R/importSource/loadBryophytes.r

In richardjtelford/seedclimComm: Code for Cleaning SeedClim data

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# load data for different analyses
#load trait data
#zap dummy taxon bryoMeasured


###############################################
##moss data
mossQ <- "SELECT sites.siteID, blocks.blockID, turfs.TTtreat,turfs.turfID, dest_blocks.blockID AS destBlockID, (SELECT Count(subTurfEnvironment.bad) AS CountOfbad
FROM subTurfEnvironment where (subTurfEnvironment.year = new_TurfCommunity.year) AND (subTurfEnvironment.turfID = new_TurfCommunity.turfID)
 AND ( (subTurfEnvironment.bad)='')) AS notbad, sites.Temperature_level, sites.Precipitation_level, new_TurfCommunity.Year, new_TurfCommunity.species, new_TurfCommunity.cover, turfEnvironment.recorder , dest_blocks.siteID as destSiteID
FROM (((blocks AS dest_blocks INNER JOIN plots AS dest_plots ON dest_blocks.blockID = dest_plots.blockID) INNER JOIN (((sites INNER JOIN blocks ON sites.siteID = blocks.siteID) INNER JOIN plots ON blocks.blockID = plots.blockID) 
INNER JOIN turfs ON plots.plotID = turfs.originPlotID) ON dest_plots.plotID = turfs.destinationPlotID) INNER JOIN new_TurfCommunity ON turfs.turfID = new_TurfCommunity.turfID) INNER JOIN turfEnvironment ON (turfEnvironment.year = new_TurfCommunity.Year) AND (turfs.turfID = turfEnvironment.turfID)
WHERE NOT turfs.TTtreat='' AND ((Not (new_TurfCommunity.Year)=2010));"
moss.thin <- dbGetQuery(con, mossQ)
       
head(moss.thin)
                                       
#correct for stomping
table(cover.thin$notbad)
stompingQ <- "SELECT blocks.siteID, blocks.blockID, turfs.turfID, subTurfEnvironment.year, turfs.TTtreat, Count(subTurfEnvironment.bad) AS CountOfbad
FROM blocks INNER JOIN (plots INNER JOIN (turfs INNER JOIN subTurfEnvironment ON turfs.turfID = subTurfEnvironment.turfID) ON plots.plotID = turfs.destinationPlotID) ON blocks.blockID = plots.blockID
GROUP BY blocks.siteID, blocks.blockID, turfs.turfID, subTurfEnvironment.year, turfs.TTtreat, subTurfEnvironment.bad
HAVING (((subTurfEnvironment.bad)='x'));"
dbGetQuery(con, stompingQ) 

 #delete turfs with too much stomping  
cover.thin <- cover.thin[cover.thin$notbad > 10,]
sort(cover.thin$notbad, decreasing = TRUE)
                                 
 #correct covers for stomping
 max(cover.thin$cover)
cover.thin$cover <- cover.thin$cover*25/cover.thin$notbad
sort(cover.thin$cover, decreasing = TRUE)[1:10]      
cover.thin$cover[cover.thin$cover > 80] <- 80 #stop doubtfully high values                                

#correct for botanist effects
#PM
cover.thin$cover[cover.thin$recorder == "PM"] <- cover.thin$cover[cover.thin$recorder == "PM"]*1.20
#Siri
siriQ<-"SELECT turfs.turfID, new_TurfCommunity.Year, turfEnvironment.date, Sum(new_TurfCommunity.cover) AS SumOfcover, turfEnvironment.totalVascular, turfs.TTtreat, sites.Temperature_level
FROM ((sites INNER JOIN blocks ON sites.siteID = blocks.siteID) INNER JOIN plots ON blocks.blockID = plots.blockID) INNER JOIN ((turfs INNER JOIN turfEnvironment ON turfs.turfID = turfEnvironment.turfID) INNER JOIN new_TurfCommunity ON (new_TurfCommunity.Year = turfEnvironment.year) AND (turfs.turfID = new_TurfCommunity.turfID)) ON plots.plotID = turfs.destinationPlotID
WHERE (((turfEnvironment.recorder)='Siri'))
GROUP BY turfs.turfID, new_TurfCommunity.Year, turfEnvironment.date, turfEnvironment.totalVascular, turfs.TTtreat, sites.Temperature_level
HAVING ((Not (turfs.TTtreat)=''))
ORDER BY new_TurfCommunity.Year, turfEnvironment.date, Sum(new_TurfCommunity.cover) DESC;"

siri<-dbGetQuery(con, siriQ)
siriLOW <- siri[siri$SumOfcover/siri$totalV < 1.35,]
siriLOW$turfID <- as.character(siriLOW$turfID)

siri.fix <- paste(as.character(cover.thin$turfID), cover.thin$Year) %in% paste(siriLOW$turfID, siriLOW$Year)

table(siri.fix, cover.thin$recorder)

cover.thin$cover[siri.fix] <- cover.thin$cover[siri.fix]*1.3



# make fat table

cover <- xtabs(cover ~ paste(turfID, Year, sep = "_") + species, data = cover.thin)
cover <- as.data.frame(unclass(cover))
dim(cover)



#make meta data
cover.meta <- unique(cover.thin[,c("siteID", "TTtreat", "Year", "blockID", "turfID","Temperature_level",  "Precipitation_level", "destBlockID", "recorder", "notbad", "destSiteID")])
cover.meta <- cover.meta[order(paste(cover.meta$turfID, cover.meta$Year)),]
cover.meta$TTtreat <- factor(as.character(cover.meta$TTtreat), levels = c("TTC","TT1", "TT2", "TT3", "TT4"))

turfs <- cover.meta[!duplicated(cover.meta$turfID),]
turfs <- turfs[order(turfs$turfID),]

#verify
all(paste(cover.meta$turfID, cover.meta$Year, sep = "_") == rownames(cover))

#clear up
rm(cover.thin)
         
#set NID.seedling to  0/1
cover$NID.seedling <- ifelse(cover$NID.seedling > 0,1,0)
         
table(cover.meta$turfID, cover.meta$Year)   
table(cover.meta$Year, cover.meta$siteID, cover.meta$TTtreat)         
                                       
alltaxa<-TRUE
propertaxa <- !names(cover) %in% c("NID.seedling", "Car.sp", "Hie.sp", "Luz.sp", "NID.gram" , "NID.herb", "NID.rosett", "Pyr.sp")
noNIDseedlings <- !names(cover) %in% c("NID.seedling")

turfs$newTT <- turfs$TTtreat  #alternative TTtreat with combined controls
levels(turfs$newTT)[1:2] <- "control"