Smathermather's Weblog

Remote Sensing, GIS, Ecology, and Oddball Techniques

Archive for the ‘National Park’ Category

Gorilla Food Plants Biomass and Ranging

Posted by smathermather on July 4, 2017

The last two days, I have been working with Olivier Jean Leonce Manzi here at Karisoke Research Center on the question of the relationship between gorilla food plants biomass and the ranging patterns of gorillas outside Volcanoes National Park (VNP) in Rwanda.

A view from the edge of VNP looking toward Mounts Mgahinga and Muhabura

A view from the edge of VNP looking toward Mounts Mgahinga and Muhabura

Even though Volcanoes National Park is set aside and gorillas thrive inside, they don’t strictly stay within the bounds of the park — often leaving the park to forage in the adjacent farming communities. This tendency is an opportunity for human / wildlife conflict, and thus it is important to understand the relationship between gorilla browsing habits outside the park and their food resources in these farming communities.

Among the food plants in the study, eucalyptus, a non-native, is planted widely in Rwanda as a fast growing timber source. Gorillas like to climb up eucalyptus, stripping the outer bark, and use their teeth to scrape the inner bark from the tree. For larger trees, this seems to have little effect. For smaller trees, it can kill the tree easily, either by the weight of the gorilla on the tree or the damage to the vascular system of the tree.

 

Eucalyptus trees planted near VNP. Eating the inner bark of Eucalyptus is a favorite food of gorillas. For larger trees, this seems to have no effect. For smaller trees, this can maim or kill the non-native tree plantings.

Eucalyptus trees planted near VNP. Eating the inner bark of Eucalyptus is a favorite food of gorillas. For larger trees, this seems to have no effect. For smaller trees, this can maim or kill the non-native tree plantings.

Bamboo, native to the region, is widely planted outside VNP (and grows in forests inside VNP). As it sprouts during rainy season, it is a favorite food of gorillas both inside and outside the park.

Small bamboo stand outside VNP.

Small bamboo stand outside VNP.

Olivier’s study area is in the farming area along the base of Karisimbi and Bisoke Volcanoes just outside VNP.  (Quick aside: it was a combination of Karisimbi and Bisoke names that formed Karisoke Research Center’s name).

Map of study area near Karisimbi and Bisoke Volcanoes outside Volcanoes National Park.

Map of study area near Karisimbi and Bisoke Volcanoes outside Volcanoes National Park.

The two datasets we want to compare for the study are counts of gorillas ranging outside the park and transects of gorilla plant food biomass, also outside the park.

Gorilla from the Amahoro (Peace) group in a bamboo stand during rainy season. (Amahoro group is not part of this study.)

Gorilla from the Amahoro (Peace) group in a bamboo stand during rainy season. (Amahoro group is not part of this study.)

 

study_area_inset

Map of gorilla sightings outside VNP within our study area.

The measurements that Olivier made on gorilla plant food biomass is that of herbs (overall), trees (overall), eucalyptus, bamboo, and rubus (a group commonly known as raspberries, blackberries, dewberries, etc.) — favored foods for gorillas especially outside the park.

vegetation_plots.png

Vegetation plot locations along border of VNP

For the purposes of analysis, Olivier grouped the vegetation plots and gorilla counts into 18 approximately equal zones. Gorilla counts and vegetation plots were summarized per zone and compared.

vegetation_plot_zones.png

I remember his project as one of the more difficult ones to wrap my head around when I was here in December. In summary, here’s the problem that we wanted to solve: given a dataset of gorilla food biomass outside the park, and counts of gorillas outside the park, can we establish a relationship between the two. It should be an easy problem: on one side of the equation, we have count data, on the other ratio data. My first thought would be to apply a Poisson approach.

Gorilla.count ~ Herbs.biomass + Tree.biomass + Eucalyptus.biomass + Bamboo.biomass + Rubus.biomass

But we quickly run into a problem: our data are not independent in time or in space, and so a simple Poisson approach is likely not appropriate.

For as much work as I’ve done in the geospatial space, I have done precious little with spatial statistics, so this posed a conundrum to me. I can’t remember now if it was through much googling, or the great stewardship of Dr. Patrick Lorch, the research manager at my institution, that we settled upon using a Markov chain Monte Carlo (MCMC) approach to the problem. The advantage to this approach is that we can do the analysis using a Poisson distribution without regard to autocorrelation. In the R statistical package, this is an easy analysis to set up.

