis centered on the remnant trees (points with status = “Remnant” treated as event type i).

1)   i = Remnant, j = Regen

The first analysis between remnant and regeneration trees demonstrate that there is dependence on the two events to each other. At fairly small distances, or values of r, infected western hemlocks that have regenerated after the 1892 fire cluster around infected remnant western hemlocks that survived the 1892 fire. This stands to reason because we assume that infected trees will be near other infected trees, and that infection centers start usually with a “mother tree.” In this case the remnant trees serve as the start of the new infection centers. The Jcross output also shows me that the two types of trees are clustered using the frequency of the shortest distances. After ~8 meters the two tree types exhibit definite clustering. In terms of the function, the Gij(r) in the numerator of the Jij(r) function is approaching 1, or the highest frequency of very short distances.

2)   i = Remnant, j = Uninfected

The Kcross plot from the second set of analyses between remnant and uninfected trees demonstrates that there is independence between the two events up to ~15 meters. After that, the trees exhibit slight clustering effects. The lack of dispersal tendencies is strange for these two types of trees because we expect uninfected trees to be furthest away from the center of infection centers. The presence of clustering may be indicative of the small spatial scale of my study site. It may also be that the size of the infection centers are only about 15 meters (if we assume that remnant trees are the center). The Jcross plot shows something similar: at small distances the types of trees seem independent and then around 8 meters they exhibit clustering.

3)   i = Remnant, j = NonHost

The Kcross from the last set of analyses between the remnant trees and the non-hosts demonstrates a similar pattern exhibited by the regeneration trees. After about 4 meters, the trees tend to be clustered. This is an interesting find because if the non-hosts cluster to remnant trees but uninfected trees are independent, then the non-hosts may be playing a role in this. The Jcross plot shows the same: the two types of trees exhibit clustering.

4)   Comparing Kcross Functions with eval.fv()

A useful way to compare patterns of Kcross functions is using the eval.fv function. The titles of each plot tell which Kcross was subtracted from which; note the difference in scales. The first plot shows that the regenerating trees’ spatial pattern as related to remnant trees is very different from the uninfected trees’ pattern. The regenerating trees’ spatial pattern is much more similar to the non-hosts’ spatial pattern at short distances, until about 15 meters. Then the patterns differ with the regenerating trees exhibiting more of a clustering tendency. However the scale is much smaller than the other two graphs. Lastly, the third plot shows the difference between the non-host trees’ spatial pattern and the uninfected trees’ spatial pattern. There appears to be a stepwise relationship where, at very near and very far distances the non-host trees are much more clustered, but at moderate distances the differences may be less dramatic.

Critique of Cross-Type Functions

The amount of easily interpretable literature on the spatstat package as a whole is sparse, although a wealth of very technical information exists. The function was easy to use and execute though and so was the process of creating the point pattern object. These two functions can clearly show how the spatial patterns of the two types of events change with scale. It would be helpful if there was a way to compare three or more types of events. The last drawback is that there is a lack of specific information for each point on your map or study site. This pattern that is generalizable to a whole set of points may not be as useful when trying to put together a story, such as the story of a stand’s development through time.

Additional Raster Analysis

The last critique of the cross-type functions led me to attempt a visualization of these patterns on my stand. Very briefly, I determined densities of the infected, uninfected, and the non-host trees using the Kernel Density function in ArcMap. Then I classified these densities using natural breaks and coded these for raster addition. After adding all three density rasters together, I coded each unique density classification combination to tell me how the densities of the populations appeared in the study site.

It appears that there are distinct patches of high density separated by areas of low density. On the eastern side of my study site, it appears that the high density areas of infected trees cluster with the remnant infected trees. An interesting interaction is occurring between the high density patches of uninfected trees and infected trees in the western portion of my study site. The mechanism for the seemingly clear divide may be the non-TSHE trees.

Fire Refugia’s Effects on Clustering of Infected and Uninfected Western Hemlock Trees

Overview

For Exercise 1, I wanted to know about the spatial pattern of western hemlock trees infected with western hemlock dwarf mistletoe. I used a hotspot analysis to determine where clusters of infected and uninfected trees were in my 2.2 ha study area (Map 1). I discovered a hot spot and a cold spot, indicating two clusters, one of high values (infected) and one of low values (uninfected).

