Tag Archives: Yaquina

Manipulating salinity to create a better fit habitat suitability model for Olympia oysters

Follow-up from Exercise 2
In Exercise 2, I compared Olympia oyster location data to the model of predicted suitable habitat that I developed in Exercise 1. Results from that analysis showed that 13 of the 18 observations within or near areas of high-quality habitat (type 4) indicated the presence of Olympia oysters (72%) versus 5 locations where oysters were not found (28%). No field survey locations fell within areas of majority lowest quality habitat (type 1). Seven observations were found within the second lowest quality habitat type (2), with 2 of those observations indicating presence (29%) and 5 indicating absence (71%).

Habitat suitability
4 3 2 1
Presence 13 [0.72] 4 [0.4] 2 [0.29] 0 [0]
Absence 5 [0.28] 6 [0.6] 5 [0.71] 0 [0]
Total (n = 35*) 18 [1.0] 10 [1.0] 7 [1.0] 0 [0]

*3 data points removed from analysis due to inconclusive search results.

To expand on this analysis, I used a confusion matrix to further examine the ‘errors’ in the data, or the observations that did not correlate with my model of predicted suitable habitat. For ease of interpretation, I removed habitat suitability type 1 since there were not observations in this category, and type 3 since it fell in between high and low-quality habitat.

Habitat suitability
4 (high) 2 (low)
Presence 0.37 0.06
Absence 0.14 0.14

Decimals reported indicate the proportion of total observations (n = 35) that fell within this category. The habitat suitability model predicted that oysters would be present within the highest quality habitat type and absent in low-quality habitat. The confusion matrix shows that the model was successful in predicting that 37% of the total observations where oysters were present were found within habitat type 4 (high), and 14% of the observations where oysters were absent were found in habitat type 2 (low).

In the type 4 habitat, 14% of the total observations found that oysters were absent, which goes against the model prediction. I suspect this is partly due to the patchy nature of substrate availability in Yaquina Bay and the low-resolution quality of the substrate raster layer used for analysis. For the 6% of observations that show oyster presence within habitat type 2, it’s possible that these points were juvenile oysters that were able to settle in year-1, but are less likely to survive into adulthood. Both of these errors could also indicate issues with the weights assigned in the model back in Exercise 1.

Question asked
For exercise 3, I wanted to expand on the habitat suitability analysis to see if I could more accurately predict oyster locations and account for the errors found in exercise 2. Here I asked:

Can the spatial pattern of Olympia oyster location data be more accurately described by manipulating the spatial pattern of one of the parameters of suitable habitat (salinity)?

I decided to modify the rank values of one of the model parameters: salinity. Based on my experience collecting oyster location data in the field, it seemed that salinity was the biggest influence in where oysters would be found. It was also the easiest parameter to change since it had the fewest rank categories. The excerpt below comes from the ranking value table I established for the habitat parameters in Exercise 1. Changes to rank value for salinity are indicated in the right-most column.

Habitat parameter Subcategories Subcategory variable range Olympia oyster tolerance Rank value applied
Mean wet-season salinity (psu) Upper estuary < 16 psu somewhat, but not long-term 1 –> 2
Upper mid estuary 16.1 – 23 psu yes 4 –> 3
Lower mid estuary 23.1 – 27 psu yes 3 –> 4
Lower estuary > 27 psu somewhat 2 –> 1

Name of tool or approach
I combined my approach from exercise 1 and exercise 2 to create a different model output based on the new rank values applied to the salinity parameter. The analysis was completed in ArcGIS Pro and the table of values generated was reviewed in Excel.

Brief description of steps to complete the analysis

  1. After assigning new rank values to the salinity parameter, I applied a new ‘weighted overlay’ to the salinity raster layer in ArcGIS. As I did in exercise 1, I used the ‘weighted overlay’ tool again to combine the weighted substrate and bathymetry layers with the updated salinity layer. A new map of suitable habitat was created based on these new ranking values.
  2. Then, I added the field observation data of oyster presence/absence to the map and created a new map of all the data points overlaid on habitat suitability.
  3. I then created buffers around each of the points using the ‘buffer’ tool. In the last analysis, I used the ‘multiple ring buffer’, but was only able to analyze the largest buffer (300m). This time, I created only the one buffer around each point.
  4. Using the ‘Zonal Statistics’ tool, I overlaid the newly created buffers on the updated raster of habitat suitability and viewed the results. I again chose ‘majority’ as my visual represented statistic, which categories the buffer based on the habitat suitability type occupying the largest area.
  5. I also created a results table using the ‘Zonal Statistics as Table’ tool, then copied it over to Excel for additional analysis.