Finally, we’ll close with a picture of Olivier working on his literature review for the methods section:

olivier.jpg

Posted in Ecology, Gorillas, Karisoke, National Park, R | Tagged: , , , , , , | 1 Comment »

A little Gorilla Time

Posted by smathermather on June 12, 2017

I miss my mountain gorilla friends in Rwanda. Let’s write a little more code to support them. I’ll be visiting Karisoke again next week, so it seems timely to post a little more code (HT Jean Pierre Samedi Mucyo for working with me on this one).

The problem today is simple — given a time series of gorilla locations and dates, can we calculate rate of travel using PostgreSQL? Well, of course we can. We can do anything in Postgre.

We have two tricks here:

  1. The first is to order our data so we can just compare one row to the next.
  2. Once we do that, we need simply to use PostGIS to calculate distance, and ordinary time functions from Postgres to calculate time difference.

This is my first use of WITH RECURSIVE, and it’s probably unnecessary (could be replaced with windowing functions), but I was very proud to finally get over my fear of WITH RECURSIVE . (We actually use one windowing function in our prep of the data. But there we are… ).

snip

For the record, WITH RECURSIVE isn’t recursive, but it is useful here in allowing us to compare the current row with the previous.

Posted in Database, Ecology, Gorillas, Karisoke, National Park, PostgreSQL, SQL | Tagged: , , , , | Leave a Comment »

Korean Drumming at FOSS4G Seoul

Posted by smathermather on October 3, 2015

Korean Drumming at FOSS4G Seoul:

Posted in Conference, FOSS4G, FOSS4G, National Park, Other | Tagged: , , | Leave a Comment »

Pictures from my last few weeks.

Posted by smathermather on October 3, 2015

Posted in Conference, FOSS4G, FOSS4G, National Park, Other | Tagged: , , | Leave a Comment »

Mini-series on Korean words, part 3: Agglutinative language

Posted by smathermather on August 31, 2015

Short linguistics aside

For me, understanding a language, beyond a memorization of terms, is predicated on the idea that I understand something of the underlying logic to the language. So today, instead of a Korean word, we’ll talk about the term agglutinative. (bless you)

In short, what it means is that a language uses a lot of prefixes, stem words, and suffixes, and that these components of larger words don’t change their sound in order to be put together.

Let’s take some English words as a counter example. When we look at English numbering, we have this weird thing that happens in the teens. The first thing we notice, is that for numbers between 10 and 20, we call them teens not tens. English is not agglutinative, it is fusional. When prefixes and suffixes come into play, often (but not always) the sounds change. Think of thirteen (not three-ten or three-teen) vs. Fourteen.  Fifteen is another departure — we might expect five-teen.

And don’t even get me started on twenty (two tens), or thirty (three tens)… .

Korean Numerals

By contrast, Sino-Korean numerals are agglutinative.

FYI, in the Korean Language, there are two numbering systems: the native Korean system, and the Sino-Korean system. More on that another time.

So, if I say the number three (sam), the number ten (sheep), and the number three again (still sam), I get 33, or sam sheep sam: 삼십삼. If I want to say 13, that’s just sheep sam, or 십삼. You prefer the number 88? Well that’s 팔십팔, or pal sheep pal.

FYI, the proper romanization of the word 10 (십) is “sip”, but as the s sound in front of the long e sound is pronounced sh, we’ll just consider the whole process an homage to counting sheep. Somehow apropos given the nation is 13 time zones away from me… .

 

Posted in Conference, FOSS4G, FOSS4G, National Park, Other | Tagged: , , , , | Leave a Comment »

Mini-series on Korean words, part 2: Land of Mountains and Sea

Posted by smathermather on August 30, 2015

A good logo is hard to come by. I love the logo of Korean National Park Service. It’s simple, beautiful, has elements of complexity to it, and makes a simple statement: land of mountains and sea. The mountains and the sea are sources of life in Korea, from the resources and farming found on the edge of the mountains, the peace found hiking and visiting temples in the mountains, to the resources and seafood found in the sea. More to the point with KNPS, many of the national parks lands are reserves of mountains or protected ocean.

Today we will look at the second word in our mini-series on Korean words (see the first here): the Korean word for mountain: san.

The Korean character 'san'

Look to the individual characters that make up the syllable, and we see ㅅ(s),ㅏ(ah),ㄴ(n). This is a simple enough word.

As Seoul is surrounded by mountains, you will encounter san as a syllable in many contexts. Take for example a mountain to the north of Seoul, Bukhan Mountain, or Bukhansan: 북한. This name mirrors one of the names of North Korea: Bukhan. Buk means north, Han is the river that flows through Seoul. So the full name is “Mountain north of the Han”.