In my study site, 2 fires burned. Once in 1829, burning most of the stand, and then again in 1892, burning everywhere except the fire refugia (polygons filled in blue). This created a multi-storied forest with remnant trees located in the fire refugias. One component of the remnant forest are infected western hemlocks. These remnant hemlocks serve as the source of inoculum for the hemlocks regenerating after the 1892 fire.

For Exercise 2, my research question was: How does the spatial pattern of fire refugia affect the spatial pattern of western hemlock dwarf mistletoe?

I predicted that a cluster of infected western hemlocks are more likely to be next to a fire refugia than a cluster of uninfected trees. In order to assess this relationship, I used the geographically weighted regression tool in ArcMap.

Geographically Weighted Regression

Geographically weight regression (GWR) works by creating a local regression equation for each feature in a data set you want to analyze, using an explanatory variable(s) to predict values for the response variable, using the least squares method. The Ordinary Least Squares (OLS) tool differs from GWR because OLS creates a global regression model (one model for all features) whereas GWR creates local models (one model per feature) to account for the spatial relationship of the features to each other. Because the method of least squares is still used, assumptions should still be met for statistically rigorous testing. The output of the GWR tool is a feature class of the same type as the input, with a variety of attributes for each feature. These attributes summarize the ability of the local regression model to predict the actual observed value at that feature’s location. If you have an explanatory variable that explains a significant amount of the variation of the response variable, this is useful for seeing how its coefficient varies spatially.

Execution of GWR

To use this tool, I quantified the relationship between the trees and the fire refugia. I used the “Near” tool for this to calculate the nearest distance to a fire refugia polygon’s edge. This was my explanatory variable. My response variable was the z-score that was output for each tree from the Optimized Hot Spot Analysis. Then I ran the GWR tool. I then used the Moran’s I tool to check for spatial autocorrelation of the residuals. This is to check the clustering of residuals. Clustering indicates I may have left out a key explanatory variable. The figure below displays my process.

I tested the relationship between nearest distance to a fire refugia polygon’s edge and the z-score that was output for each tree from the Optimized Hot Spot Analysis using OLS, which is necessary to develop a well specified model. My R2 value for this global model was 0.005, which is incredibly small. Normally I would have stopped here and sought out other variables to explain this pattern, but for this exercise I continued the process. 

Results

This GWR produced a high global R2 value of 0.98 (Adj R2 0.98) indicating that distance to refugia does a good job of explaining variance in the spatial pattern of infected and uninfected trees. However, examining the other metrics for the local model performance gives a different picture of model performance.

Map 2 displays results for the coefficients for the explanatory variable of distance to nearest refugia. As this variable changes, the z-score increases or decreases. These changes in z-scores indicate a clustering of high or low values. From examining the range of coefficient values, the range is quite small, -0.513 to 0.953. This means that across my study site, the coefficient only changes slightly from positive to negative. In the north western corner, we see a cluster of positive coefficient values. Here, as distance to refugia increases, the z-score of trees increases, predicting a clustering of infected trees. These values are associated with high local R2 values (Map 4). In other places of the stand we see slight clustering of negative coefficients, indicating distance to refugia decreases the z-score of trees, predicting a clustering of uninfected trees.

Map 3 displays the standardized residuals for each tree. Blue values indicate where the local model over-predicted what the actual observed value was, and red values are under-predictions. When residuals from the local regression models are distributed randomly (i.e. not clustered or dispersed) over the study area, then the geographically weighted regression model is fit well, or well specified. The residuals of the local regression models were significantly clustered. (Moran’s Index of 0.265, p-value of 0.000, z-score of 24.344). Because we can observe clustering in my study area of residuals, there is another phenomenon driving the changes in z-scores; in other words, driving the clustering of infected and uninfected trees.

