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Mapmaking with ggmap

I am always looking for free alternatives to ArcGIS for making pretty maps. R is great for graphics and the new-to-me ggmap package is no exception.

I’m working with some data from Botswana for a contract and needed to plot maps for several years of count based data, where the GPS coordinates for facilities were known. ArcGIS is unwieldy for creating multiple maps of the same type of data based on time points, so R is an ideal choice…. the trouble is the maps I can easily make don’t look all that good (though with tweaking can be made to look better.)

ggmap offered me an easy solution. It downloads a topographic base map from Google and I can easily overlay proportionally sized points represent counts at various geo-located points. This is just a map of Botswanan health facilities (downloaded from Humanitarian Data Exchange) with the square of counts chosen from a normal distribution. The results are rather nice.

BotswanaHF

library(rgdal)
library(ggmap)
library(scales)

#read in grographic extent and boundary for bots
btw <- admin<-readOGR(“GIS Layers/Admin”,”BWA_adm2″) #from DIVA-GIS

# fortify bots boundary for ggplot
btw_df <- fortify(btw)

# get a basemap
btw_basemap <- get_map(location = “botswana”, zoom = 6)

# get the hf data
HFs.open.street.map<-read.csv(“BotswanaHealthFacilitiesOpenStreetMap.csv”)
# create random counts
HFs.open.street.map$Counts<-round((rnorm(112,mean=10,sd=5))^2,0)

# Plot this dog
plot
ggmap(btw_basemap) +
geom_polygon(data=btw_df, aes(x=long, y=lat, group=group), fill=”red”, alpha=0.1) +
geom_point(data=HFs.open.street.map, aes(x=X, y=Y, size=Counts, fill=Counts), shape=21, alpha=0.8) +
scale_size_continuous(range = c(2, 12), breaks=pretty_breaks(5)) +
scale_fill_distiller(breaks = pretty_breaks(5))

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“Homicidal Snakebite in Children”

Currently, I’m doing a research project on snakebites and found this gem in the literature, of which there is little:

“Snake bites are common in many regions of the world. Snake envenomation is relatively uncommon in Egypt; such unfortunate events usually attract much publicity. Snake bite is almost only accidental, occurring in urban areas and desert. Few cases were reported to commit suicide by snake. Homicidal snake poisoning is so rare. It was known in ancient world by executing capital punishment by throwing the victim into a pit full of snakes. Another way was to ask the victim to put his hand inside a small basket harboring a deadly snake. Killing a victim by direct snake bite is so rare. There was one reported case where an old couple was killed by snake bite. Here is the first reported case of killing three children by snake bite. It appeared that the diagnosis of such cases is so difficult and depended mainly on the circumstantial evidences.”

When does a person “ask” someone to “put his hand inside a small basket harboring a deadly snake?” Does that ever happen? Apparently so.

Apparently a man killed his three children using a snake.

It gets better:

“In deep police office investigations, it was found that the father disliked these three children as they were girls. He married another woman and had a male baby. The father decided to get rid of his girl children. To achieve his plan, he trained to become snake charmer and bought a snake (Egyptian cobra). The father forced the snake to bite the three children several times and left them to die. At last, he burned the snake.”

Paulis, M. G. and Faheem, A. L. (2016), Homicidal Snake Bite in Children. J Forensic Sci, 61: 559–561. doi:10.1111/1556-4029.12997

Kenya 2017 Election Violence: Some Data Analysis

I’m getting used to the new version of ArcGIS (which is a vast improvement!) and gave it a test run on some data from the ACLED (Armed Conflict Location & Event Data Project) database, specifically on this years round of violence surrounding the Kenyan election. ACLED keeps real time data on violence and conflict around the globe, the latest entry in 2017 is Nov 24, just five days ago.

KenyaViolence2017

The first election occurred on August 8th, 2017. The opposition contested the results of the election, claiming problems in vote tallying by the IEBC, resulting in a nullification by the Supreme Court. A new election was called and was to be conducted within 60 days of the nullification. Raila Odinga, the opposition leader, claimed that the election again would not be fair, dropped out of the race and called for a national boycott. The election went ahead as place on October 26, 2017 and Uhuru Kenyatta was declared the winner.

NairobiViolence

 

 

There was violence at every stage of the process, both by rioters in support of the opposition and by the police and military who were known to fire live rounds into groups of demonstrators. Opposition supporters were known to set fire to Kikuyu businesses. Local Kikuyu gangs were reported to be going house to house rooting out people from tribal groups from the West and beating them in the street. Tribal groups in rural areas were reported to be fighting amongst one another. The police response has been heavy handed and disproportionate leading to a national crisis.