Results
An updated table based on manipulated salinity rank values was generated to compare to the table created from exercise 2 and displayed at the top of this blog post. Results from this analysis showed that only 2 of the 35 total observations fell within or near areas of high-quality habitat (type 4), one indicated presence and the other absence. The adjustments to the salinity rank value allowed the habitat type 3 to dominate the map, with 31 of the total 35 observations falling in this category. Of the 31 points, 18 showed presence data (58%) and 13 were absence data (42%). Again, no field survey locations fell within areas of majority lowest quality habitat (type 1). Two observations were found within the second lowest quality habitat type (2), both indicating absence (100%).

Habitat suitability
4 3 2 1
Presence 1 [0.5] 18 [0.58] 0 [0] 0 [0]
Absence 1 [0.5] 13 [0.42] 2 [1.0] 0 [0]
Total (n = 35) 2 [1.0] 31 [1.0] 2 [1.0] 0 [0]

Again, I used a confusion matrix to further examine the ‘errors’ in the data, or the observations that did not correlate with my model of predicted suitable habitat. I removed habitat suitability type 1 since there were not observations in this category.

Habitat suitability
4 (high) 3 2 (low)
Presence 0.03 0.51 0
Absence 0.03 0.37 0.06

 

Decimals reported indicate the proportion of total observations (n = 35) that fell within this category. The confusion matrix shows that the model fit nearly all observations (31) into the type 3 habitat category, with a near even split between presence (18) and absence (13). In reference to the confusion matrix from exercise 2 at the top of this blog, it is difficult to make a direct comparison of the errors since most of the observations fell into type 3.

Critique of the method
I was surprised to see how drastically the map of suitable habitat changed by manipulating only one of the habitat parameters. The adjustment of the rank values for salinity resulted in a vast reduction in area attributed to the highest quality habitat (type 4). The results indicate that choosing the salinity parameter to manipulate did not result in a better fit model and that changes to salinity rank values were too drastic. Since the salinity parameter contains only 4 subcategories, or 4 different weighted salinity values, the impacts to the habitat suitability map were greater than if the parameter had had more nuance. For example, the bathymetry parameter has 10 subcategories and a reworking of the ranking values within could have made more subtle changes to the habitat suitability map.

The next steps would be to examine another parameter, either substrate or bathymetry, to see if adjustments to ranking values result in a more appropriate illustration of suitable habitat. Additionally, the collection of more oyster location data points will help in creating a better fit model and understanding the nuances of suitable habitat in Yaquina Bay.

 

Does the presence of Olympia oysters correspond with predicted suitable habitat?

Question explored
In my last blog post, I mapped habitat suitability for Olympia oysters in Yaquina Bay, OR by assessing three environmental parameters: salinity, substrate availability, and elevation. In exercise 2, I brought in oyster location data points collected from field surveys of the intertidal zone to compare against the map of suitable habitat. The question I am examining in this exercise is:

How does the spatial pattern of Olympia oyster location data correspond to the spatial pattern of suitable habitat in Yaquina Bay?

Field surveys of the intertidal zone of Yaquina Bay were conducted on April 19-20 and May 17, 2019 during low tides. Oysters were characterized as ‘present’ if evidence of at least one oyster (living or dead) was detected within the predefined search area.

Name of tool or approach
I first uploaded the data points collected in the field into Google Earth where I could easily verify the locations against my field notes and photos, as well as perform some minor quality control. The points were imported into ArcGIS Pro for spatial analysis. Statistical information was reviewed and plotted in Excel.