From the previous two map evaluations I saw that the distance of a tree to fire refugia was not the only explanatory variable necessary to explain why infected and uninfected trees clustered. Map 4 displays the local R2 values for each feature. The areas in red are high local R2 values. We see the northwestern corner has a large number of large values which correspond to a cluster of small residuals and positive coefficients. Here, distance to fire refugia explains the clustering of infected trees well. The reverse is observed in several other places (clusters of blue) where distance to fire refugia does not explain why infected or uninfected trees cluster. In fact the majority of observations had a local R2 of 0.4 or less. From this evaluation, I believe this GWR model using distance to refugia does a good job of explaining the clustering of infected trees, but not much else.

Critique

GWR is useful for determining how the coefficient of an explanatory variable can change across an area. One feature in a specified area may have a slightly different coefficient from another feature, indicating these two features are experiencing different conditions in space. This allows the user to make decisions about where the explanatory has the most positive or negative impact. This result is not something you can derive from a simple OLS global model. This local regression process is something you could do manually but the tool in ArcMap makes this process easy. The output of GWR is also easy to interpret visually.

Some drawbacks are that you need to run the OLS model first for your data to determine which variables are significant in determining your response variable. If not, then a poorly specified model can lead to inappropriate conclusions about the explanatory variable (i.e. high R2 values). Also, the evaluation of how the features interact in space is not totally clear. The features are evaluated within a fixed distance or number of neighbors, but there is no description for how weights are applied to each neighboring feature. Lastly, for incidence data, this tool is much harder to use if you want to determine what is driving the spatial pattern of your incidence data. Some other continuous metric (in my case a z-score) must be used as the response variable, making results harder to interpret.

Model Results Follow-Up

After finding that distance to a refugia was not a significant driver for the majority of trees, I examined my data for other spatial relationships. After a hotspot analysis on solely the infected trees, I found that the dispersal of infected trees slightly lined up with the fire refugia drawn on the map (Map 5).

Among other measures, forest structure was used to determine where fire refugia were located. Old forest structure is typically more diverse vertically and less clustered spatially. Also infected western hemlocks are good indicators of fire refugia boundaries because as a fire sensitive tree species, they would not survive most fire damage and the presence of dwarf mistletoe indicates they have been present on the landscape for a while. From the map we can see that the dispersal of infected trees only lines up with the refugia in a few places. This mis-drawing of fire refguia bounds may be a potential explanation for under-performance of the GWR model.

Exercise 1: What is the spatial pattern of western hemlock dwarf mistletoe at the Wolf Rock reference stand?

For Exercise 1, I wanted to analyze the spatial pattern of western hemlock dwarf mistletoe infections in live western hemlocks on my 2.2 ha reference stand (Wolf Rock). This was without considering any attributes of the western hemlock trees themselves. Simply, what was the spatial pattern of infection?

To answer this I used the “Average Nearest Neighbor” tool in the Spatial Statistics toolbox in ArcMap. This tool calculates a z-score and a p-value from that z distribution. This is a commonly used method in dwarf mistletoe literature for assessing the clustering of infection centers. Also, the equations for this tool assume that points are free to locate wherever in space and that there are no barriers to spread.

ArcMap makes running these analyses very simple so I created a selection of infected trees (red dots), created a new feature, and then ran the tool. The p-value from my test was 0.097 and my Nearest Neighbor Index was 0.970, indicating that the spatial pattern of the infections are somewhat clustered with an alpha of 0.10.

Average Nearest Neighbor is a good test for analyzing whether or not a set of coordinates are clustered. The degree of clustering of may be harder to interpret as a lower p-value may not necessarily mean points are more clustered. Also I was unable to see where my clusters are, and if my intuitions match the analysis (see map). One other important consideration is the study area. Changes in analysis area can drastically change the result of your clustering analysis (i.e. larger study areas may make data look more clustered). Lastly, there was no option for edge correction. This may have skewed some of the clustering results along the edge of my study site and 2.2 ha is pretty small to be subsampled without losing a lot of my data.

