diff --git a/merge.data.NZ.R b/merge.data.NZ.R
index 8c5ab3413aed43dd7073e467567513eb418b1de0..fb49cfdf504204039a880c6b0a7ae96d0beb30fa 100644
--- a/merge.data.NZ.R
+++ b/merge.data.NZ.R
@@ -41,12 +41,13 @@ data.nz$D <- data.nz[["D0"]] ## diameter in cm
data.nz$dead <- as.numeric(is.na(data.nz[["D1"]])) ## dummy variable for dead tree 0 alive 1 dead
data.nz$plot <- data.nz$plid; data.nz$plid <- NULL
data.nz$htot <- rep(NA, nrow(data.nz)) ## Max height is already available so have as missing
-data.nz$tree.id <- rep(NA, nrow(data.nz))
-#data.nz$tree.id <- gsub("__", "_", data.nz$tree.id)
-#data.nz$tree.id <- gsub("_", ".", data.nz$tree.id) ## tree unique id
+data.nz$tree.id <- data.nz$tag
+head(subset(data.nz,subset=data.nz$tag %in% names(table(data.nz$tag))[table(data.nz$tag)==2])) ### 3 individuals with two observation with strange value check with Daniel and David add an issue
+data.nz$obs.id <- 1:nrow(data.nz)
+data.nz$census <- re(1,nrow(data.nz)) # only one census NEED TO CHECK WITH DANIEL AND DAVID add issue
data.nz$weights <- 1/(20*20) ## need to check with david
-########################################## CHANGE COORDINATE SYSTEM DON'T KNOW THE EPSG CODE HERE change coordinates
+########################################## CHANGE COORDINATE SYSTEM
########################################## system of Easting Northing to be in lat long WGS84
library(sp)
library(dismo)
@@ -71,8 +72,13 @@ dev.off()
rm(data.sp, data.sp2)
-###################### ECOREGION merge greco to have no ecoregion with low number of observation
+###################### ECOREGION merge to have no ecoregion with low number of observation
table(data.nz$Broad)
+## merging two ecoregion based on Daniel Laughlin advice.
+data.nz$Broad[data.nz$Broad=="Wetland"] <- "BeechHumid"
+data.nz$Broad[data.nz$Broad=="ConiferDry"] <- "BeechHumid"
+
+
###################### PERCENT DEAD
perc.dead <- tapply(data.nz[["dead"]], INDEX = data.nz[["plot"]], FUN = function.perc.dead2)
@@ -81,10 +87,26 @@ data.nz <- merge(data.nz, data.frame(plot = names(perc.dead), perc.dead = perc.d
########################################################### PLOT SELECTION FOR THE ANALYSIS
vec.abio.var.names <- c("MAT", "MAP")
-vec.basic.var <- c("tree.id", "sp", "spname", "plot", "ecocode", "D", "G", "dead",
- "year", "htot", "Lon", "Lat", "perc.dead")
+vec.basic.var <- c("obs.id","tree.id", "sp", "spname", "plot", "ecocode", "D", "G", "dead",
+ "year", "htot", "Lon", "Lat", "perc.dead","weights","census")
data.tree <- subset(data.nz, select = c(vec.basic.var, vec.abio.var.names))
+### read TRAITS data TODO
+
+#### GENERATE ONE OBJECT PER ECOREGION
+
+# vector of ecoregion name
+ecoregion.unique <- unique(data.tree[["ecocode"]])
+
+
+#### lapply function
+
+
+system.time(lapply(ecoregion.unique, FUN = fun.data.per.ecoregion, data.tot = data.tree,
+ plot.name = "plot", weight.full.plot = NA, name.country = "NZ", data.TRY = NA,
+ species.lookup = species.clean))
+
+
############################################## COMPUTE MATRIX OF COMPETITION INDEX WITH SUM OF BA PER SPECIES IN EACH PLOT in
############################################## m^2/ha without the target species
data.BA.SP <- BA.SP.FUN(id.tree = as.vector(data.nz[["tree.id"]]), diam = as.vector(data.nz[["D"]]),
diff --git a/merge.data.US.R b/merge.data.US.R
index 9091f2934dcd08a2117daf97c48fbd0b91e1f2d5..307cfcc9c334ff3b366941f8844e834f58df9c7f 100644
--- a/merge.data.US.R
+++ b/merge.data.US.R
@@ -37,6 +37,7 @@ data.us$subplot <- paste(as.character(data.us[["PlotID"]]), as.character(data.us
sep = ".") ## plot code
data.us$htot <- rep(NA, length(data.us[["Species"]])) ## height of tree in m - MISSING
data.us$tree.id <- as.character(data.us$TreeID)
+data.us$obs.id <- 1:nrow(data.us)
## tree unique id
data.us$sp.name <- NA
## census is missing use as only one census and check with mark
@@ -84,13 +85,10 @@ data.us[["sp"]] <- paste("sp", data.us[["sp"]], sep = ".")
