diff --git a/R/format.data/BCI.R b/R/format.data/BCI.R
index a64b9a070424597dee0be0d8428c116ea749b686..e6eaaa936453bb13140c67c836bf0f2d8c1dc2ef 100644
--- a/R/format.data/BCI.R
+++ b/R/format.data/BCI.R
@@ -77,5 +77,7 @@ vec.basic.var <- c("obs.id","tree.id", "sp", "sp.name","plot", "subplot", "D", "
"year", "htot", "x", "y", "census")
data.tree <- subset(data.bci, select = c(vec.basic.var))
-
+data.tree[["Lon"]] <- -79.8461
+data.tree[["Lat"]] <- 9.1543
+data.tree[["ecocode"]] <- "tropical"
write.csv(data.tree,file="output/formatted/BCI/tree.csv",row.names = FALSE)
diff --git a/R/format.data/Fushan.R b/R/format.data/Fushan.R
index b2cd1ac7e0f4879359ee5cc8cf7c7d9dc8546718..c237a67dda0e83c40a093e7197201f050e4aa412 100644
--- a/R/format.data/Fushan.R
+++ b/R/format.data/Fushan.R
@@ -45,6 +45,11 @@ data.fushan <- subset(data.fushan,subset=data.fushan$status1!="P")
vec.basic.var <- c("obs.id","tree.id", "sp", "sp.name","plot", "subplot", "D", "G", "dead",
"year", "htot", "x", "y", "census")
data.tree <- subset(data.fushan, select = c(vec.basic.var))
+
+data.tree[["Lon"]] <- 121.555
+data.tree[["Lat"]] <- 24.7614
+data.tree[["ecocode"]] <- "tropical"
+
write.csv(data.tree,file="output/formatted/Fushan/tree.csv",row.names = FALSE)
diff --git a/R/format.data/Paracou.R b/R/format.data/Paracou.R
index 60457745124cb6b3e24afe1798caa7451beb8d66..98bf88b215b8eb4b4685302744b5e4dccf4e4991 100644
--- a/R/format.data/Paracou.R
+++ b/R/format.data/Paracou.R
@@ -95,6 +95,11 @@ data.paracou$sp.name <- data.paracou$Latin_name
vec.basic.var <- c("obs.id","tree.id", "sp", "sp.name","plot", "subplot", "D", "G", "dead",
"year", "htot", "x", "y", "census")
data.tree <- subset(data.paracou, select = c(vec.basic.var))
+
+data.tree[["Lon"]] <- -52.900002
+data.tree[["Lat"]] <- 5.38
+data.tree[["ecocode"]] <- "tropical"
+
write.csv(data.tree,file="output/formatted/Paracou/tree.csv",row.names = FALSE)
diff --git a/R/process.data/analysis.R b/R/process.data/analysis.R
index ad760c78f48040124b1ba4d5fb1a92a488db321e..06a13f0a8a72d587e8ffb0b27eb6f65bb3ea4ebe 100644
--- a/R/process.data/analysis.R
+++ b/R/process.data/analysis.R
@@ -2,8 +2,9 @@
############################################# MERGE FRENCH DATA
path.formatted <- "output/formatted"
path.processed <- "output/processed"
+library(plyr)
-source("analysis-fun.R")
+source("R/process.data/analysis-fun.R")
## load all sites
data <- load_all_formatted_data(path.formatted)
@@ -11,32 +12,19 @@ data <- load_all_formatted_data(path.formatted)
source("R/utils/plot.R")
source("R/utils/maps.R")
-# Map for single site
-# to.dev(world.map(data[["US"]]$tree[["Lon"]], data[["US"]]$tree[["Lat"]], group = NULL, cols = NULL),
-# png,file="map.png", height =800, width = 800)
+get_unique_plot_coords <- function(set, data){
+ i <- !duplicated(paste(data[[set]]$tree$Lon, data[[set]]$tree$Lat)) #find duplicates
+ data.frame(set = set, Lon = data[[set]]$tree$Lon[i], Lat = data[[set]]$tree$Lat[i], ecocode = data[[set]]$tree$ecocode[i], stringsAsFactors=FALSE)
+}
+
+x <- rbind.fill(lapply(names(data), get_unique_plot_coords, data=data))
# Map for all sites
-to.dev(world.map.all.sites(data),
+to.dev(world.map.all.sites(x, add.legend =TRUE),
png,file=file.path(path.processed, "world_map_all.png"), height =2000, width = 2000)