Prologue

After confirming that my infections were clustered, I wanted to see if the pattern I saw in my map, was actually on the ground. I wanted to know, where are infected trees clustered with infected trees and where are uninfected trees clustered with uninfected trees? Again, this was without considering any attributes of the western hemlock trees themselves.

I used the “Optimized Hot Spot Analysis” tool in the Mapping Clusters toolbox to analyze the incidence of infection data (0 = absence, and 1 = presence). The Optimized Hot Spot Analysis tool can automatically aggregate incidence data that are normally not appropriate for hot spot analysis. It also calculates several other metrics for me that made analysis easy. I could take these automatically calculated metrics and alter them in a regular hot spot analysis if needed.

This map displays clustering that matched up closely with my intuitions from Map 1. On the left, the blue values show a cluster of uninfected trees that are closely clustered with other uninfected trees. The larger swath on the right show a cluster of trees that are closely clustered with other infected trees. In the middle a mix of uninfected trees and infected trees are mixed without displaying any significant clustering. Lastly, small clusters in the top left and bottom left of infected trees were identified. These clusters may be edge of larger clusters outside my stand, or lightly infected trees that are starting a new infection center. These results will be extremely valuable in informing my steps for Exercise 2 because I can assess the conditions of both patches and determine differences between the two. I can also determine if distance to the refugia impact the clustering of infection because it appears the infected cluster is closer to the fire refugia.

The hot spot analysis was extremely useful for analyzing and displaying the information I needed about the clustering and was very useful for building off of the Average Nearest Neighbor analysis.

My data set also included a severity rating for dwarf mistletoe infected western hemlocks in my study site. I ran a similar hot spot analysis to above to determine if there were any similarities with how severity played out in the stand compared to solely incidence data. My data ranged from 0 – 5, 0 indicating uninfected trees and 5 indicating most heavily infected. These are classified data, not continuous but still appropriate for the optimized hot spot analysis. Western hemlock dwarf mistletoe forms infection centers, starting from a residual infected western hemlock that survived some disturbance. From there the infection spreads outwards. Another facet of infection centers is that the most heavily infected trees are almost always aggregated in the center of the infection center and infection severity decreases as you move towards the outside of the infection center. This is intuitive when you think about infected trees in terms of the time they’ve been exposed to a dwarf mistletoe seed rain: the trees in the center of the infection center likely have been exposed to infectious seed the longest. These trees can be rated using a severity rating system that essentially determines the proportion of tree crown infected. This is calculated in a way that gives a rating that is easily interpretable, in this case, 0-5.

This third map tells me about how severity is aggregated in the stand. I can see that the wide swath in the middle of the stand, associated with the fire refugia, has the largest aggregation of severely infected trees. This is what I expected in the stand because the trees in the fire refugia survived the fire and provide an infectious seed source for the post-fire regeneration. Also, on the edges of this high severity cluster, are lower severity values indicating the expected pattern of infection centers are playing out. The west side of the stand shows a large clustering of low severity ratings. We can see that the high density of uninfected trees, falls into our cold spot of low or no severity. Interestingly, the hot spot of trees found previously  in the southwest corner, is actually a cluster of low severity trees. This may be a new infection center forming or an exterior edge of another infection center outside the plot.  Lastly, the two pockets of low severity on the east side of the stand are more distinct when considering their severity.

This second application of hot spot analysis tells another story about my data and how dwarf mistletoe is patterned spatially. The non-significant swath in the center of my stand using the incidence data turns out to be a significant clustering of highly infected trees among other new observations.

 

Cross-sectional Change in the Andrews Forest

Background and Research Questions

This project explores stream bed mobility in the HJ Andrews experimental forest in relationship to peak discharge events and channel geometry. The HJ Andrews Experimental Forest is a Long Term Ecological Research (LTER) Site located east of Eugene on the western slope of the Cascade Range. The site has been managed since the 1950s for ecological and forestry research, and the largest stream in the forest has been gauged since 1950. From 1978 to 2011, researchers conducted repeated cross sectional surveys on five reaches in three different creeks in the forest. An analysis of these cross-sectional profiles will help researchers and managers gain a better understanding of how, when, and where stream beds responds to extreme hydrologic events.