As of now, though not nearly as violent as the post election violence of 2007-08, the violence has not yet abated.

In the database, there were 420 events logged, including rioting, protests and violence against civilians by the state, police and local tribal militias. There are 306 recorded fatalities in the data base, but this number should be approached with some caution. There were likely more. The database is compiled from newspaper reports, which don’t count fatalities and don’t cover all events.
ViolentTSI made two maps (above), one for Nairobi, and the other for Kenya. They include all non Al-Shabaab events (a Somali Islamist group the Kenya Defense Force has been fighting for several years.) I also included a time series of both events and fatalities.

Some excerpts from the notes:

“Police raided houses of civilians in Kisumu, beating civilians and injuring dozens. Live bullets were used on some civilians, including a 14 year old boy. Of the 29 people injured, 26 had suffered gun shots.”

“One man was found dead in a sugar cane plantation one day after ethnic tensions between the Luo and Kalenjin communities got into an ethnic clash. The body had been hacked with a panga.”

“Rioters started throwing stones at the police in the morning, protesting against the elections to be held the next day. The police responded with teargas and water canons. The rioters were mostly from the Luo ethnic group and they took the opportunity to loot several stores, attack residents and to burn a store owned by an ethnic Kikuyu. One woman was raped.” *This was in Kawangware, not far from my apartment. I was eating at a local bbq place when this happened. 

 

 

“Police forces attacked supporters of the opposition that went to the Lucky Summer neighbourhood to check on a ritual of beheading of a sheep that was taking place (suspectedly by the Mungiki sect). The police shot at the civilians. The police confirmed that it shot a man and that the group performing the ritual had sought protection.”

“As a revenge to the previous event, the Kikuyu joined forces and attacked the Luo. The ethnic tensions and violence led to one severely injured person. Residents claims three were killed and dozens, including three school children, were injured.”

A visit to the local witchdoctor: treating snakebites in Kwale, Kenya

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Wound from a puff adder bite

Humans have had to deal with the threat of snakebites as long as humans have existed. While deaths from snakebites are rare, the outcomes are so severe and the nature of the animal so mysterious, that humans have developed all sorts of ways of dealing with them.

Witchdoctors, or Mganga as they are known in East Africa, are the first line for snakebite treatment here. The Waganga are fairly useless for treating many serious health issues, but they have carved out a niche for themselves for a few public health problems.

Our survey in Western Kenya confirms that nearly 100% of people who have been bitten by a snake visit the Mganga, regardless of whether they visit a formal health facility or not.

I went and sat down with an established Mganga here in Kwale and he was gracious enough to answer all of my questions openly and (mostly) honestly.

Hello, thank you for taking the time to speak with me today. Is English OK?

No, my English is not very good. Can we do this through a translator?

Of course. So, what happens when a patient comes in for treatment for a snakebite?

When the patient comes in, I first apply the “njiwe na njoka” (lit: snake stone). The stone sucks all the poison out of the wound. When you put it on the bite, it will stick. When the stone has absorbed all the poison, it will fall off.

What do you mean? Like it just sticks to the flesh without tying it?

Yes, if there is poison, the stone will stick to the body. When all the poison is gone, the stone will fall off. After it is done, I take the stone and wash it with milk several times and then use it again for the next patient.

What is the snake stone? Is it like a rock? I’ve seen people use charcoal in the villages. They tie it to the wound, it doesn’t appear to stick on its own.

No, this is different. This is a stone from the snake. The stone is in the skull of the snake, like that of a fish.

(Note: I did not know this, but some species of snakes have otoliths, like most fish. Snakes (and fish) are deaf in the traditional sense. The otolith is a piece of calcium which grows as the animal ages and sit on top of a bed of nerves. When there are vibrations, the otolith vibrates, stimulating the nerve bed so that the animal can “hear” motion around it. Not all snakes have otoliths but some species of burrowing snakes do.)

Where do you get the stone? Can you just buy it in the market?

The snake stones come from the Maasai, from big snakes in Maasai land. My teacher travels to Maasai land to get them and brings them back.

If the wound is fresh, I apply the stone. However, if it has been two or three days since the bite, I can’t use the stone anymore. Then I have to use a special medicine made from herbs and crushed snake heads. I mix it all together, then crush it into a powder and keep in a gourd.

When the patient comes in, I use a new razor blade to make small scratches on the wound. Then I rub the powder in it and bandage the wound. The wound will try to heal over time, so you have to make the scratches to be able to apply the powder.

