I have nothing to say, I just want to see if this works
I found this post and wanted to see if it actually works (sometimes the code included in blog posts does not…actually, this code in this one did not. I had to make some modifications to get this to work.).
Apprently, I can include images, so I’ll include the most popular image on my site:
I can include R code
Which is great, because I do a lot of R work
So here’s some R code. You can see that it is formatted properly:
summary(mtcars) plot(mtcars$mpg, mtcars$cyl, main="myplot", xlab="mpg", ylab="cyl")
2. I can even include videos (I think), like this horrifying clip from Slithis Survival Kit:
Well, two packages, at least. Having not posted in well… forever… this is a decent move back into the world of blogging (which is far harder in 2018 than it was in, say, 2009.)
I have been working on Shiny based mapping apps recently and found the Zip Radius Package potentially convenient. I even made a map of zip codes and population within 100 miles of 48104.
The fieldRS package provides a convenient way of classifying and mapping remote sensing data, which will be extremly handy when doing the snake project, for example. An open question was how to access localized risk based on topography and landuse. I had no convenient way of assessing this at the time.
While other blog posts will do a much better job of explaining the Data Explorer package in R, it still seemed useful to mention it here.
A huge hurdle to data analysis is data cleaning, and to effectively develop a strategy to efficiently prepare data for analysis, a basic snapshot of the data is helpful.
Enter the Data Explorer package, a set of tools that can provide minimal descriptive information for not much effort at all. With a single command, you can take a raw dataset, and produce a useful report that you can use to start working on your plan of data cleaning attack.
I downloaded a portion of the Social Indicators Survey from Columbia University, and picked a small subset of variables.
Using this small set of code, I produced the report below.
sis_sm <- as.data.frame(with(sis, cbind(sex, race, educ_r, r_age, hispanic, pearn,
Data Profiling Report
The data is 34.8 Kb in size. There are 453 rows and 12 columns (features). Of all 12 columns, 9 are discrete, 3 are continuous, and 0 are all missing. There are 1,245 missing values out of 5,436 data points.
Data Structure (Text)
## 'data.frame': 453 obs. of 12 variables: ## $ sex : Factor w/ 2 levels "1","2": 2 1 2 1 2 2 1 2 2 1 ... ## $ race : Factor w/ 4 levels "1","2","3","4": 3 1 1 2 3 3 3 4 1 4 ... ## $ educ_r : Factor w/ 4 levels "1","2","3","4": 4 4 2 2 2 1 1 4 4 2 ... ## $ r_age : num 40 28 22 24 31 42 36 63 69 24 ... ## $ hispanic: Factor w/ 2 levels "0","1": 2 1 1 1 2 2 2 1 1 1 ... ## $ pearn : num 14400 14400 12000 15000 8000 9600 2400 9600 NA NA ... ## $ assets : num 5000 50000 4000 NA NA 6000 NA 1250 100000 NA ... ## $ poor : Factor w/ 2 levels "0","1": 1 1 1 2 2 2 2 2 2 2 ... ## $ read : Factor w/ 4 levels "1","2","3","4": NA NA NA NA NA NA NA NA NA NA ... ## $ homework: Factor w/ 4 levels "1","2","3","4": NA NA NA NA 4 1 1 NA NA NA ... ## $ black : Factor w/ 2 levels "0","1": 1 1 1 2 1 1 1 1 1 1 ... ## $ police : Factor w/ 2 levels "0","1": 2 2 1 1 2 2 1 NA 2 2 ...
Data Structure (Network Graph)
The following graph shows the distribution of missing values.
Continuous Features (Histogram)
Discrete Features (Bar Chart)
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.
#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
# create random counts
# Plot this dog
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))
I keep staring at this picture, which appeared on “Economist’s View” last March and wondering exactly what I’m supposed to learn from this, aside from the obvious fact that health care in the US is too expensive.
We have known that health care in the US is too expensive for a long while now. We are also pretty sure of the reasons why, none of which are easily solved.
But we shouldn’t assume that there is a causal relationship between health care expenditures and life expectancy. The message here seems to be that other countries increase their health budgets and their citizens live progressively longer, but for some reason it doesn’t work in the US. Well, I don’t think it works anywhere.
There’s no evidence to suggest that extra spending this year will increase life expectancy this year. If anything, it is long past expenditures and improvements to health care that will increase life expectancy today. I think that if we looked at overall economic growth and life expectancy, we would see the same trend. Most of us will live longer, because we were born under better conditions than our grandparents, not because of government spending for health care, the vast majority of which goes to the elderly.
What this tells us, though, is two things: one, that health care in the US costs too much and seems to be increasing without bound (math talk). Second, that life expectancy in the US is shorter than these other countries. This is true, but the US is a fundamentally different place than any of the countries on that list, some of which has to do with social problems (racism) and some of which likely has to do with the fact that we take in larger numbers of immigrants from countries which have low life expectancies than any country on that list. These places aren’t comparable. While solving the problem of racism is noble, I don’t think that many people (except our President and his bigoted minions) want to suggest that we increase US life expectancy by deporting immigrants or closing the door to people from, say, Africa.
But we should be careful not to take home the message that there is an intrinsic relationship between spending and lifespan because that would be just misleading in my opinion.
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
I was reading Chris Blattman‘s blog this morning where he had a cool post on the increasing use of development jargon in published material. Words like “impact,” “stakeholder,” and “capacity” are all over the place here on the continent.
These terms are so pervasive, that people drop them in everyday conversation, almost creating a language on their own.