## variables to keep
vec.abio.var.names <- c("MAT", "MAP")
-vec.basic.var <- c("tree.id", "sp", "plot", "subplot", "ecocode", "D", "G", "dead",
+vec.basic.var <- c("obs.id","tree.id", "sp", "plot", "subplot", "ecocode", "D", "G", "dead",
"year", "htot", "Lon", "Lat", "perc.dead", "weights","census")
data.tree <- subset(data.us, select = c(vec.basic.var, vec.abio.var.names))
rm(data.us)
-
-## creat row unique id
-data.tree$obs.id <- as.character(1:nrow(data.tree))
gc()
### read TRY data
diff --git a/ms/Makefile b/ms/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..30a9f5a14ef026faac5a48e6b184b28e15a7a2ba
--- /dev/null
+++ b/ms/Makefile
@@ -0,0 +1,14 @@
+all: metadata base
+
+base: data.format.pdf
+
+%.pdf: %.md
+ pandoc $< -V linkcolor:black -V geometry:a4paper -V geometry:margin=1in --listings --include-in-header=include.tex -o $@
+
+metadata:
+ Rscript knit_site_description.R
+
+clean:
+ rm -f *.pdf
+
+.PHONY: all base metadata clean
diff --git a/ms/requirements/include.tex b/ms/include.tex
similarity index 100%
rename from ms/requirements/include.tex
rename to ms/include.tex
diff --git a/ms/metadata/France/files/dataIFN.FRANCE.csv b/ms/metadata/France/files/dataIFN.FRANCE.csv
index b3c662ecf081ff4d5536a6ed502fdedbc29a1a34..67d58d41864250465734f39520d4b19a61fb187a 100644
--- a/ms/metadata/France/files/dataIFN.FRANCE.csv
+++ b/ms/metadata/France/files/dataIFN.FRANCE.csv
@@ -1,36 +1,36 @@
-use var units description
-1 idp NA plot number (a single census)
-1 a NA tree number within the plot
-1 veget NA 1 alive 2 or 3 dead
-1 simplif NA indicator with tree with only dbh measurement no growth
-1 acci NA 0 tree not damaged else tree damaged (1 broken 2 partil unrooten 3 bended 4 burned)
-1 espar NA species code
-1 ori NA origin of the tree (0 resprout 1 from seed 2 resprout from windthrown tree)
-0 lib NA percentage of canopy in full light in three class (0 between 0 and 2/3 more than 2/3)
-0 mortb NA percentage of branch mortality in 5 classes
-1 c13 cm circumference at 1m30
-1 ir5 mm radial growth over 5 years ( !!! not diameter growth)
-1 htot m height
-0 r % percentage of wood of bad quality
-1 age yr age
-1 w 1/ha weighting fqtcor to convert qt hectqr bqsis
-1 YEAR yr year of measurment
-1 datemort NA died less than 5 years ago =1 more than 5 years ago =2
-1 dead NA 0 alive 1 dead
-1 SER NA ecoregion (first letter large scale ecoregion number smaller division)
-1 sgdd ?/day sum of degree days above 5.56?C
-1 WB.y mm water budget in mm over the year
-1 WB.s mm water budget in mm over the growing season
-1 WS.y NA water stress index over the year
-1 WS.s NA water stress index over the growing season
-1 MAT ?C mean annual temperature
-1 SAP mm annual sum of precipitation
-1 xl93 m x in lambert 93
