Skip to content
GitLab
Select Git revision
  • master default
  • BRIEFCOM
  • ctfs
  • test.dplyr
  • package
Find file BlameHistoryPermalink
READ.DATA.NFI.FRANCE.R 25.36 KiB
1 
############################################################ READ, MERGE AND CLEAN ALL NFI DATA NEW METHODS
2
3 
### read TREE table downloaded from the web
4 
arbre2005 <- read.csv("./data/raw/DataFrance/2005/arbres_foret_2005.csv", sep = ";",
5 
    stringsAsFactors = FALSE)
6 
summary(arbre2005)
7 
arbre2006 <- read.csv("./data/raw/DataFrance/2006/arbres_foret_2006.csv", sep = ";",
8 
    stringsAsFactors = FALSE)
9 
summary(arbre2006)
10 
arbre2007 <- read.csv("./data/raw/DataFrance/2007/arbres_foret_2007.csv", sep = ";",
11 
    stringsAsFactors = FALSE)
12 
summary(arbre2007)
13 
arbre2008 <- read.csv("./data/raw/DataFrance/2008/arbres_foret_2008.csv", sep = ";",
14 
    stringsAsFactors = FALSE)
15 
summary(arbre2005)
16 
arbre2009 <- read.csv("./data/raw/DataFrance/2009/arbres_foret_2009.csv", sep = ";",
17 
    stringsAsFactors = FALSE)
18 
summary(arbre2009)
19 
arbre2010 <- read.csv("./data/raw/DataFrance/2010/arbres_foret_2010.csv", sep = ";",
20 
    stringsAsFactors = FALSE)
21 
summary(arbre2010)
22 
arbre2011 <- read.csv("./data/raw/DataFrance/2011/arbres_foret_2011.csv", sep = ";",
23 
    stringsAsFactors = FALSE)
24
25
26
27
28
29 
#### ALL TREE after 2007 don't have the veget value as in 2005 aned 2006 because new
30 
#### variable ACCI for tree with accident (trunk broken ...)  NEED TO UPDATE VEGET
31 
#### FROM ACCI
32 
arbre2007$veget[arbre2007$acci > 0] <- 1
33 
arbre2008$veget[arbre2008$acci > 0] <- 1
34 
arbre2009$veget[arbre2009$acci > 0] <- 1
35 
arbre2010$veget[arbre2010$acci > 0] <- 1
36 
arbre2011$veget[arbre2011$acci > 0] <- 1
37 
##
38 
arbre2005$veget <- unclass(arbre2005$veget) - 1
39 
arbre2006$veget <- unclass(arbre2006$veget) - 1
40
41 
###### ORI NEED TO BE DEGRADED SINCE 2007 to two level from resprout or from seed
42 
arbre2007$ori[arbre2007$ori == 2] <- 0
43 
arbre2008$ori[arbre2008$ori == 2] <- 0
44 
arbre2009$ori[arbre2009$ori == 2] <- 0
45 
arbre2010$ori[arbre2010$ori == 2] <- 0
46 
arbre2011$ori[arbre2011$ori == 2] <- 0
47
48
49 
############################## merge all table adding NA when no variable for that year
50 
arbre.tot <- data.frame(idp = c(arbre2005$idp, arbre2006$idp, arbre2007$idp, arbre2008$idp,
51 
    arbre2009$idp, arbre2010$idp, arbre2011$idp), a = c(arbre2005$a, arbre2006$a,
52 
    arbre2007$a, arbre2008$a, arbre2009$a, arbre2010$a, arbre2011$a), veget = c(arbre2005$veget,
53 
    arbre2006$veget, arbre2007$veget, arbre2008$veget, arbre2009$veget, arbre2010$veget,
54 
    arbre2011$veget), simplif = c(rep(NA, length(arbre2005$idp)), rep(NA, length(arbre2006$idp)),
55 
    rep(NA, length(arbre2007$idp)), rep(NA, length(arbre2008$idp)), arbre2009$simplif,
56 
    arbre2010$simplif, arbre2011$simplif), acci = c(rep(NA, length(arbre2005$idp)),
57 
    rep(NA, length(arbre2006$idp)), arbre2007$acci, arbre2008$acci, arbre2009$acci,
58 
    arbre2010$acci, arbre2011$acci), espar = c(as.character(arbre2005$espar), as.character(arbre2006$espar),
59 