Brief description of steps to complete the analysis

  1. After validating the data point locations and performing some minor quality control in Google Earth, I saved the points as a KML file. In ArcGIS Pro, I used the geoprocessing tool ‘KML to layer’ to convert them for analysis. Once I added the data points onto the map as a layer, I edited the symbology to display the points as ‘Present’ or ‘Absent’.
  2. To assess the neighboring habitat, defined by 4 class types from least suitable to most suitable, surrounding each of the data points, I used the ‘Multiple Ring Buffer’ tool to create 3 buffer rings around each of the points at distances of 75, 150, and 300 meters. For the results in this blog post, only the 300-meter buffer was used. I selected ‘overlapping (disks)’ in the dissolve option to assess the habitat around each data point individually.
  3. Once the buffers were created, I used the ‘Zonal Statistics’ tool to overlay the buffered areas onto the raster of habitat suitability. This tool allows the user to select by statistic desired (mean, median, etc.) to generate a spatial output. I chose ‘majority’, which categorizes the buffer zones based on dominant habitat suitability type within the buffer. Majority also represented the median in this output. For example, if the majority of the suitable habitat within the buffer area is class 4 (most suitable) then the buffer display is shown as ‘4’.
  4. In addition to the ‘Zonal Statistics’ spatial output, I used the tool ‘Zonal Statistics as Table’ to generate a table of all the statistical information relevant to this analysis. The same input data is used (overlaying the buffered zones on the habitat suitability raster) to create this table.
  5. I copied the table generated into Excel where I split up the data on a couple levels: 1) Presence vs. Absence and 2) North shore vs. South shore for comparison. The north and south shores are managed very differently: the north shore is largely composed of rip rap and steeper slopes because Yaquina Bay Road runs right along the edge, whereas the south shore is more natural and less developed. I created box and whisker plots of the majority habitat suitability type, minority, variety, and mean.

Results

The results show some mixed information. When looking ‘Presence’ data points, the majority habitat types surrounding these points on both the north and south shore are 3 or 4, most suitable areas. The minority habitat type is very different between the north and south shore, with the south, more natural shoreline showing a stronger correlation with low suitability habitat being found less often around presence data points. The means for presence data points generally correspond with greater habitat suitability.

However, the absence data points show that the majority habitat type tends to be more closely aligned with predicted most suitable habitat, especially on the south shore. Additionally, the minority habitat types surrounding the absence data points are 1, 2, and 3, indicating that the least suitable habitat does not constitute much of the area. This could be partly due to low coverage by the least suitable habitat type overall (see maps). There appears to be very weak correlation between absence of oysters and location of suitable habitat. Absence of oysters is likely to be recorded in both suitable and unsuitable habitat.

Critique of the method
This method further revealed to me that the importance of the resolution of the baseline data. Based on field observations and conversations with shellfish biologists, the distribution of Olympia oysters is very patchy due to substrate availability. The oysters may be found attached to a pile of rocks in the middle of the mud flat, but will not be found elsewhere in the mud flat. The raster layer I have available for substrate has classified substrate into large generalized categories, which does not reflect the nuanced nature of their opportunistic settling strategy. Dividing habitat suitability into only 4 categories limits the complexity of the analysis which can be helpful, but also means that there’s not a lot of distinction between suitable and unsuitable. Additionally, more data points will help make this analysis more robust.

Using the buffers and the ‘Zonal Statistics’ tools created a generalized output that provides some useful information for analyzing habitat suitability for the oysters. The approach is easily duplicated, which was helpful as I needed to add my field data points in batches as I collected them. What would be more informative for the next iteration is to be able to analyze multiple buffers side-by-side; how does the smallest neighborhood around each point compare to the larger ones?

Determining suitable habitat for Olympia oysters in Yaquina Bay, OR

Exercise #1

Question that you asked:
My goal for my thesis work is to evaluate the distribution of native Olympia oysters in Yaquina Bay, Oregon by assessing habitat suitability through spatial analysis of three habitat parameters: salinity, substrate availability, and elevation. A map of predicted suitable habitat as a result of the spatial analysis will be compared with field observations of oyster locations within Yaquina Bay. The main research question I am examining in this project is:

How is the spatial pattern of three habitat parameters (salinity, substrate, elevation) [A] related to the spatial pattern of Olympia oysters in the Yaquina estuary [B] over time [C]?

For this blog post, I will be evaluating the [A] portion of this question and the three habitat parameters simultaneously to identify where habitat is least suitable to most suitable. To better understand the spatial pattern of the habitat parameters, I am evaluating a raster layer for each parameter, then combining them to determine where overlap between the layers shows the best environmental conditions for oysters to survive.