-1 yl93 m y in lambert 93
-0 dep NA French department (admin region)
-0 csa NA type of forest 1 closed forest 2 small patch 3 open forest
-1 plisi NA presence of forest edge
-1 sfo NA forest structure in 5 class
-0 incid NA percentage of disturbance in 5 classes only after 2009
-1 dc NA type of harvesting 0 = no harvesting orther harvesting
-1 tplant NA type of plantation 0 = no plantation other plantation
+use,var,units,description
+1,idp,NA,plot number (a single census)
+1,a,NA,tree number within the plot
+1,veget,NA,1 alive 2 or 3 dead
+1,simplif,NA,indicator with tree with only dbh measurement no growth
+1,acci,NA,0 tree not damaged else tree damaged (1 broken 2 partil unrooten 3 bended 4 burned)
+1,espar,NA,species code
+1,ori,NA,origin of the tree (0 resprout 1 from seed 2 resprout from windthrown tree)
+0,lib,NA,percentage of canopy in full light in three class (0 ; between 0 and 2/3 ;m ore than 2/3)
+0,mortb,NA ,percentage of branch mortality in 5 classes
+1,c13,cm,circumference at 1m30
+1,ir5,mm,radial growth over 5 years ( !!! not diameter growth)
+1,htot,m,height
+0,r,%,percentage of wood of bad quality
+1,age,yr,age
+1,w,1/ha,weighting fqtcor to convert qt hectqr bqsis
+1,YEAR,yr,year of measurment
+1,datemort,NA,died less than 5 years ago =1 more than 5 years ago =2
+1,dead,NA,0 alive 1 dead
+1,SER,NA,ecoregion (first letter large scale ecoregion number smaller division)
+1,sgdd,C/day,sum of degree days above 5.56?C
+1,WB.y,mm,water budget in mm over the year
+1,WB.s,mm,water budget in mm over the growing season
+1,WS.y,NA,water stress index over the year
+1,WS.s,NA,water stress index over the growing season
+1,MAT,Degree C,mean annual temperature
+1,SAP,mm,annual sum of precipitation
+1,xl93,m,x in lambert 93
+1,yl93,m,y in lambert 93
+0,dep,NA,French department (admin region)
+0,csa,NA,type of forest 1 closed forest 2 small patch 3 open forest
+1,plisi,NA,presence of forest edge
+1,sfo,NA ,forest structure in 5 class
+0,incid,NA,percentage of disturbance in 5 classes only after 2009
+1,dc,NA,type of harvesting 0 = no harvesting orther harvesting
+1,tplant,NA,type of plantation 0 = no plantation other plantation
diff --git a/ms/metadata/France/files/species.csv b/ms/metadata/France/files/species.csv
index 41f2a604c4c48988e0ed01a521c74a9992fc2d86..cd8fc5d4df7d122fd4830f60f01e4a0bfef3d00b 100644
--- a/ms/metadata/France/files/species.csv
+++ b/ms/metadata/France/files/species.csv
@@ -1,4 +1,4 @@
-use var units description
-1 code NA species code = espar in IFN file
-1 Latin_name NA Latin name
-0 Exotic_Native_cultivated NA exotic native
+use,var,units,description
+1,code,NA,species code = espar in IFN file
+1,Latin_name,NA,Latin name
+0, Exotic_Native_cultivated,NA,exotic native