    as.character(arbre2007$espar), as.character(arbre2008$espar), as.character(arbre2009$espar),
60 
    as.character(arbre2010$espar), as.character(arbre2011$espar)), ori = c(arbre2005$ori,
61 
    arbre2006$ori, arbre2007$ori, arbre2008$ori, arbre2009$ori, arbre2010$ori, arbre2011$ori),
62 
    lib = c(arbre2005$lib, arbre2006$lib, arbre2007$lib, arbre2008$lib, arbre2009$lib,
63 
        arbre2010$lib, arbre2011$lib), forme = c(arbre2005$forme, arbre2006$forme,
64 
        arbre2007$forme, arbre2008$forme, arbre2009$forme, arbre2010$forme, arbre2011$forme),
65 
    tige = c(arbre2005$tige, arbre2006$tige, arbre2007$tige, arbre2008$tige, arbre2009$tige,
66 
        arbre2010$tige, arbre2011$tige), mortb = c(rep(NA, length(arbre2005$idp)),
67 
        arbre2006$mortb, arbre2007$mortb, arbre2008$mortb, arbre2009$mortb, arbre2010$mortb,
68 
        arbre2011$mortb), sfgui = c(rep(NA, length(arbre2005$idp)), rep(NA, length(arbre2006$idp)),
69 
        rep(NA, length(arbre2007$idp)), arbre2008$sfgui, arbre2009$sfgui, arbre2010$sfgui,
70 
        arbre2011$sfgui), sfgeliv = c(rep(NA, length(arbre2005$idp)), rep(NA, length(arbre2006$idp)),
7172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140
rep(NA, length(arbre2007$idp)), arbre2008$sfgeliv, arbre2009$sfgeliv, arbre2010$sfgeliv, arbre2011$sfgeliv), sfpied = c(rep(NA, length(arbre2005$idp)), rep(NA, length(arbre2006$idp)), rep(NA, length(arbre2007$idp)), arbre2008$sfpied, arbre2009$sfpied, arbre2010$sfpied, arbre2011$sfpied), sfdorge = c(rep(NA, length(arbre2005$idp)), rep(NA, length(arbre2006$idp)), rep(NA, length(arbre2007$idp)), arbre2008$sfdorge, arbre2009$sfdorge, arbre2010$sfdorge, arbre2011$sfdorge), sfcoeur = c(rep(NA, length(arbre2005$idp)), rep(NA, length(arbre2006$idp)), rep(NA, length(arbre2007$idp)), rep(NA, length(arbre2008$idp)), arbre2009$sfcoeur, arbre2010$sfcoeur, arbre2011$sfcoeur), c13 = c(arbre2005$c13, arbre2006$c13, arbre2007$c13, arbre2008$c13, arbre2009$c13, arbre2010$c13, arbre2011$c13), ir5 = c(arbre2005$ir5, arbre2006$ir5, arbre2007$ir5, arbre2008$ir5, arbre2009$ir5, arbre2010$ir5, arbre2011$ir5), htot = c(arbre2005$htot, arbre2006$htot, arbre2007$htot, arbre2008$htot, arbre2009$htot, arbre2010$htot, arbre2011$htot), hdec = c(rep(NA, length(arbre2005$idp)), rep(NA, length(arbre2006$idp)), rep(NA, length(arbre2007$idp)), arbre2008$hdec, arbre2009$hdec, arbre2010$hdec, arbre2011$hdec), decoupe = c(rep(NA, length(arbre2005$idp)), rep(NA, length(arbre2006$idp)), rep(NA, length(arbre2007$idp)), arbre2008$decoupe, arbre2009$decoupe, arbre2010$decoupe, arbre2011$decoupe), q1 = c(arbre2005$q1, arbre2006$q1, arbre2007$q1, arbre2008$q1, arbre2009$q1, arbre2010$q1, arbre2011$q1), q2 = c(arbre2005$q2, arbre2006$q2, arbre2007$q2, arbre2008$q2, arbre2009$q2, arbre2010$q2, arbre2011$q2), q3 = c(arbre2005$q3, arbre2006$q3, arbre2007$q3, arbre2008$q3, arbre2009$q3, arbre2010$q3, arbre2011$q3), r = c(arbre2005$r, arbre2006$r, arbre2007$r, arbre2008$r, arbre2009$r, arbre2010$r, arbre2011$r), lfsd = c(arbre2005$lfsd, arbre2006$lfsd, arbre2007$lfsd, arbre2008$lfsd, arbre2009$lfsd, arbre2010$lfsd, arbre2011$lfsd), age = c(rep(NA, length(arbre2005$idp)), rep(NA, length(arbre2006$idp)), rep(NA, length(arbre2007$idp)), arbre2008$age, arbre2009$age, arbre2010$age, arbre2011$age), v = c(arbre2005$v, arbre2006$v, arbre2007$v, arbre2008$v, arbre2009$v, arbre2010$v, arbre2011$v), w = c(arbre2005$w, arbre2006$w, arbre2007$w, arbre2008$w, arbre2009$w, arbre2010$w, arbre2011$w), YEAR = c(rep(2005, length(arbre2005$idp)), rep(2006, length(arbre2006$idp)), rep(2007, length(arbre2007$idp)), rep(2008, length(arbre2008$idp)), rep(2009, length(arbre2009$simplif)), rep(2010, length(arbre2010$simplif)), rep(2011, length(arbre2011$simplif)))) rm(arbre2005, arbre2006, arbre2007, arbre2008, arbre2009, arbre2010, arbre2011) gc() ######################################################## #### check problem of unit for c13 ir5 and htot by plotting the data ######################################################## plot(arbre.tot$c13,arbre.tot$ir5,col=unclass(factor(arbre.tot$YEAR)),cex=0.1) ######################################################## boxplot(arbre.tot$c13~arbre.tot$YEAR,ylab='c13') ######################################################## boxplot(arbre.tot$ir5~arbre.tot$YEAR,ylab='ir5') ######################################################## boxplot(arbre.tot$htot~arbre.tot$YEAR,ylab='htot') ######################################################## boxplot(arbre.tot$age~arbre.tot$YEAR,ylab='age') ##### SOMETHING VERY STRANGE ######################################################## FOR THE AGE WITH SEVERAL TREE OVER 1000 YEARS OLD ######################################################## boxplot(arbre.tot$mortb~arbre.tot$YEAR,ylab='mortality branche') ######################################################## boxplot(arbre.tot$veget~arbre.tot$YEAR,ylab='accident') ######################################################## boxplot(arbre.tot$simplif~arbre.tot$YEAR,ylab='accident') ######################################################## boxplot(arbre.tot$w~arbre.tot$YEAR,ylab='accident') ######################################################## boxplot(arbre.tot$ori~arbre.tot$YEAR,ylab='accident') ######################################################## boxplot(arbre.tot$lib~arbre.tot$YEAR,ylab='accident') ######################################################## boxplot(arbre.tot$forme~arbre.tot$YEAR,ylab='accident') ######################################################## boxplot(arbre.tot$tige~arbre.tot$YEAR,ylab='accident') ### NEED TO USE ONLY THE ######################################################## TIGE == 1 in the ANALYSIS ######################################################## boxplot(arbre.tot$sfgui~arbre.tot$YEAR,ylab='accident') ######################################################## boxplot(arbre.tot$sfgeliv~arbre.tot$YEAR,ylab='accident') ## ##### CHECK OTHER VARIABLE OK DONE ### USE BRANCH MORTALITY AS AN INDICATOR OF ## MORTALITY ?? ABIOTIC STRESS ? ## x11() plot(arbre.tot$c13,arbre.tot$htot,col=unclass(factor(arbre.tot$YEAR))) save(arbre.tot, file = "./data/process/arbre.tot.Rdata") ######################################### DEAD ############################################################## READ AND MERGE DEAD DATA MERGE WITH DEAD TREE and MERGE WITH PLOT DATA!! ### read DEAD TREE table downloaded from the web arbre_mort2005 <- read.csv("./data/raw/DataFrance/2005/arbres_morts_foret_2005.csv",