Name of the tool or approach that you used:
For this portion of my research analysis, I wanted to be able to make an educated guess about where the best and worst habitat for Olympia oysters would be located within Yaquina Bay by ranking different subcategories within each of the salinity, substrate, and elevation datasets.

To do this, I started by looking through the available literature on the subject and consulting with shellfish biologists to get an idea of what conditions oysters prefer in order to apply a ranking value. The following table is a compilation of that information:

Habitat parameter Subcategories Subcategory variable range Olympia oyster tolerance Rank value applied
Mean wet-season salinity (psu) Upper estuary < 16 psu somewhat, but not long-term 1
Upper mid estuary 16.1 – 23 psu X 4
Lower mid estuary 23.1 – 27 psu X 3
Lower estuary > 27 psu somewhat 2
 
Substrate availability 1.2 Unconsolidated mineral substrate possible 3
1.2.1.3.3 Gravelly mud unlikely 2
1.2.2.4 Sandy mud no 1
2 Biogenic substrate yes 4
3 Anthropogenic substrate yes 4
3.1 Anthropogenic rock yes 4
3.1.2 Anthropogenic rock rubble unlikely 2
3.1.3 Anthropogenic rock hash no 1
9.9.9.9.9 Unclassified uncertain —
 
Bathymetric depth (compared to MLLW) 1.5 – 2.5m supratidal no 1
1 – 1.5m supratidal no 1
0.5 – 1m intertidal maybe 2
0 – 0.5m intertidal yes 3
-2 – 0m intertidal yes 4
-3 – -2m subtidal yes 4
-4 – -3m subtidal yes 4
-6 – -4m subtidal yes 4
-8 – -6m subtidal yes 3
-12.5 – -8m subtidal yes 3
 

Once I established my own ranking values, I decided to use the ‘weighted overlay’ function, found within the Spatial Analyst toolbox in ArcGIS Pro. Weighted overlay applies a numeric rank to values within the raster inputs on a scale that the ArcGIS user is able to set. For example, on a scale from 1-9 ranking 1 as areas of least fit and 9 as areas of best fit. This can be used to determine the most appropriate site or location for a desired product or phenomenon. I used the ranking value scale 1-4 where 1 indicates the lowest suitability of subcategories for that parameter and 4 indicates the highest suitability.

Brief description of steps you followed to complete the analysis:

To apply the weighted overlay function:

  1. Open the appropriate raster layers for analysis in ArcGIS Pro. Weighted overlay will only work with a raster input, specifically integer raster data. Here, I pulled all three of my habitat parameter raster layers from my geodatabase into the Contents pane and made each one visible in turn as I applied the weighted overlay function.
  2. In the Geoprocessing pane, type ‘weighted overlay’ into the search box. Weighted overlay can also be found in the Spatial Analyst toolbox.
  3. Once in the weighted overlay window within the Geoprocessing pane, determine the appropriate scale or ranking values for the analysis. I used a scale from 1-4, where 1 was low suitability and 4 was high suitability.
  4. Add raster layers for analysis by selecting them from your geodatabase and adding them into the window at the top left. To add more than one raster, click ‘Add raster’ at the bottom of the window.
  5. Select one of the raster inputs and see the subcategories for that raster appear on the upper right. Here, ranking values within the predetermined can be individually applied to the subcategories by clicking from a drop-down list. Do this for each subcategory within each raster input. I ranked each subcategory within each of my habitat rasters according to the ranks listed on the table above.
  6. Determine the weights of each raster input. The weights must add up to 100, but can be manipulated according to the needs of the analysis. A raster input can be given greater or lesser influence if that information is known. For my analysis, I made all three of my habitat raster inputs nearly equal weight (two inputs were assigned a weight of 33, one was weighted 34 to equal 100 total).
  7. Finally, run the tool and assuming no errors, an output raster will appear in the Contents pane and in the map window.

Brief description of results you obtained:

The first three images show each habitat parameter weighted by suitability, with green indicating most suitable and red indicating least suitable.