Water flowing through streams exerts stresses on the bed material. Whether or not these stresses have the capacity to mobilize sediment and change the shape of a stream bed depends on the amount of water moving through the stream along with other factors. As with many geomorphological processes, bed sediment transport is dominated by movement during extreme events. Although cross sectional changes overall appear to be strongly related to the magnitude of greatest flow between measurements, I am interested in investigating confounding factors including the extent of temporal and spatial autocorrelation in the data set.

I would like to explore (a) if and (b) in what manner aggradation or erosion in one cross section might be related to changes in adjacent cross sections. I would also like to know if aggradation or erosion in one cross section in one year are related to changes in the same cross section in an adjacent year.

Data

I am analyzing cross sectional measurements of five reaches within the Andrews Forest, which range from 12 m to 55 m in horizontal extent and 1.2 to 7.3 meters in vertical extent. The cross sections are variously spaced along an along-stream dimension, and they are were surveyed every one to five years over a period of 30 years between 1978 and 2011. The vertical precision of the data set is roughly 1 cm (though the data are unlikely to be accurate to 1 cm) and the horizontal precision varies from 1 cm to several decimeters.

The cross sectional change between two adjacent pairs of years at one cross section is shown below. Areas of erosion are shown in red and areas of aggradation are shown in green.

Hypothesis and Approach

I predict that there will be a relationship between changes at one cross section during one year and the same cross section at another year. Portions of the stream bed that have been recently scoured or contain newly emplaced sediment may be less armored than undisturbed portions of the stream bed. These less armored portions of the stream bed may be more susceptible to future disturbance. Alternately, changes at a cross section may represent longer-term processes related to channel geometry: e.g. a series of cross sections could show continued incision of a cut bank over multiple years.

I do not expect to see a detectable relationship between changes at adjacent cross sections because I expect that the most important geographic controls on channel change are either smaller (e.g. pools) or much larger (e.g. along-stream variation in discharge) than the distance between cross sections.

I want to use this class as an opportunity to explore statistical relationships, but I don’t know yet what kinds of analyses are best suited to this problem. I’d like to learn more in general about how to handle spatial autocorrelation, and when it is and isn’t a statistical issue.

Justification
This project could be scientifically useful for improving our understanding of sediment transport in Pacific Northwest mountain streams. Resource managers may also have an interest in sediment transport because it relates to stream channel mobility (“How much can we depend on this creek staying in the same place?”) and ecology (“How vulnerable is stream life to disruption via bed transport?”). From a resource management perspective, it is becoming increasingly useful to study peak flow events because downscaled climate models for our region predict increased frequencies of large storms.

Preparation

I feel good about my experience with spatial technology, and I’m most interested in learning about how to use that technology to answer statistical questions. I am highly proficient with Arc software. I have TAed one undergraduate class and independently taught another short undergraduate class in ArcGIS. I have a working knowledge of ArcPy, but I still need to use references regularly to write code. I conducted some undergraduate remote sensing research using ArcPy and used ArcPy for research at a government science agency. I work extensively in R. I’ve done image processing using Arc software, Python, ENVI, ImageJ, and raster tools in R, but it’s a very broad field, and I definitely think I could learn more.

 

Epidemiology of Western Hemlock Dwarf Mistletoe Post – Mixed Severity Fire

Description of the Research Question

My study site is located in the HJ Andrews Experimental Forest, where the two most recent mixed severity fires burned leaving a sizable fire refugia in the middle of the stand. Western hemlock dwarf mistletoe (WHDM) survived the fire in this refugia. WHDM spreads via explosively discharged seed and rarely by animals. This means that for the pathogen to spread, the seed must reach susceptible hosts. WHDM is a obligatory parasite of western hemlock. The regeneration post fire may pose a barrier to the pathogens spread because of the structure and composition. Lastly, the structure of the fire refugia may determine the rate of spread. This is because the structure largely determines where infections exist in the vertical profile of the canopy.