Honestly, I’m not really sure what “capacity” is supposed to mean, let alone am I able to identify who is and who isn’t a “stakeholder.” The cynical me says that a “stakeholder” is a person who is able to scrape off development funds into their own pockets, which seems to be a national pastime here. “Capacity” is as condescending as it sounds. Who decides who has the “capacity” to do things anyway? Are people who lack skills “incapacitated?”
The most annoying to me are “self help groups” which are, in essence, simply small business cooperatives. Not sure why their existence has to be treated as writing some past individual wrong. Given that it is mostly illegal to have a business here in Kenya (due to onerous laws on trade left over from the Brits and overzealous bureaucrats looking for bribes), it is possible that a “self help group” simply avoids many of the most costly permitting laws but more likely that a development group felt the need to give a fancy name to something completely normal.
That, however, is an aside.
If Google Trends is to be believed, interest in the development industry is waning in Kenya. I searched for trends in four terms, “capacity,” “sustainable development,” “stakeholder,” and the almighty “per diem.”
Development organizations often pay people to attend “seminars” on this or that topic in the form of “per diems” which are often not small. A fairly educated Kenyan can make a decent wage from attending these seminars on a regular basis. Harry Englund of Churchill College wrote a cool book on the subject called “Prisoners of Freedom.”
Anyway, here’s the graph. I found it kind of reassuring. Countries like Kenya can’t claim independence while holding out their hands waiting for development money to come through. Kenya is not a poor country. It doesn’t need many of these development projects when it is perfectly able to stand on its own. If these trends are to be believed, there is reason to be hopeful.
As I’ve noted in previous posts, we’re doing some research on snakebites in two areas of Kenya. I came out to Mbita in Western Kenya to do some routine management things for the demographic surveillance system that I run. This gave me an opportunity to go out and visit some houses of people who had indicated that someone in the family had been bitten by a snake in the past.
Today brought us to the Gembe East area of Mbita District in Homa Bay County, an area most associated with malaria transmission (of which I’ve written papers on). The Usao area we visited today is probably the poorest area of Gembe East. Roads are almost non-existent and the cell network is even harder to find. Among kids, skin infections are common, as are untreated wounds and eye infections. One kid has an eyeball so swollen that he couldn’t blink.
Discarded Coartem and Artefan packs litter the area. When I’m in the villages I always check the trash. It’s a great indicator of the public health situation. I often think that people should give up on surveys and just start mapping drug waste out here. At least we wouldn’t need to go through any (or at least few) bureaucratic hurdles.
We hired a single staff member at the last minute, assisted by a graduate student from Japan, hired a car and took off this morning to get here.
To find the snakebites, we compiled a list of houses where people had reported snakebites and then coordinated with our DSS staff to find them. Our registration system allows us to easily find houses in our survey areas, a real asset when one is doing these kinds of follow up surveys.
The first house we went to was vacant, everyone had taken off to do their daily chores. I became worried at this point since this area is so challenging to get to. Our list indicated that the neighboring house had a snakebite victim so we went over there and found the lady more than willing to talk.
Her son had been bitten ten years earlier by a puff adder in the space between her house and the water. Fortunately he didn’t suffer any permanent damage, but given that two houses right next to one another both experience snakebites, the area has to be considered somewhat dangerous.
She didn’t take the child to a clinic, instead enlisting the help of the local witchdoctor. Local practitioners treat snake bites by making small cuts around the wound, ostensibly to cut off routes that the venom can use to spread, then they apply a salve containing local herbs. The nature of the herbs is unknown. I plan to try and find one of these guys and see what it could possibly be.
Giving up, we returned to the market area, and suddenly several people came out of the woodwork claiming to have been bitten in the past. Some of them were in our list. Lucky day.
One gentleman had been bitten on the leg several years previous. He didn’t suffer any major damage, but the skin surrounding the wound is now scaly and tend to come off. Again, the culprit was a puff adder. The locals claim that the snake causes a persons skin to become snake-like, even shedding occasionally, just as a dog bite (rabies) causes a person to bite like a dog (it’s disconcerting how familiar people are with the symptoms of rabies here).
Our regular DSS survey worker pointed out that many people don’t want to report snakebites, presumably because of the associations with witchcraft. He also noted that when people hear about other people reporting bites, they tend to want to report them too. We had one lady who claimed that she hadn’t been bitten, but today was eager to talk about it. Just about everyone has some story about a snake, it appears.
After doing about six surveys, almost all of which were puff adder bites, we moved on. Most of the wounds we saw were minor. Some wasting of the legs, some skin problems, but no paralysis or debilitating long term issues.
A 12 year old boy, however, had been bitten on the hand by a puff adder about three years ago. Fortunately, his mother took him to the clinic immediately. He spent a month in the hospital, likely on intravenous antibiotics because the venom had destroyed most of the tissues in his left arm. Amputation was avoided, but he no long has full use of the arm and the hand is permanently deformed.
The survey worker tried to get the child to identify the snake by showing him a picture of other many kinds of snakes, but it had all the hallmarks of a serious puff adder bite. Clearly there was rotting of the tissue all the way up to shoulder and the joints were permanently bent. The elbow no longer moves due to the lack of muscle tissue and cartilage. The kid otherwise is a normal 12 year old boy. He is lucky to be alive.
Only two of the ten surveys today indicated that people went to a clinic for treatment. Someone noted that getting to the clinic is nearly impossible unless you have a motorcycle, and most of the people here just don’t have the means to call one. They opt for the witchdoctors, who make snakebites a principal part of their practice. Whether it is effective or not is unknown. Likely many minor bites might have resolved themselves on their own. Serious bites likely result in death so we’ll never know.