Do you use the razor blade again?

No, I always use a new blade. (He was emphatic on this point.)

What is the powder made from?

Snakeheads. When we kill a snake, we keep the heads to make the powder. We mix it with roots, bark and leaves from special plants from deep in the forest. My teacher is a security guard in one of the forests and can get them when he can find them.

Wait, so your teacher is a forest ranger? Can’t he get by being an Mganga?

Yes. He is a forest ranger.

So he took the job so that he can get the plants from the forest whenever he needs them.

 (Silence)

OK, so how many bites do you see per month?

It depends, some months I get more than others but mostly one every three months or so.

Do you refer them to the health facility for formal treatment?

Yes, I do. I treat them, then they go to the facility, then they come back to me. (I’m suspicious on this point, though the Mganga in question appears more together than most.)

Is there a religious component to this?

Well, there are two kinds of bites, those where the snake just bites and there is no witchcraft and those where someone has used magic to send the snake to bite you.

How do you know the difference?

If the bite heals quickly, there is no witchcraft. But if the bite is treated and does not improve then there is definitely witchcraft involved. At that time, I have to use powerful magic to get rid of the curse.

What do you do?

I send the snake back to the person who applied the curse. When we hear that someone nearby has been bitten, we know who applied the curse.

(Note: this is not uncommon. Witchcraft is often associated with hatred and revenge but the person applying the curse risks becoming cursed themselves. It is possible that snakebites are seen as a never ending battle of malevolent spiritual forces. What this does is sow distrust among people, even families and the Mganga is seen as the only cure. The result is that the Mganga are never without work.)

How did you learn this craft?

I was sick for a long time with stomach and head problems. I went to the hospital and it never got better so then I went to an Mganga. I improved. The Mganga suggested that I become on and I started training under him.

Thank you very much for your time.

 

 

10 things about the Kenyan Coast

I made this trip out to the coast, first to do some damn work and second because I can get out of Nairobi and be spared spending Nairobi money for a while. A week’s worth of not-Nairobi-money is money in the bank. In Nairobi, you simply walk outside and 1000 schilling notes start flying away.

Some things I noticed (I’ll get to the snakes in a minute):

  1. It’s damn hot out here. Nairobi is cold. Here, it’s like being immersed in a sauna continuously, except for the hours of 3 to 5 am, which become cold for some reason.
  2. Fish from the sea is good. There are ample stocks of mackerel out here. I always want to make 塩サバ and have a side of okra. Or ゴーヤ. Or 山芋. Or something.
  3. Somalis are cool dudes. As in, they want to do business, they want to make sure you are happy and that you come back again. Kenyan business people are really just interested in getting your money right then probably because they might be out of business tomorrow. They don’t care if you come back. But then, if you don’t keep customers, you will go out of business. Welcome to the world of business in Kenya.
  4. Somalis make somali coffee, as in, not Nescafe. They put coffee grounds in hot water and steam the shit out of it. It’s refreshing. Though I noticed that they were pulling water from a plastic jerry can on the floor. One has to wonder where the water comes from.
  5. As much as possible, avoid the tomatoes and onions they put on the pilau (a dish like 混ぜご飯.) Yesterday, as I was eating my pilau, I ate the tomatoes and onions. I knew that things would turn out badly. Imodium is my friend right now.
  6. Mombasa is a weird place. I always expect to see people with dancing monkeys or snake charmers on the street, but then you look closer and it really is Kenya. They really tried to make a nice city at one point, but the city services never caught up. Trash is a constant problem. But there’s this weird mix of Arab, Brit and Indian architecture. It truly is an international city. They also like perfume. And they love ice cream. I think because they don’t drink and smoke, they can actually smell and taste things.
  7. Tarbousch: I always used to get the Biryani there, but the waiter convinced me to try the chicken schwarma. Perhaps the best shwarma I’ve ever had. I ordered two in the end.
  8. Police: Are stupid. Like really dumb. My tuk tuk driver failed to stop for the police, likely because he couldn’t here them over the cacophony of tuktuk motors everywhere. I apologized to the policemen to be friendly. He tried to arrest me for the tuk tuk driver’s failure to stop. The policeman was obviously a complete moron. I had to start fake calling the Kenyan Ministry of Health to “report him.” Eventually he let me go. I hate those guys. Likely, he wanted money.
  9. Mombasa is remarkably music free. Given Somalia’s rich musical history and the ubiquity of Taraab music in Zanzibar, you would assume the Mombasa might have some kind of musical culture, but it does not. Plenty of people seem to buy stereos and the matatus blast out Bongo (TZ) music, but there’s a stunning lack of performance culture of any kind here. Again, I blame Moi.
  10. Living in Nairobi will make you really mean. You just stop being nice to people you don’t know. It’s a cancer really.

