Get the coordinates of Volcanos from Wikipedia page

You can find many information in Wikipedia pages but sometimes in can be long to gather them manually. R can be used as a sucker of information. Let see how it can retrieve the coordinates of volcanos in Central America. The web pages are here:
https://en.wikipedia.org/wiki/List_of_volcanoes_in_Mexico
https://en.wikipedia.org/wiki/List_of_volcanoes_in_Guatemala
https://en.wikipedia.org/wiki/List_of_volcanoes_in_El_Salvador
https://en.wikipedia.org/wiki/List_of_volcanoes_in_Nicaragua
https://en.wikipedia.org/wiki/List_of_volcanoes_in_Costa_Rica


 library(maps)
library(mapdata)
library(maptools)
library(XML)
# Note a problem in readHTMLTable. It cannot be used directly with url:
# readHTMLTable(url, header=FALSE, stringsAsFactors = FALSE) generates an error # load a file in temporary directory
url <- "https://en.wikipedia.org/wiki/List_of_volcanoes_in_Mexico"
dest <- paste(tempdir(), "/List_of_volcanoes_in_Mexico.html", sep="")
download.file(url, dest)

 tables <- readHTMLTable(dest, header=FALSE, stringsAsFactors = FALSE)
tables <- tables[unlist(lapply(tables, function(x) !is.null(x)))]
Volcano <- cbind(tables[[3]][-c(1,2),], Country="Mexico")
url <- "https://en.wikipedia.org/wiki/List_of_volcanoes_in_Guatemala"
dest <- paste(tempdir(), "/List_of_volcanoes_in_Guatemala.html", sep="")
download.file(url, dest)

 tables <- readHTMLTable(dest, header=FALSE, stringsAsFactors = FALSE)
tables <- tables[unlist(lapply(tables, function(x) !is.null(x)))]
Volcano <- rbind(Volcano, cbind(tables[[2]][-1,], Country="Guatemala"))

 url <- "https://en.wikipedia.org/wiki/List_of_volcanoes_in_El_Salvador"
dest <- paste(tempdir(), "/List_of_volcanoes_in_El_Salvador.html", sep="")
download.file(url, dest)

 tables <- readHTMLTable(dest, header=FALSE, stringsAsFactors = FALSE)
tables <- tables[unlist(lapply(tables, function(x) !is.null(x)))]
Volcano <- rbind(Volcano, cbind(tables[[2]][-1,], Country="El Salvador"))

 url <- "https://en.wikipedia.org/wiki/List_of_volcanoes_in_Nicaragua"
dest <- paste(tempdir(), "/List_of_volcanoes_in_Nicaragua.html", sep="")
download.file(url, dest)

 tables <- readHTMLTable(dest, header=FALSE, stringsAsFactors = FALSE)
tables <- tables[unlist(lapply(tables, function(x) !is.null(x)))]
Volcano <- rbind(Volcano, cbind(tables[[2]][-1,], Country="Nicaragua"))

 url <- "https://en.wikipedia.org/wiki/List_of_volcanoes_in_Costa_Rica"
dest <- paste(tempdir(), "/List_of_volcanoes_in_Costa_Rica", sep="")
download.file(url, dest)

 tables <- readHTMLTable(dest, header=FALSE, stringsAsFactors = FALSE)
tables <- tables[unlist(lapply(tables, function(x) !is.null(x)))]
Volcano <- rbind(Volcano, cbind(tables[[2]][-c(1,2),], Country="Costa Rica"))

 colnames(Volcano) <- c("Name", "Altitude", "Elevation", "Coordinates", "Eruption", "Country")
row.names(Volcano) <- as.character(seq(from=1, to=nrow(Volcano), by=1))
Volcano[Volcano[, "Coordinates"]=="-" | Volcano[, "Coordinates"]=="—" | is.na(Volcano[, "Coordinates"]), "Coordinates"] <- NA
Volcano <- Volcano[!is.na(Volcano[, "Coordinates"]), ]