Salinity —

Bathymetry —

Substrate —

The results of the final weighted overlay show that the oysters are most likely to be in the mid estuary where salinity, bathymetry, and substrate are appropriate.

 

Critique of the method – what was useful, what was not?:

The weighted overlay was a simple approach to combining all of the raster layers for habitat and creating something spatially meaningful for my research analysis. The areas indicated in green in the resulting map generally reinforce what was found in the literature and predicted by local shellfish biologists. While the weighted overlay tool did generate a useful visual, it is highly dependent on the quality of the raster inputs. In my analysis, the detailed resolution of the bathymetry layer was very helpful, but the substrate layer is a more generalized assessment of sediment types within Yaquina Bay. It doesn’t show the nuances of substrate availability that might be important for finding exactly where an opportunistic species like Olympia oysters might actually have settled. For example, in Coos Bay Olympia oysters have been found attached to shopping carts that have been dumped. The substrate raster is a generalized layer that uses standardized subcategories and does not pinpoint such small features.

Additionally, the salinity layer is an average of wet-season salinity, but it can change dramatically throughout the year. Some in situ measurements from Yaquina Bay this April showed that the surface salinity with the subcategory range of 16-23 psu were actually <10 psu. While it is more reasonable to generalize salinity for the purposes of this analysis, it is important to note that the oysters are exposed to a greater range over time.

This spatial information serves as a prediction of suitable oyster habitat. The next step is to compare this predicted suitability to actual field observations. I’ve recently completed my first round of field surveys and will be analyzing how closely the observations align with the prediction in Exercise #2.

Predicting spatial distribution of Olympia oysters in the Yaquina estuary, OR

My spatial problem

  • A description of the research question that you are exploring.

My research aims to determine the current abundance and spatial distribution of native Olympia oysters in Yaquina Bay, Oregon. This oyster species has experienced massive decline in population due to overharvest during European settlement of the western United States. Yet its value to the ecosystem, its cultural importance, and its tastiness have made the Olympia oyster a current priority for population enhancement. For my research, I will be focusing on a local population of Olympia oysters in the Yaquina estuary. The goal of my project is to gather baseline information about their current abundance and spatial distribution, then develop a repeatable biological monitoring protocol for assessing this population in the future. Using spatial technology, I will first assess whether the distribution of Olympia oysters can be predicted using three habitat parameters: salinity, substrate availability, and elevation. In collaboration with the Oregon Department of Fish and Wildlife (ODFW), I will use the results of this spatial analysis and field surveys to determine ‘index sites’, which are specific locations within the estuary that are indicative of the larger population. These index sites will be revisited in the future by ODFW’s Shellfish and Estuarine Assessment of Coastal Oregon (SEACOR) team to assess changes in population size and spread over time. If predictions of Olympia oyster distribution are accurate based on the habitat parameters I’ve identified, then I’d also like to analyze potential species distribution under future environmental conditions and under different management scenarios, including habitat restoration and population enhancement.

For this course, I will be exploring this main research question:

How is the spatial pattern of Olympia oysters in the Yaquina estuary [A] related to (caused by) the spatial pattern of three habitat parameters (salinity, substrate, elevation) [B]?

 

  • A description of the dataset you will be analyzing, including the spatial and temporal resolution and extent.

I will be using three spatial datasets, representing each of the habitat parameters, overlaid on one another to rank most to least likely locations for Olympia oyster presence. The salinity dataset is based on historical measurements (1960-2006) and represents a gradient from highest salinity (~32psu) at the mouth of the estuary to fresher water up stream (<16psu). Elevation is represented through a bathymetric dataset from 2001-2002, sourced from the Environmental Protection Agency office in Newport, OR. The substrate data comes from the Oregon ShoreZone mapping effort in 2014, which is managed and updated by the Oregon Coastal Management Program. There’s a couple different ways this data can be used, either as a substrate layer that characterizes substrate type broadly (low resolution) or through vector data with associated data tables that describe the substrate within a tidal zone along the shoreline (higher resolution, but spatial extent is limited).

The images here show the three habitat parameter spatial datasets:

Yaquina Bay bathymetry derived from subtidal soundings in 1953, 1999, 1998, and 2000 by U.S. Army Corps of Engineers.
Data from EPA.