141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210
sep = ";", stringsAsFactors = FALSE) ## summary(arbre_mort2005) arbre_mort2006 <- read.csv("./data/raw/DataFrance/2006/arbres_morts_foret_2006.csv", sep = ";", stringsAsFactors = FALSE) ## summary(arbre_mort2006) arbre_mort2007 <- read.csv("./data/raw/DataFrance/2007/arbres_morts_foret_2007.csv", sep = ";", stringsAsFactors = FALSE) ## summary(arbre_mort2007) arbre_mort2008 <- read.csv("./data/raw/DataFrance/2008/arbres_morts_foret_2008.csv", sep = ";", stringsAsFactors = FALSE) ## summary(arbre_mort2005) arbre_mort2009 <- read.csv("./data/raw/DataFrance/2009/arbres_morts_foret_2009.csv", sep = ";", stringsAsFactors = FALSE) ## summary(arbre_mort2009) arbre_mort2010 <- read.csv("./data/raw/DataFrance/2010/arbres_morts_foret_2010.csv", sep = ";", stringsAsFactors = FALSE) ## summary(arbre_mort2010) arbre_mort2011 <- read.csv("./data/raw/DataFrance/2011/arbres_morts_foret_2011.csv", sep = ";", stringsAsFactors = FALSE) ## names(arbre_mort2005) names(arbre_mort2006) names(arbre_mort2007) ## names(arbre_mort2008) names(arbre_mort2009) names(arbre_mort2010) ## names(arbre_mort2011) ### merge 2005 2006 2007 to compute c13 arbre_mort05_07 <- rbind(arbre_mort2005, arbre_mort2006, arbre_mort2007) arbre_mort05_07$c13 <- rep(NA, length(arbre_mort05_07$c0)) arbre_mort05_07$espar2 <- as.numeric(substr(arbre_mort05_07$espar, 1, 2)) arbre_mort05_07$year <- c(rep(2005, length = length(arbre_mort2005[, 1])), rep(2006, length = length(arbre_mort2006[, 1])), rep(2007, length = length(arbre_mort2007[, 1]))) #### NEED TO CONVERT c0 into c13 before 2008 before 2008 no date dead but all tree #### died less than 5 years ago. need to do convertion between c0 and c13. for #### that use the NFI data from previous inventory that were reporting both c0 and #### c13 for all species fit an allometric relationship and then use it to predict #### c13 in this data base ### READ DATA CYCLE 3 ORGINAL /// NEED TO CONVERT C0 and C13 in cm *100 arbre.cycle3 <- read.table("./data/raw/DataFrance/cycle3/data.arbre.tot.txt", sep = " ", stringsAsFactors = FALSE) ### change the C from m to cm arbre.cycle3$C0 <- arbre.cycle3$C0 * 100 arbre.cycle3$C13 <- arbre.cycle3$C13 * 100 ## LOAD library RMA regression library(lmodel2) ## the regression between C13 and C0 vary between species, but not same species in ## cycle 3 because less details (the classification is only based on number and no ## letters remove the letters and apply the same model to all species that have ## the same number code species.list <- c(as.numeric(names(table(substr(arbre_mort05_07$espar, 1, 2))))[-1]) ## length(table(arbre.cycle3$ESS)) for (i in species.list) { if (sum(arbre.cycle3$ESS == i) > 50) { lmodel2.res <- lmodel2(C13 ~ C0, data = arbre.cycle3[arbre.cycle3$ESS == i, ], range.x = "relative", range.y = "relative") arbre_mort05_07$c13[arbre_mort05_07$espar2 == i & !is.na(arbre_mort05_07$espar2)] <- lmodel2.res$regression.results[4, 2] + arbre_mort05_07$c0[arbre_mort05_07$espar2 == i & !is.na(arbre_mort05_07$espar2)] * lmodel2.res$regression.results[4, 3] print(i) print(lmodel2.res$regression.results[4, 2:3]) print(range(arbre_mort05_07$c13[arbre_mort05_07$espar2 == i & !is.na(arbre_mort05_07$espar2)], na.rm = T)) } else {
