required <- c("raster", "rgdal", "rgeos") if (!all(unlist(lapply(required, function(pkg) requireNamespace(pkg, quietly = TRUE))))) knitr::opts_chunk$set(eval = FALSE, collapse = TRUE, comment = "#>", fig.align = "center")
The IRRI (International Rice Research Institute) survey loop in Central Luzon is a study that aims to monitor the changes in rice farming in the major rice producing area of the Philippines - the Central Luzon region, which is called as the "rice bowl of the Philippines". Data have been collected in this project since the 1960s. See, http://ricestat.irri.org/fhsd/php/panel.php?page=1&sortBy=title&sortOrder=ascending# for the panel data.
This vignette details how to find and retrieve weather data for the area that this survey covers for the time period of 1960-2016. Methods that are detailed include:
retrieving a spatial object of provincial level data;
sub-setting this data for the provinces of interest;
merging the polygons into one object;
finding the centroid of this resulting polygon;
using the centroid of the polygon to find stations within 100km of this point;
determining which stations provide data for the specified time-period, 1960-2015; and
downloading the station files and creating a single CSV file of the data for analysis.
As a first step, we'll use the raster package to retrieve data from GADM that will provide the provincial spatial data for the survey area. We will then use this to find the centroid of the area of interest, which will be used to find the nearest stations. Using
raster::getData() fetch level 0 (national) and 1 (provincial) data for the Philippines.
library(raster) RP0 <- raster::getData(country = "Philippines", level = 0) RP1 <- raster::getData(country = "Philippines", level = 1)
Now we will select the provinces involved in the survey and make a new object called
Central_Luzon from the provincial level data,
Central_Luzon <- RP1[RP1@data$NAME_1 == "Pampanga" | RP1@data$NAME_1 == "Tarlac" | RP1@data$NAME_1 == "Pangasinan" | RP1@data$NAME_1 == "La Union" | RP1@data$NAME_1 == "Nueva Ecija" | RP1@data$NAME_1 == "Bulacan", ]
Next, create a map inset showing where the Central Luzon Loop survey takes place.
First we'll use
gSimplify() from rgeos to simplify the map of the Philippines to make the map generation in the next few steps quicker.
RP0 <- rgeos::gSimplify(RP0, tol = 0.05)
library(ggplot2) library(grid) library(gridExtra) CL_names <- data.frame(coordinates(Central_Luzon)) # get center coordinates of provinces in Central Luzon CL_names$label <- Central_Luzon@data$NAME_1 # Main Map p1 <- ggplot() + geom_polygon(data = Central_Luzon, aes(x = long, y = lat, group = group), colour = "grey10", fill = "#fff7bc") + geom_text(data = CL_names, aes(x = X1, y = X2, label = label), size = 2, colour = "grey20") + theme(axis.text.y = element_text(angle = 90, hjust = 0.5)) + ggtitle("Central Luzon Provinces Surveyed") + theme_bw() + xlab("Longitude") + ylab("Latitude") + coord_map() # Inset p2 <- ggplot() + geom_polygon(data = RP0, aes(long, lat, group = group), colour = "grey10", fill = "#fff7bc") + coord_equal() + theme_bw() + labs(x = NULL, y = NULL) + geom_rect(aes(xmin = extent(Central_Luzon), xmax = extent(Central_Luzon), ymin = extent(Central_Luzon), ymax = extent(Central_Luzon)), alpha = 0, colour = "red", size = 0.7, linetype = 1) + theme(axis.text.x = element_blank(), axis.text.y = element_blank(), axis.ticks = element_blank(), axis.title.x = element_blank(), axis.title.y = element_blank(), plot.margin = unit(c(0, 0, 0 ,0), "mm")) grid.newpage() v1 <- viewport(width = 1, height = 1, x = 0.5, y = 0.5) # plot area for the main map v2 <- viewport(width = 0.28, height = 0.28, x = 0.67, y = 0.78) # plot area for the inset map print(p1, vp = v1) print(p2, vp = v2)
Now that we have the provincial data that we want, we will dissolve the polygons that represent the individual provinces in Central Luzon and find the centroid of all of them, which we will use as the central point for querying stations from the GSOD data set.