Salinity figure digitized from Lewis et al. (2019) based on Oregon’s wet-season salinity measurements (average salinity November-April).
Lewis, N. S., E. W. Fox, and T. H. DeWitt. 2019. Estimating the distribution of harvested
estuarine bivalves with natural history-based habitat suitability models. Estuarine, Coastal and Shelf Science, 219: 453-472.

Substrate component classes of Yaquina Bay based on data classifications from Coastal and Marine Ecological Classification Standard (CMECS) ‘Estuarine Substrate Component’ layer.
Data from Oregon Coastal Management Program.

  • Predict the kinds of patterns you expect to see in your data, and the processes that produce or respond to these patterns.

I am hypothesizing that the distribution/spread of Olympia oysters in Yaquina Bay is influenced by availability of appropriate habitat parameters; where these parameters align within the appropriate range will determine where the oysters can be found. However, I think that I will find that not all of the parameters equally influence oyster distribution. For example, Olympia oysters have been observed to tolerate a broad salinity range, but are absolutely not present without suitable substrate. I am expecting to see that the influence of a particular habitat parameter changes depending on where the oysters are located within the estuary. I’m curious to see, if possible, which parameter will be most important at what life stage and what may drive changes in population per specific site in the estuary.

I do expect that I will be able to make a prediction about where the oysters will be located based on the habitat parameters, though I am uncertain that the resolution of the spatial data is sophisticated enough to capture nuances in distribution. For example, Olympia oysters are known to be opportunistic in finding suitable substrate and will settle on a wide variety of hard surfaces, including derelict boating equipment, discarded shopping carts, and pilings.

 

  • Describe the kinds of analyses you ideally would like to undertake and learn about this term, using your data.

I want to be able to produce a model that can predict where the oysters are located based not just on the three habitat parameters of interest, but under various environmental conditions and different management scenarios. For example, where might the oysters settle in a given year if rainfall is substantially higher, or if adult oysters spawn earlier, or if oyster growers create Olympia oyster beds for harvest, or if a new habitat restoration site is established, etc.

I’m not especially handy at statistical analysis, so I would like to gain a better understanding of statistics through spatial data. I know that I will need to use statistics to determine how successfully the prediction of Olympia oysters aligns with actual observations in the field, but currently unsure how to do that. A recent study in Yaquina estuary was just released using a similar approach for predicting the distribution of five other bivalve species. This study used R to generate a logistic regression model to determine the probability of each species presence within a given area. I would like to do something similar for my analysis, but need some help.

 

  • What do you want to produce — maps? statistical relationships?

The desired products of this research are habitat suitability maps of the current and future (pending the success of the initial effort) distribution of native Olympia oysters for use by ODFW. As a part of this effort, I will create a map of index site locations to be used in future species monitoring. I would also like to generate a predictive model that can determine distribution of oysters based on annual changes in the local environment (El Nino conditions, heavy rainfall, restoration efforts, introduction of invaders, etc.). While salinity, substrate, and elevation seem to be the main factors influencing oyster distribution, there are a number of other factors that can have effects, including temperature, proximity to the mouth of the estuary, and tidal retention.

 

  • How is your spatial problem important to science? To resource managers?

ODFW currently does not have reliable baseline information on the distribution of Olympia oysters in Oregon. As an ecological engineer, the species provides a number of important benefits to the ecosystem, including water filtration and habitat for other marine creatures. It is culturally significant to local tribes, including the Confederated Tribes of Siletz. This species is not currently listed as threatened or endangered, but if it becomes listed one day, then that designation will trigger a number of mitigation and conservation measures that will be difficult and expensive for agencies and private landowners. Additionally, there’s been some exploration that if the population can become robust again, there is potential to grow and harvest this species as a specialty food product. Given the current slow food movement and interest in local products, Olympia oysters could fit well in this niche.

 

  • How much experience do you have with:

(a) Arc-Info – Little experience, used a bit with older versions of ArcMap.

(b) Modelbuilder and/or GIS programming in Python – I am comfortable with ModelBuilder, but have no experience with Python.

(c) R – Some experience; I took Stats 511 where we used R heavily in a series of lab exercises. I have not applied my own data in R.

(d) Image processing – I have used a variety of Adobe products for graphic design, including Photoshop and InDesign.