211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280
lmodel2.res <- lmodel2(C13 ~ C0, data = arbre.cycle3, range.x = "relative", range.y = "relative") arbre_mort05_07$c13[arbre_mort05_07$espar2 == i & !is.na(arbre_mort05_07$espar2)] <- lmodel2.res$regression.results[4, 2] + arbre_mort05_07$c0[arbre_mort05_07$espar2 == i & !is.na(arbre_mort05_07$espar2)] * lmodel2.res$regression.results[4, 3] print(i) print(lmodel2.res$regression.results[4, 2:3]) print(range(arbre_mort05_07$c13[arbre_mort05_07$espar2 == i & !is.na(arbre_mort05_07$espar2)], na.rm = T)) } } ### for species with NO DATA in cycle 3 apply mean model over all species lmodel2.res <- lmodel2(C13 ~ C0, data = arbre.cycle3, range.x = "relative", range.y = "relative") arbre_mort05_07$c13[is.na(arbre_mort05_07$espar2)] <- lmodel2.res$regression.results[4, 2] + arbre_mort05_07$c0[is.na(arbre_mort05_07$espar2)] * lmodel2.res$regression.results[4, 3] ## check predicted C13 from C0 head(cbind(arbre_mort05_07$c13, arbre_mort05_07$c0, arbre_mort05_07$espar)) ### ok donne c13 added ######################## MERGE WITH other dead data arbre_mort_tot <- data.frame(idp = c(arbre_mort05_07$idp, arbre_mort2008$idp, arbre_mort2009$idp, arbre_mort2010$idp, arbre_mort2011$idp), a = c(arbre_mort05_07$a, arbre_mort2008$a, arbre_mort2009$a, arbre_mort2010$a, arbre_mort2011$a), espar = c(as.character(arbre_mort05_07$espar), as.character(arbre_mort2008$espar), as.character(arbre_mort2009$espar), as.character(arbre_mort2010$espar), as.character(arbre_mort2011$espar)), ori = c(arbre_mort05_07$ori, arbre_mort2008$ori, arbre_mort2009$ori, arbre_mort2010$ori, arbre_mort2011$ori), veget = c(arbre_mort05_07$veget, arbre_mort2008$veget, arbre_mort2009$veget, arbre_mort2010$veget, arbre_mort2011$veget), datemort = c(rep(NA, length(arbre_mort05_07$ori)), arbre_mort2008$datemort, arbre_mort2009$datemort, arbre_mort2010$datemort, arbre_mort2011$datemort), c13 = c(arbre_mort05_07$c13, arbre_mort2008$c13, arbre_mort2009$c13, arbre_mort2010$c13, arbre_mort2011$c13), v = c(arbre_mort05_07$v, arbre_mort2008$v, arbre_mort2009$v, arbre_mort2010$v, arbre_mort2011$v), w = c(arbre_mort05_07$w, arbre_mort2008$w, arbre_mort2009$w, arbre_mort2010$w, arbre_mort2011$w), YEAR = c(rep(2005, length(arbre_mort2005$idp)), rep(2006, length(arbre_mort2006$idp)), rep(2007, length(arbre_mort2007$idp)), rep(2008, length(arbre_mort2008$idp)), rep(2009, length(arbre_mort2009$idp)), rep(2010, length(arbre_mort2010$idp)), rep(2011, length(arbre_mort2011$idp)))) rm(arbre.cycle3, arbre_mort2005, arbre_mort2006, arbre_mort2007, arbre_mort2008, arbre_mort2009, arbre_mort2010, arbre_mort2011) gc() save(arbre_mort_tot, file = "./data/process/arbre_mort_tot.Rdata") ################################################################################ MERGE DEAD AND ALIVE TREE head(arbre_mort_tot) head(arbre.tot) arbre.ALIVE.DEAD <- data.frame(idp = c(arbre.tot$idp, arbre_mort_tot$idp), a = c(arbre.tot$a, arbre_mort_tot$a), veget = c(arbre.tot$veget, arbre_mort_tot$veget), simplif = c(arbre.tot$simplif, rep(NA, length = length(arbre_mort_tot$idp))), acci = c(arbre.tot$acci, rep(NA, length = length(arbre_mort_tot$idp))), espar = c(as.character(arbre.tot$espar), as.character(arbre_mort_tot$espar)), ori = c(arbre.tot$ori, arbre_mort_tot$ori), lib = c(arbre.tot$lib, rep(NA, length = length(arbre_mort_tot$idp))), forme = c(arbre.tot$forme, rep(NA, length = length(arbre_mort_tot$idp))), tige = c(arbre.tot$tige, rep(NA, length = length(arbre_mort_tot$idp))), mortb = c(arbre.tot$mortb, rep(NA, length = length(arbre_mort_tot$idp))), sfgui = c(arbre.tot$sfgui, rep(NA, length = length(arbre_mort_tot$idp))), sfgeliv = c(arbre.tot$sfgeliv, rep(NA, length = length(arbre_mort_tot$idp))), sfpied = c(arbre.tot$sfpied, rep(NA, length = length(arbre_mort_tot$idp))), sfdorge = c(arbre.tot$sfdorge, rep(NA, length = length(arbre_mort_tot$idp))), sfcoeur = c(arbre.tot$sfcoeur, rep(NA, length = length(arbre_mort_tot$idp))), c13 = c(arbre.tot$c13, arbre_mort_tot$c13),
281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350
ir5 = c(arbre.tot$ir5, rep(NA, length = length(arbre_mort_tot$idp))), htot = c(arbre.tot$htot, rep(NA, length = length(arbre_mort_tot$idp))), hdec = c(arbre.tot$hdec, rep(NA, length = length(arbre_mort_tot$idp))), decoupe = c(arbre.tot$decoupe, rep(NA, length = length(arbre_mort_tot$idp))), q1 = c(arbre.tot$q1, rep(NA, length = length(arbre_mort_tot$idp))), q2 = c(arbre.tot$q2, rep(NA, length = length(arbre_mort_tot$idp))), q3 = c(arbre.tot$q3, rep(NA, length = length(arbre_mort_tot$idp))), r = c(arbre.tot$r, rep(NA, length = length(arbre_mort_tot$idp))), lfsd = c(arbre.tot$lfsd, rep(NA, length = length(arbre_mort_tot$idp))), age = c(arbre.tot$age, rep(NA, length = length(arbre_mort_tot$idp))), v = c(arbre.tot$v, arbre_mort_tot$v), w = c(arbre.tot$w, rep(10000/(pi * (c(15))^2), length = length(arbre_mort_tot$w))), YEAR = c(arbre.tot$YEAR, arbre_mort_tot$YEAR), datemort = c(rep(NA, length = length(arbre.tot$YEAR)), arbre_mort_tot$datemort), dead = c(rep(0, length = length(arbre.tot$YEAR)), rep(1, length = length(arbre_mort_tot$idp)))) ## dead: 1 = dead w: assume that all dead tree are sampled on the whole plot as ## explained in the method ## delete plot with DEAD tree missing because of no C13 or no espar arbre.ALIVE.DEAD2 <- arbre.ALIVE.DEAD[!(arbre.ALIVE.DEAD$idp %in% unique(c(names(tapply(is.na(arbre.ALIVE.DEAD$c13), INDEX = arbre.ALIVE.DEAD$idp, FUN = sum))[tapply(is.na(arbre.ALIVE.DEAD$c13), INDEX = arbre.ALIVE.DEAD$idp, FUN = sum) > 0], names(tapply(is.na(arbre.ALIVE.DEAD$espar), INDEX = arbre.ALIVE.DEAD$idp, FUN = sum))[tapply(is.na(arbre.ALIVE.DEAD$espar), INDEX = arbre.ALIVE.DEAD$idp, FUN = sum) > 0]))), ] save(arbre.ALIVE.DEAD2, file = "./data/process/arbre.ALIVE.DEAD2.Rdata") ######################################################################################## LOAD DATA FOR PLOT INFO read DEAD TREE table downloaded from the web placette2005 <- read.csv("./data/raw/DataFrance/2005/placettes_foret_2005.csv", sep = ";", stringsAsFactors = FALSE) ## summary(placette2005) placette2006 <- read.csv("./data/raw/DataFrance/2006/placettes_foret_2006.csv", sep = ";", stringsAsFactors = FALSE) ## summary(placette2006) placette2007 <- read.csv("./data/raw/DataFrance/2007/placettes_foret_2007.csv", sep = ";", stringsAsFactors = FALSE) ## summary(placette2007) placette2008 <- read.csv("./data/raw/DataFrance/2008/placettes_foret_2008.csv", sep = ";", stringsAsFactors = FALSE) ## summary(placette2005) placette2009 <- read.csv("./data/raw/DataFrance/2009/placettes_foret_2009.csv", sep = ";", stringsAsFactors = FALSE) ## summary(placette2009) placette2010 <- read.csv("./data/raw/DataFrance/2010/placettes_foret_2010.csv", sep = ";", stringsAsFactors = FALSE) ## summary(placette2010) placette2011 <- read.csv("./data/raw/DataFrance/2011/placettes_foret_2011.csv", sep = ";", stringsAsFactors = FALSE) ## names(placette2005) ## uta -> uta1 ## sfo NA ## plisi NA names(placette2006) ## ## plisi NA names(placette2007) ## dcespar1 dcespar2 tpespar1 tpespar2 iti pentexp ## NA ## deleted acces names(placette2008) ## gest incid peupnr portance asperite ## names(placette2009) names(placette2010) names(placette2011) placette2005$tplant <- as.character(placette2005$tplant) placette2005$tplant[placette2005$tplant == ""] <- 0 placette2006$tplant[placette2006$tplant == ""] <- 0 ### for selection of plot use plisi=0 dc=0 tplant=0 incid indicateur d incident ### récent utilisé ou pas ?? avec ou sans perturbatrion naturelle placette_tot <- data.frame(idp = c(placette2005$idp, placette2006$idp, placette2007$idp, placette2008$idp, placette2009$idp, placette2010$idp, placette2011$idp), xl93 = c(placette2005$xl93, placette2006$xl93, placette2007$xl93, placette2008$xl93, placette2009$xl93, placette2010$xl93, placette2011$xl93), yl93 = c(placette2005$yl93, placette2006$yl93, placette2007$yl93, placette2008$yl93, placette2009$yl93, placette2010$yl93, placette2011$yl93), dep = c(placette2005$dep, placette2006$dep, placette2007$dep, placette2008$dep, placette2009$dep, placette2010$dep, placette2011$dep), csa = c(placette2005$csa, placette2006$csa, placette2007$csa, placette2008$csa, placette2009$csa, placette2010$csa, placette2011$csa), plisi = c(rep(NA, length(placette2005$tm2)), rep(NA, length(placette2006$idp)),
351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420
placette2007$plisi, placette2008$plisi, placette2009$plisi, placette2010$plisi, placette2011$plisi), uta1 = c(placette2005$uta, placette2006$uta1, placette2007$uta1, placette2008$uta1, placette2009$uta1, placette2010$uta1, placette2011$uta1), tm2 = c(placette2005$tm2, placette2006$tm2, placette2007$tm2, placette2008$tm2, placette2009$tm2, placette2010$tm2, placette2011$tm2), sfo = c(rep(NA, length(placette2005$tm2)), placette2006$sfo, placette2007$sfo, placette2008$sfo, placette2009$sfo, placette2010$sfo, placette2011$sfo), incid = c(rep(NA, length(placette2005$idp)), rep(NA, length(placette2006$idp)), rep(NA, length(placette2007$idp)), rep(NA, length(placette2008$idp)), placette2009$incid, placette2010$incid, placette2011$incid), dc = c(placette2005$dc, placette2006$dc, placette2007$dc, placette2008$dc, placette2009$dc, placette2010$dc, placette2011$dc), tplant = c(placette2005$tplant, placette2006$tplant, placette2007$tplant, placette2008$tplant, placette2009$tplant, placette2010$tplant, placette2011$tplant), esspre = c(placette2005$esspre, placette2006$esspre, placette2007$esspre, placette2008$esspre, placette2009$esspre, placette2010$esspre, placette2011$esspre), cac = c(placette2005$cac, placette2006$cac, placette2007$cac, placette2008$cac, placette2009$cac, placette2010$cac, placette2011$cac), ess_age_1 = c(placette2005$ess_age_1, placette2006$ess_age_1, placette2007$ess_age_1, placette2008$ess_age_1, placette2009$ess_age_1, placette2010$ess_age_1, placette2011$ess_age_1), YEAR = c(rep(2005, length(placette2005$idp)), rep(2006, length(placette2006$idp)), rep(2007, length(placette2007$idp)), rep(2008, length(placette2008$idp)), rep(2009, length(placette2009$idp)), rep(2010, length(placette2010$idp)), rep(2011, length(placette2011$idp)))) rm(placette2005, placette2006, placette2007, placette2008, placette2009, placette2010, placette2011) save(placette_tot, file = "./data/process/placette_tot.Rdata") ##################################### LOAD elevation data LOAD ALTITUDE DATA ##################################### load('./data/process/placette_tot.Rdata') alti <- read.csv("./data/raw/DataFrance/altitude/SER_alti.csv", header = T, sep = ";", stringsAsFactors = FALSE) alti2011 <- read.csv("./data/raw/DataFrance/altitude/SER_alti_2011.csv", header = T, sep = ";", stringsAsFactors = FALSE) names(alti2011) <- names(alti) alti.tot <- rbind(alti, alti2011) ## sum( placette_tot$idp %in% alti.tot$IDP)/length(placette_tot$idp) ## table(placette_tot$YEAR[! placette_tot$idp %in% alti.tot$IDP]) placette_tot.alti <- merge(placette_tot, alti.tot, by.x = "idp", by.y = "IDP") ### write csv file for Piedallu write.csv(placette_tot.alti, "./data/process/placette_tot.alti.csv") ### write new fiel for 2011 write.csv(placette_tot.alti[placette_tot.alti$YEAR == 2011, ], "./data/process/placette_tot.alti.2011.csv") ######################################### LOAD DATA ECOLOGIE read DEAD TREE table downloaded from the web ecologie2005 <- read.csv("./data/raw/DataFrance/2005/ecologie_2005.csv", sep = ";", stringsAsFactors = FALSE) ## summary(ecologie2005) ecologie2006 <- read.csv("./data/raw/DataFrance/2006/ecologie_2006.csv", sep = ";", stringsAsFactors = FALSE) ## summary(ecologie2006) ecologie2007 <- read.csv("./data/raw/DataFrance/2007/ecologie_2007.csv", sep = ";", stringsAsFactors = FALSE) ## summary(ecologie2007) ecologie2008 <- read.csv("./data/raw/DataFrance/2008/ecologie_2008.csv", sep = ";", stringsAsFactors = FALSE) ## summary(ecologie2005) ecologie2009 <- read.csv("./data/raw/DataFrance/2009/ecologie_2009.csv", sep = ";", stringsAsFactors = FALSE) ## summary(ecologie2009) ecologie2010 <- read.csv("./data/raw/DataFrance/2010/ecologie_2010.csv", sep = ";", stringsAsFactors = FALSE) ## summary(ecologie2010) ecologie2011 <- read.csv("./data/raw/DataFrance/2011/ecologie_2011.csv", sep = ";", stringsAsFactors = FALSE)
421422423424425426427428429430431432433
ecologie_tot <- rbind(ecologie2005, ecologie2006, ecologie2007, ecologie2008, ecologie2009, ecologie2010, ecologie2011) head(ecologie_tot) rm(ecologie2005, ecologie2006, ecologie2007, ecologie2008, ecologie2009, ecologie2010, ecologie2011) save(ecologie_tot, file = "./data/process/ecologie_tot.Rdata")