My research question is: How is the spatial pattern of WHDM spread extent and intensification from fire refugia related to the spatial pattern of the structure and composition of the fire refugia and the surrounding regeneration via barriers to viable seed reaching susceptible hosts?

I have three objectives related to the spatial organization or the regenerating forest surrounding the fire refugia and one related to the fire refugia itself. My objectives are to determine how fire refugia affects dwarf mistletoe’s spread and intensification through:

  1. The stand density of regenerating trees and of surviving trees, post fire.
  2. The stand age and structure of regenerating trees and surviving trees in fire refugia.
  3. The tree species composition of the regenerating trees adjacent to fire refugia.

AND…

  1. Whether intensification dynamics of WHDM inside a fire refugia resemble those of WHDM in other infection centers.

Dataset Description

Spatial locations of the extent of spread and intensity (also referred to as severity) of WHDM infection include presence/absence of infection in susceptible hosts and will have a severity rating for each infected tree. The presence/absence data will be two measurements, one from 1992 and one from 2019. The intensity rating will be from 2019 only.

Spatial locations/descriptions of the structure and composition of the fire refugia and regeneration surrounding refugia include X,Y of each tree, a variety of forest inventory attributes such as diameters, heights, and species for each tree, and delineation of the fire refugia boundaries. This data has been measured several times: 1992, 1997, 2013, and 2019. The GPS coordinates were recorded with handheld GPs units most likely under canopy cover so resolution may vary.

These data sets are bounded by a 2.2 ha rectangle that confines the study area.

Hypotheses

The spatial pattern of western hemlock dwarf mistletoe in the study site will be several discrete clusters. This arrangement forms because WHDM spreads from an initial infection point outward. The initial infection serves as an approximate center point and the cluster, or infection center, grows outward from there. Separations between clusters are maintained by forest structure and composition or disturbances. New clusters form from remnant trees surviving disturbances, or random dispersal of seed long distances by animals. In this case, the fire refugia protect the remnant trees from disturbance and these trees are the new focal points for infection centers

The spatial pattern of the forest structure and composition will drive the direction and rate of spread of WHDM because variances in these two attributes will cause varying amounts of barriers to WHDM seed dispersal. Because seeds are shot from an infected tree, that seed needs to reach a new uninfected branch. This means physical barriers to spread can affect seed dispersal and non susceptible species will stop spread.

Approaches

I would like to utilize spatial analyses that allow me to understand how the clustering of WHDM is related to the boundaries of the fire refugia. Also, how the infection centers have changed over time utilizing forest structure and composition metrics of the regeneration surrounding the refugia. Lastly, something that can incorporate a severity rating on a scale instead of simply presence/absence data and describe the distribution of severely infected trees vs lightly infected trees and how that relates to the fire refugia boundary and forest metrics of the regeneration surrounding the refugia.

Expected Outcome

I would like to produce statistical relationships that can determine the significance of forest density, species composition, age, and structure on the ability of WHDM to spread. Also, I would like to produce statistical relationships that can describe whether or not a fire refugia alters the way WHDM spreads and intensifies when compared to commonly observed models. Maps as visuals for describing the change over time would be a useful end product as well.

Significance

Understanding the spread patterns of WHDM is important for resource managers seeking to increase biodiversity and produce forest products. Focus has shifted to creating silvivultural prescriptions that emulate natural disturbances that are still economically viable and that maintain ecosystem functions. Disturbance events can control WHDM but also create opportunities to increase its spread and intensification so managers need to have an understanding of how a particular forest structure will affect WHDM. Also, if we want to maintain biodiversity, understanding how WHDM infection centers created by fire develop is important. Fire frequency and severity may be increasing in the future and the loss of mixed severity fire would mean a significant loss of WHDM. Land managers seeking to emulate burns can use this information to plan burns that preserve patches of WHDM if desired and understand how the pathogen will progress 25 years later. This is not usually the case for forest pathogens.

Level of Preparation

I have worked in ArcMap quite a bit, but I haven’t much experience with the wide range of functionality of ArcInfo. I used ModelBuilder somewhat to keep my queries and basic analyses organized. No experience programming in Python. I have taken two stats classes before this using R and feel I have a working knowledge and have no problem learning new tools in it. However, I have very little work with image processing such as working with rasters and some small exposure to LiDAR processing.