-png("output/figs/world.map.all.png",height=2000,width=2000)
-world.map.all.sites(data,legend.TF=FALSE)
-BCI <- c(-79.8461,9.1543)
-Paracou <- c(-52.900002,5.38)
-Fushan <- c(121.555 , 24.7614)
-NSW <- c(151,-33.18)
-data.bigplot <- rbind(BCI,Paracou,Fushan,NSW)
-points(data.bigplot[,1],data.bigplot[,2],col="red",cex=3,pch=16)
-
-M_baiki <- c(17.93,3.9)
-Luquillo <- c(-65.816,18.3262)
-La_chonta <- c(-62.99,-15.75)
-data.bigplot.add <- rbind(M_baiki,Luquillo,La_chonta)
-points(data.bigplot.add[,1],data.bigplot.add[,2],col="green",cex=3,pch=16)
-dev.off()
# make summary table
-library(plyr)
data.summary <- lapply(data, summarise.data)
tab.1 <- rbind.fill(lapply(data.summary,summary.table.1))
diff --git a/R/utils/maps.R b/R/utils/maps.R
index 0253f25b99443bb7824ad1f6f25513adca61a180..db2ebe9764c9d4181271b99499368094f9fe9275 100644
--- a/R/utils/maps.R
+++ b/R/utils/maps.R
@@ -3,47 +3,35 @@ library(rworldmap, quietly = TRUE)
## Plot map of distn
-world.map <- function(Lon, Lat, group = NULL, cols = NULL, add = FALSE,legend.TF=FALSE){
+world.map <- function(Lon, Lat, col = "red", add = FALSE, cex=0.2){
if(!add){
newmap <- getMap(resolution = 'low')
plot(newmap, col= "lightgrey")
}
- if(is.null(group))
- group <- rep("all", length(Lat))
-
- ngrps <- length(unique(group))
-
- if(is.null(cols)) #establish new pallettte if needed
- cols <- brewer.pal(max(ngrps,3), "Set1")
- else # check enough cols for groups
- if(length(cols) < ngrps)
- cols <- rep(cols[1], ngrps)
-
- # add data, unique points only
- i <- !duplicated(paste(Lon, Lat, group))
-
- points(Lon[i],Lat[i],pty='.',cex=.2, col = cols[as.factor(group)])
-
- if(legend.TF){
- legend('bottomleft', col = cols, legend = names(table(group)), pch = rep(19,ngrps), bty = "n")
- }
+ points(Lon,Lat,pch=19,cex=cex, col = col)
}
-world.map.all.sites <- function(data,legend.TF=FALSE){
-
+world.map.all.sites <- function(data,add.legend=FALSE){
+
+sets <- unique(data$set)
+
# list of colours
-cols <- as.list(niceColors(length(data)) )
-names(cols) <- names(data)
+cols <- as.list(niceColors(length(sets)))
+names(cols) <- sets
# new map
-world.map(NA, NA, group = NULL, cols = NULL)
+world.map(NA, NA)
-for(site in names(data))
- world.map(data[[site]]$tree[["Lon"]], data[[site]]$tree[["Lat"]], group = NULL, col = cols[[site]], add=TRUE,legend.TF)
- if(legend.TF){
- legend('bottomleft', col = unlist(cols), legend = names(cols), pch = rep(19,length(cols)), bty = "n")
+for(set in sets){
+ i <- data$set ==set
+ cex = 0.4
+ if(sum(i) ==1)
+ cex=2
+ world.map(data[i, "Lon"], data[i, "Lat"], col = cols[[set]], add=TRUE, cex=cex)
}
+if(add.legend)
+ legend('bottomleft', col = unlist(cols), legend = names(cols), pch = rep(19,length(cols)), bty = "n")
}
diff --git a/data/metadata/sites/Fushan/_site_details.JSON b/data/metadata/sites/Fushan/_site_details.JSON
index 0f9d8a93f727f78959bc9db75796263e5cff6c6d..e3a1bda099ee07371d3546c71f2120179a5b6a5f 100644
--- a/data/metadata/sites/Fushan/_site_details.JSON
+++ b/data/metadata/sites/Fushan/_site_details.JSON
@@ -10,8 +10,8 @@
"country": "Taiwan",
"climate": "",
"vegetation type": "",
- "latitude": -1,
- "longitude": -1,
+ "latitude": 24.7614,
+ "longitude": 121.555,
"minimum tree size": "",
"history": "",
"field methodology": "",