There is a new Rice Outlook report from the Economic Research Service of the USDA. I was surprised to see a forecast record harvest for the coming year, given the crazy price movements in rice this year and the dire predictions that were the rule earlier this summer. At Costco in California, they actually rationed the 25 and 50 lb bags for a while, fearing a run on fancy rice (like Jasmine and Basmati). I watched an irate shopper who was trying to buy 12 10 lb bags of rice get told that she couldn't do it. She nearly lost it.
I plotted a couple of price quote series (for Thailand Grade B and Thailand Super A1 100% Broken).
The plot shows an astounding price increase over the beginning of 2008, nearly tripling the November 2007 price before plummeting again at the end of last month.
It will be interesting to keep an eye on this. As I mentioned in a previous post, nearly three billion of the world's people rely on rice as a staple crop and most of these people are poor. When the price of rice triples, people go hungry. Roz Naylor has a nice video available on the Woods Institute for the Environment website explaining the food crisis of this spring and how it relates the the expansion of biofuels.
This may seem obvious to an expert statnet user, but it took me a bit of careful reading of Carter's paper and some trial and error to figure it out. We are using the frequency of behaviors based on ethological observations as edge weights and would like to be able to extract a matrix of the edge weights.
[r]
set.seed(123)
## generate a network with 21 nodes and 50 edges.
## some edges are either self-loops or redundant
## just a quick and dirty way to get an example network object
n1 <- round(1+20*runif(50))
n2 <- round(1+20*runif(50))
n3 <- rpois(50,3)
eee <- cbind(n1,n2)[order(n1),]
net <- network(eee,directed=FALSE)
set.edge.attribute(net,"meaningful.measure",n3)
as.matrix(net,attrname="meaningful.measure")
[/r]
This last command returns a 50x50 matrix of the edge weights.
I've been using the statnet suite of tools a lot recently. As with any powerful software, there is quite a learning curve. I will write some notes in my blog to help me remember tricks that I learn along the way. And who knows? They might even be useful to other people!
For a variety of reasons, we have found it easy to import our networks as adjacency matrices. The problem is that when there are attributes associated with the edges, it is much easier to deal with an edge list. While using summary(net) yields an edge list as part of the summary, it was not clear to me how to get such a list as a manipulable object. I wrote the statnet_help list and Carter Butts (co-author of network) pointed out to me that getting an edgelist is quite simple. Having read in our adjacency matrix
[r] mat <-read.table("mat5.txt",header=TRUE)
mat <- as.matrix(mat)
net <- network(mat, directed=FALSE)[/r]
We can get the edge list like this:
[r]bbb <- as.matrix(net,matrix.type="edgelist") [/r]
Easy...
This is an experiment to see how the WordPress plugin works. What better equation to try out than the Euler-Lotka equation:
where is age at first reproduction, is age at last reproduction, is the intrinsic rate of population increase, is the proportion surviving to exact age , and is the fertility rate of women age
A news story reports the outbreak of abalone viral ganglioneuritis in Tasmania. This is the first report of the disease in Tasmanian fisheries. In fact, the disease appears to be quite newly emergent since, according to the Department of Primary Industries for the State of Victoria, the virus was previously not described in Australia prior to 2005. Since 2005, it has been devastating abalone fisheries in Victoria. Now it's in Tasmania. One theory for the emergence of this herpes-like virus is that it is actually endemic in abalone populations and usually harmless. Environmental stress (e.g., via warming or polluted water) could induce increased virulence, leading to the high observed mortality rates. This is an outbreak to keep an eye on. The PROMED-mail moderator writes this about the virus:
Ganglioneuritis is an interesting condition causing inflammation in the nervous tissue, which swells. The result is curling of the abalone foot and swelling of the mouth. Thus, the organism cannot eat and looses its grip on the rocks it so depends on.
Abalone viral ganglioneuritis (AVG) is a highly virulent herpes-like virus, undescribed in Australia before 2005, and still not well characterized. The virus affects the nervous tissue of abalone and rapidly causes death. The virus can be spread through direct contact, through the water column without contact, and in mucus that infected abalone produce before dying. The virus is thought to survive only a short time when out of a moist environment.
A new study of tuberculosis (TB) prevalence in captive elephants (presumably Elephas maximus) in India, reported in the Times of India, shows that approximately 15% of southern India's captive elephants test positive for TB. This is a big problem for the health and well-being elephants. The study makes me wonder (1) what TB prevalence in free-ranging elephants is, and (2) how frequently TB is transmitted from elephant to humans, and (3) what the infectious organism is (M. tuberculosis vs. M. bovis), (4) where do the infections of captive elephants come from: cattle, humans, other elephants?
The PROMED-mail moderator wrote the following on the topic of TB epidemiology in elephants. Elephants are known to be susceptible to infection by both Mycobacterium tuberculosis and M. bovis. The above article does not specify the bacteria identified in the Indian elephants. A short review on tuberculosis in elephants, by Susan Mikota, was published by ProMED-mail in July 2007 (see ProMED archive 20070702.2111). It included, among other things, the following: "While most cases in the U.S. have been due to M. tuberculosis, we may find more cases of M. bovis in Asia, where elephants often share grazing land with domestic livestock." The review, to which subscribers are referred, also covered data on the sampling and laboratory techniques applicable in elephants.
OK, I understand that agricultural diseases are devastating for both the farmers and people who rely on their produce to subsist, particularly in a world where food prices have increased dramatically in part due to agricultural losses from plant pathogens. I just can't help but find the names of many agricultural diseases amusing. The one that comes immediately to mind is banana bunchy top virus, which has recently emerged in Angola.
Agricultural disease monikers seem to always be extremely descriptive. Imagine if some human scourges followed the same convention: "black sores ringing groin disease" (plague), "lungs full of mucous" (influenza/pneumonia), "pus dripping from urethra" (gonorrhea, chlamydia). Maybe not so amusing...
notes on human ecology, population, and infectious disease