Central_Luzon <- rgeos::gUnaryUnion(Central_Luzon) centroid <- rgeos::gCentroid(Central_Luzon) ggplot() + geom_polygon(data = Central_Luzon, aes(x = long, y = lat, group = group), colour = "grey10", fill = "#fff7bc") + geom_point(aes(x = centroid@coords, y = centroid@coords)) + theme(axis.text.y = element_text(angle = 90, hjust = 0.5)) + ggtitle("Centre of Survey\nArea") + theme_bw() + xlab("Longitude") + ylab("Latitude") + coord_map()
Next, make a list of stations that are within this area. First we need to fetch the station metadata, "isd-history.csv" from the FTP server and then check which stations fall within a 100km radius of the centre of the provinces we're interested in.
library(GSODR) library(readr) # Fetch station list from NCEI station_meta <- read_csv( "ftp://ftp.ncdc.noaa.gov/pub/data/noaa/isd-history.csv", col_types = "ccccccddddd", col_names = c("USAF", "WBAN", "STN_NAME", "CTRY", "STATE", "CALL", "LAT", "LON", "ELEV_M", "BEGIN", "END"), skip = 1) station_meta$STNID <- as.character(paste(station_meta$USAF, station_meta$WBAN, sep = "-")) loop_stations <- nearest_stations(LAT = centroid@coords, LON = centroid@coords, distance = 100) loop_stations <- station_meta[station_meta$STNID %in% loop_stations, ] loop_stations <- loop_stations[loop_stations$BEGIN <= 19591231 & loop_stations$END >= 20151231, ] print(loop_stations[, c(1:2, 3, 7:12)])
These are all of the stations that are available within 100km of the centroid of this area and the years for which data are available.
get_GSOD()to Fetch the Requested Station Files
This example shows how you could construct a query using the
get_GSOD() function. Be aware that it may result in incomplete data and error from the server if it stops responding. We've done our best to make GSODR handle these errors, but if it does this, see the following option for using the
PHL <- get_GSOD(station = eval(parse(text = loop_stations[, 12])), years = 1960:2015)
GSODR provides a function for dealing with local files that have been transferred from the server already as well,
reformat_GSOD(). If the previous example with
get_GSOD() does not work, this is a good alternative that takes a bit more intervention but gives the same results.
Using your FTP client (e.g., FileZilla) log into the NCEI FTP server,
years <- 1960:2015 loop_stations <- eval(parse(text = loop_stations[, 12])) # create file list loop_stations <- do.call( paste0, c(expand.grid(loop_stations, "-", years, ".op.gz")) ) local_files <- list.files(path = "./GSOD", full.names = TRUE, recursive = TRUE) local_files <- local_files[basename(local_files) %in% loop_stations] loop_data <- reformat_GSOD(file_list = local_files) readr::write_csv(loop_data, file = "Loop_Survey_Weather_1960-2015", path = "./")
90m hole-filled SRTM digital elevation (Jarvis et al. 2008) was used to identify and correct/remove elevation errors in data for station locations between -60˚ and 60˚ latitude. This applies to cases here where elevation was missing in the reported values as well. In case the station reported an elevation and the DEM does not, the station reported is taken. For stations beyond -60˚ and 60˚ latitude, the values are station reported values in every instance. See https://github.com/ropensci/GSODR/blob/master/data-raw/fetch_isd-history.md for more detail on the correction methods.
Users of these data should take into account the following (from the NCEI website):
"The following data and products may have conditions placed on their international commercial use. They can be used within the U.S. or for non-commercial international activities without restriction. The non-U.S. data cannot be redistributed for commercial purposes. Re-distribution of these data by others must provide this same notification." WMO Resolution 40. NOAA Policy
Jarvis, A., Reuter, H.I., Nelson, A., Guevara, E. (2008) Hole-filled SRTM for the globe Version 4, available from the CGIAR-CSI SRTM 90m Database (http://srtm.csi.cgiar.org)
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