Exploring spatial variation in drivers of soil CO2 efflux in HJ Andrews Forest

Description of Research Question

My objective is to capture modes of variance that exist between and within a subset of variables that I expect to correlate most strongly with soil CO2 efflux in the HJ Andrews (HJA) forest. By stratifying the forest, I plan to determine future sampling sites that will be used to explore the relationship between soil C inputs, soil C stocks and CO2 outputs. Aboveground and belowground biomass are major sources of soil carbon and drivers of soil respiration, so biomass will be used as a proxy for soil CO2 efflux for the purposes of this analysis.

Research Question: How is the spatial distribution of biomass in the HJA forest related to stand age, slope, aspect, elevation and geomorphon as a result of varying degrees of exposure to solar radiation, wind gusts, precipitation, humidity, etc.? What is the overall variance of the HJA forest along these vectors and is that variance spatially autocorrelated?

Description of Dataset

I will use LiDAR data from 2011 and 2014 at 0.3-0.5 m vertical resolution and at 1 m2 horizontal resolution covering the Lookout Creek Watershed and the Upper Blue River Watershed to the northern extent of HJA. These LiDAR data include a high hit model and a bare earth model. I will also use NAIP imagery to approximate forest stand age, which is 1 m resolution and covers years between 2002 and 2018.

Hypotheses

I expect areas containing more biomass to positively correlate with south-facing slopes due to more exposure to solar radiation resulting in faster rates of vegetation growth. I expect older stands to positively correlate with greater biomass. I expect steeper slopes to correspond to less biomass due to more weathering and thinner soil horizons, supporting less growth. I expect higher elevations to correspond to lower biomass due to greater sustained winds, higher windspeeds and more snow accumulation. As geomopohon describes the geometric structure of the terrain, it is a collection of multiple factors that could positively or negatively correlate with biomass. For example, I expect a ridge to negatively correlate with biomass because of the combination of greater slopes and more exposure to winds, while I expect a valley to positively correlate with biomass due to more wind protection and thicker soil horizons with more organic matter and more water retention.

Approaches

With an end goal of identifying sampling sites, I’ll need to cluster or stratify the HJA forest. I’ll begin with a clustering analysis, then perform supervised and unsupervised classification, followed by sensitivity analysis comparing the results of the clustering analysis and both classifications. I will need to address spatial autocorrelation either as part of the clustering analysis or separately. I’ll need to plan sampling by accessibility, so I’ll examine an HJA roads layer as well.

Expected Outcome

I plan to produce maps (or use/improve on already available ones) at a spatial scale relevant to my study so I can identify potential sampling sites. I plan to map biomass across the HJA forest and produce a stratification of factors most closely related to soil CO2 efflux. Depending on resolution of the data and the results of the stratification, I may need to constrain my analysis. I plan to produce a statistical summary of the strata relating and describing the covariates and how much variance is explained by the stratification.

Significance

Carbon sequestration is a highly relevant research area where many unknowns still exist. Given that soil is an enormous C reservoir, small changes in soil C stocks can have huge impacts on the rest of the C cycle. As CO2 is a potent greenhouse gas, more release of C from soil can cause greater warming of our planet and can lead to a positive feedback loop where the warming cycle is amplified. It is in our best interest to have a good understanding of current soil C stocks and fluxes in forested systems so we can hypothesize how they might change under different or future conditions. By using biomass as a proxy for soil CO2 efflux, I will identify locations that are likely to have greater CO2 efflux and I will be able to make informed predictions about which drivers are most significantly correlated to CO2 efflux. I will be able to test these analyses in the future using field sampling techniques.

My level of preparation/proficiency

I have limited experience with Arc-Info (GEOG 560) and I’ve used Modelbuilder a few times. I have no experience with GIS programming in Python or R, but am proficient with coding in R (3 statistics courses and my own data analysis) and am comfortable seeking answers to questions in the R environment. I have no experience image processing.