Buhkansan 북한산 is also the name of the national park that contains the mountain it is named for.

If you visit Seoul for FOSS4G, I highly recommend a hike in the mountains. It’s a rare megacity and capital that contains a 30 square mile national park inside its boundary. If you do visit, I recommend doing so during the week — weekend visits are very busy.

Posted in Conference, FOSS4G, FOSS4G, National Park, Other | Tagged: , , , , | Leave a Comment »

Bukhansan National Park, Seoul, Pt Two — on to Dobongsan Mountain

Posted by smathermather on September 5, 2014

Fewer words, more pictures this time. On to Dobongsan Mountain. This time, I went through a different entrance just to the north and east of the previous entrance.

DSC05134 DSC05135 DSC05136 DSC05140 DSC05144 DSC05164 DSC05167 DSC05169 DSC05235 DSC05237 DSC05239 DSC05263 DSC05279 DSC05285

Posted in Conferences, FOSS4G Korea, National Park | Tagged: , , | Leave a Comment »

Bukhansan National Park, Seoul, Pt Two — off to the base of Dobongsan Mountain

Posted by smathermather on September 4, 2014

In my previous post on Bukhansan National Park, I had the blessings of a guide, ilJumun Jingwansa, who is a KNPS ranger. My second time in the National Park, I took a subway train by myself to explore. This was a quick hike to familiarize myself with getting to the mountain, rather than an in depth exploration.

Photo along Teheran-ro in Gangam District, Seoul

Photo along Teheran-ro in Gangam District, Seoul

Photo from train while crossing the Han River.

Photo from train while crossing the Han River.

I took a train from my hotel in the Gangnam district to the Dobong Station, which is the closest subway station to Bukhansan National Park.

Photo near Dobong Station

Photo near Dobong Station

One thing that I noticed most everywhere in Seoul was the use of the small narrow spaces along rivers, under expressways, and other nooks and crannies that serve as linear parks with multi-purpose trails connecting them. Next time I am there, I hope to rent a bike and do some serious exploration of these,

From Dobong Station, I wandered up a stream along a multi-purpose trail, passed a narrow band of agriculture, to the foot of the mountain.

This adventure ended up being more about the edges of the city, and how they feather into the edges of the National Park and less about the National Park itself. But, it did give me the confidence to navigate to the Bukhansan and to the base of Dobongsan Mountain.

 

Posted in Conferences, FOSS4G Korea, National Park | Tagged: , , | Leave a Comment »

Bukhansan National Park, Seoul

Posted by smathermather on September 4, 2014

For all the time I spent in the city of Seoul, I was able to make three trips into Bukhansan National Park which is partially inside the boundary of the city. It can be both a remote space, and a space overrun by visitors from the cities around. Seoul contains more the 10 million residents, and the metropolitan region is the third largest in the world with more than 25 million.snapshot of bing map of Bukhansan National Park

The park itself is two mountains, Bukhansan Mountain itself and Dobongsan Mountain, although there are many named peaks along the two ridges. The valley containing the Bukhansanseong fortress divides the two mountains, and is said, due to natural springs, to have had the capacity to hold 50,000 people.

5 Ridges as viewed from the road at the southern end of Bukhansan National Park

Credit: ilJumun Jingwansa

IlJumun Jingwansa was my guide on the south end of Bukhansan Mountain (any history or natural history I get right is due to him — anything wrong is mine). We hiked up onto the side of the Bukhansan of the National Park, between Hyangnobong and Jokduribong peaks. Jingwansa was incredibly knowledgeable about the cultural and natural history, and as we walked and I peppered him with questions which he answered, for biological questions looking up English name equivalents of Latin names where they existed.

Image of side of mountain with Jingwansa

We saw two oaks along the way, Quercus acutissima and Quercus mongolica.

Image of Quercus acutissima acorn

We talked about crows and wildfires, trails, and the difficulty of maintaining the natural resources of a park under the constraints of heavy use and a loving public.

These mountains are made of granite, hard, and warm, and dry on the days I saw them. And they overlook the cities around them. It was here that first understood how mountainous Korea is, and something of the relationship between the Korea people, their mountains and their sea. The Korea National Park Service (KNPS) logo reflects this:

KNPS Logo

KNPS Logo

More soon… .

Posted in Conferences, FOSS4G Korea, National Park | Tagged: , , | Leave a Comment »