Snake Bites in Kwale, Kenya: Into the Field

snakebitesWe just spent the day driving around Kwale looking for snakes, and/or people who had been bitten by snakes. As the last post showed, snakebites are a persistent problem along the Kenyan Coast, with more then 5% of the households we survey indicating that at least one person in the household had been bitten in the past two years.

It wasn’t difficult to find them.

Snakes are universally feared all over Africa and the associations with witchcraft make it a common topic of discussion. Everyone knows someone who has been bitten. They often know all the details, including where it happened and what occurred following the bite. It’s never a happy story.

We went deep into Kinango, an extremely rural area west of Kwale Town and found a friendly lady who seemed to know everything about everyone. She was incredibly jolly, pulled out some plastic chairs for us to sit under and cracked jokes the whole time. I even got to copy her collection of Sangeya music which she had recorded on her phone (another post but you can hear some of it here) at some local music festivals. In total I got more than five hours of live Sengeya and Chilewa music. In the music world, these would be called “field recordings.” Here, this is just music she cooks and cleans to.

Switching back and forth between snakes and Sengenya (in Africa it seems to be possible to have multiple conversations at once), she told us about a kid who had been bitten two days previous. She even told us where to find her, so off we went.

The child was collecting firewood around a mango tree near her home, when she was suddenly bitten by a large green snake, not once but three times on the foot. The snake bit once skated away, decided it wasn’t enough and came back and bit her twice more.

Ants had moved into the dead tree and hollowed out the area underneath. Presumably, the snake moved in previously and came out to warm up during the day.

The mother thankfully took the child immediately to Kinango Hospital and treated was administered. The child was given a three day course of antivenom injections and charcoal was wrapped around the wounds to absorb any venomous discharge. Though the child complains of some numbness in the area, it looks as if there won’t be any permanent damage. Thankfully.

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Snake bite (species unknown). Note the charcoal. Victim is a 10 year old girl.

We were also told of an old woman who had been bitten more than 20 years ago, and was badly scarred, figured out where she was and off we went again.

As we pulled up a friendly young lady came out to greet us, and showed us the way to the house out back. In the distance, we could see an old lady walking with a limp. Otherwise, she was completely fit and seemed to be cutting her own firewood with a panga.

She brought us out some chairs and sat down to chat. In 1992, she had been out back collecting firewood (a pattern) and was bitten on the foot by puff adder, one of the deadliest snakes in the world. She was bitten on the foot, and became immobile for nearly a week. A series of witch doctors were brought in, who administered charcoal rubbed into small cuts in the skin.

Necrosis set in, and watery blood erupted out of the wound site. A large number of maggots appeared. Finally, someone had the good sense to take her to the hospital, where she spent an entire year.

The details were unclear, but it appeared that the gangrene was so severe that multiple infections were presents. They likely had her on intravenous antibiotics for an extended amount of time. Despite this, the foot did not heal. Some Christian missionaries came, and convinced her to convert to Christianity, which, she claimed, improved her condition. This is likely coincidental.

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Puff Adder wound. Note the permanent curvature of the foot. She continues to have to wrap it and use topical medication, 24 years following the bite.

The doctors suggested a skin graft to improve the foot, but she refused. Necrosis was so deep that it permeated the bone and the foot is permanently curved as a result. The leg still shows sign of swelling even more than 24 years after the bite. In most cases, they probably would have simply amputated.

The lady was born in 1948, bore ten children, one of which was born just as she was bitten. She was unable to breast feed or care for the child. Regardless, the daughter has two children of her own now.

Snakebites are bad news. In this woman’s case, the disregard for proper medical care simply made a bad situation worse. She is truly lucky to be alive. If she had died, it is doubtful that the Mgangas would have admitted any responsibility.

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Puff Adder victim, born in 1948. Ten kids. Still going strong.

Snakebites in Kwale, Kenya

I sent our DSS out looking for snake bites, and they found them! We simply asked households if anyone in the household had been bitten by a snake in the past five years. More then 5% of them said “yes” and since we know the locations of the households, we were able to make this cool map. Note that the snake bites tend to cluster around two large areas and are noticeably absent from others.

Kenya hosts many varieties of extremely poisonous snakes included the Puff Adder, the Black and Green Mamba and the spitting Cobra. Snakes are universally feared here and often killed on sight by the locals.

Snakebites

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