 lcoordinates <- strsplit(Volcano[, "Coordinates"], " / ")
lcoordinates2 <- lapply(lcoordinates, function(x) gsub(" \\(.+\\)", "", x[3]))
lcoordinates3 <- lapply(lcoordinates2, function(x) unlist(strsplit(x, "; ")))
lcoordinates4 <- lapply(lcoordinates3, function(x) ifelse(is.na(x), return(c(NA, NA)), x))
lcoordinates5 <- lapply(lcoordinates4, function(x) iconv(x, "", "ASCII", ""))
lc <- matrix(unlist(lcoordinates5), ncol=2, byrow=TRUE)
Volcano <- cbind(Volcano, latitude=as.numeric(lc[,1]), longitude=as.numeric(lc[,2]))

 map('worldHires', xlim=range(Volcano[,"longitude"], na.rm=TRUE), ylim=range(Volcano[,"latitude"], na.rm=TRUE), mar=c(4, 5, 1, 1))
points(Volcano[,"longitude"], Volcano[,"latitude"], col="red", pch=19)
grid()

 degAxis(1)
degAxis(2, las=1)

Commentaires

Enregistrer un commentaire

Posts les plus consultés de ce blog

Standard error from Hessian Matrix... what can be done when problem occurs

An Hessian matrix is a square matrix of partial second order derivative. From the square-root of the inverse of the diagonal, it is possible to estimate the standard error of parameters. Let take an example: val=rnorm(100, mean=20, sd=5) # Return -ln L of values in val in Gaussian distribution with mean and sd in par fitnorm<-function(par, val) {   -sum(dnorm(val, par["mean"], par["sd"], log = TRUE)) } # Initial values for search p<-c(mean=20, sd=5) # fit the model result <- optim(par=p, fn=fitnorm, val=val, method="BFGS", hessian=TRUE) # Inverse the hessian matrix to get SE for each parameters mathessian <- result$hessian inversemathessian <- solve(mathessian) res <- sqrt(diag(inversemathessian)) # results data.frame(Mean=result$par, SE=res)   library(MASS) (r<-fitdistr(val, "normal")) It works well. However, the inverse of the matrix cannot be calculated if the second order derivative for some paramete
Lire la suite

stepAIC from package MASS with AICc

Due to a bug in dropterm() and addterm() in package MASS, it is impossible to use AICc with stepAIC() . Here is a solution. Enter these commands and now you can use: stepAIC(g0, criteria="AICc") or stepAIC(g0, criteria="BIC") For example: datax <- data.frame(y=rnorm(100), x1=rnorm(100),                     x2=rnorm(100), x3=rnorm(100), x4=rnorm(100)) g0 <- glm(y ~ x1+x2+x3+x4, data=datax) gx_AICc <- stepAIC(g0, criteria="AICc") gx_AIC <- stepAIC(g0, criteria="AIC") gx_AIC <- stepAIC(g0, criteria="BIC")
Lire la suite

Install treemix in ubuntu 20.04

Informations are available here  https://bitbucket.org/nygcresearch/treemix/downloads/ In terminal, enter for  Ubuntu 20.04: wget https://bitbucket.org/nygcresearch/treemix/downloads/treemix-1.13.tar.gz tar -xvf treemix-1.13.tar.gz sudo apt-get install libgsl-dev sudo apt install libboost-dev sudo apt install libboost-all-dev cd treemix-1.13/ ./configure make sudo make install And it works: $ treemix TreeMix v. 1.13 $Revision: 231 $ Options: -h display this help -i [file name] input file -o [stem] output stem (will be [stem].treeout.gz, [stem].cov.gz, [stem].modelcov.gz) -k [int] number of SNPs per block for estimation of covariance matrix (1) -global Do a round of global rearrangements after adding all populations -tf [file name] Read the tree topology from a file, rather than estimating it -m [int] number of migration edges to add (0) -root [string] comma-delimited list of populations to set on one side of the root (for migration) -g [vertices file name] [edges file name] read the g
Lire la suite