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updateMongoDB.R
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updateMongoDB.R
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# # uncomment 544 for taxize function
#
# Leave the 3-19 lines commented!
# library(rgdal); library(raster); library(RMySQL); library(rgeos); library(mongolite); library(httr); library(lubridate)
# conMSQ <<- dbConnect(dbDriver("MySQL"), user = "root", password = "root", dbname = "col2015ac", host = "localhost")
# mongoConectRec <<- mongo(db = "records", collection = "records", url ="mongodb://192.168.11.81:27017", verbose = FALSE)
# mongoConectSpe <<- mongo(db = "records", collection = "species", url ="mongodb://192.168.11.81:27017", verbose = FALSE)
# iucnShapes <- read.csv('D:/dbDownload/nwDB/spp&TaxonomyCol2015.csv', as.is = TRUE)
# iucnShapesPath <- 'D:/dbDownload/nwDB/bySppClipCol_UTM'
# load('D:/dbDownload/CIT_IUCN_END_INV_tables.RData')
# load('D:/dbDownload/climaticNE.RData')
# prjUTM <- "+proj=utm +zone=18 +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0"
# load('D:/dbDownload/verifGeoMongo.RData')
# load('D:/dbDownload/nwDB/TAXnwDb.RData')
# id <<- raster('D:/dbDownload/nwDB/aoiId.tif')
# aoi <- readOGR('D:/dbDownload/nwDB', 'aoi', verbose = FALSE)
# tstdat <- read.csv('D:/dbDownload/nwDB/uploadsPath/Zamias2017/Zamias2017.csv', as.is = TRUE)
# record <- tstdat[1, ]
# source('D:/dbDownload/nwDB/updateMongoDB.R')
## Functions -----
updateMongoDB <- function(record, aoi, .PrivateData = 0, onlySp = FALSE,
.tempTaxValidation, .tempDirRecords, .dupDirRecords, .update = TRUE){
# .PrivateData = 0; .update = TRUE; onlySp = TRUE
# rec <- .recT <- origRec <- record
# rec <- .recT <- origRec <- record <- data.frame(species = 'Ateles hybridus', acceptedNameUsage = 'Ateles hybridus', country = 'CO', lat = 4, lon = -70,stringsAsFactors=F)
## Take the original record and structure it using some parameters
formRecord <- formatRecord(rec = record, aoi, .privateData = .PrivateData, fr.onlySp = onlySp)
## Check if species is not accepted and save it and the record in a temporal folder
if (is.na(formRecord$acceptedNameUsage) | formRecord$acceptedNameUsage == ''){
currSpe2Validate <- list.files(path = .tempDirManualTaxValidation, pattern = '.csv')
csvFiles <- gsub('.csv', '', currSpe2Validate)
if(!formRecord$species %in% csvFiles){
taxRec <- formRecord[, c('species', 'speciesOriginal', 'kingdom', 'phylum',
'class', 'order', 'family', 'acceptedNameUsage')]
write.csv(taxRec, paste0(.tempDirManualTaxValidation, '/', formRecord$species,'.csv'), row.names = FALSE, na = '')
}
write.csv(formRecord, paste0(.tempDirRecords, '/', formRecord$species,'-', basename(tempfile(formRecord$species)),'.csv'), row.names = FALSE, na = '')
cat(formRecord$species, ' saved in temporal records and taxonimc folder ')
## If species exist then the record is uploaded into mongoDB
} else {
existsID <- specAlreadyInDb(rec = formRecord)[1]
## Is the species new in mongoDB? If not then add it
if (is.logical(existsID) & existsID == FALSE){
formRecord$taxID <- (mongoConectSpe$count() + 1)
if (.update == TRUE){
formRecord$consecutivoID <- (mongoConectSpe$count() + 1)
updateSpeciesTable2(rec = formRecord)
cat(formRecord$species, 'upload in species table')
} else{
cat(formRecord$species, 'upload in species table (FAKE - change to .update = TRUE)')
}
} else {
formRecord$taxID <- existsID
}
if (is.data.frame(formRecord)){
if(.update == TRUE & onlySp == FALSE){
if(formRecord$dbDuplicate == FALSE) {
formRecord$consecutivoID <- (mongoConectRec$count() + 1)
updateRecordsTable2(rec = formRecord)
cat(' - ', formRecord$species, 'upload in records table ')
} else {
write.csv(formRecord, paste0(.dupDirRecords, '/', formRecord$species,'-', basename(tempfile(formRecord$species)),'.csv'), row.names = FALSE, na = '')
cat(formRecord$species, ' saved in temporal records and taxonimc folder ')
}
} else {
cat(' - ', formRecord$species, 'upload in records table (FAKE - change to .update = TRUE)')
}
}
cat(' Success! \n')
}
}
## Insert record in species table
updateSpeciesTable <- function(rec){
taxCols <- c('species', 'originalGenus', 'originalSpecificEpithet',
'taxonomicStatus', 'originalScientificNameID',
'scientificNameID', 'acceptedNameUsage', 'scientificNameAuthorship',
'kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'specificEpithet',
'nameAccordingTo', 'TaxVerifSource', 'sppInCol', 'speciesInCountry', 'validName',
'bmClass', 'invasive', 'endemic', 'iucn', 'cites', 'taxID', 'consecutivoID')
speciesTable <- rec[, taxCols]
speciesTable[1, is.na(speciesTable[1, ]) | speciesTable[1, ] == ''] <- 'NULL'
#mongoConectSpe <- mongo(db = 'records', collection = 'species', url = 'mongodb://192.168.11.81:27017', verbose = FALSE)
mongoConectSpe$insert(speciesTable)
}
## Insert record in records table
updateRecordsTable <- function(rec){
taxCols <- c('species', 'originalGenus', 'originalSpecificEpithet',
'taxonomicStatus', 'originalScientificNameID',
'scientificNameID', 'acceptedNameUsage', 'scientificNameAuthorship',
'kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'specificEpithet',
'nameAccordingTo', 'TaxVerifSource', 'sppInCol', 'speciesInCountry', 'validName', 'taxID', 'consecutivoID')
recordsTable <- rec[, c('species', 'acceptedNameUsage', 'taxID', 'consecutivoID', colnames(rec)[!(colnames(rec) %in% taxCols)])]
recordsTable[1, is.na(recordsTable[1, ]) | recordsTable[1, ] == ''] <- 'NULL'
colnames(recordsTable)[grep('collection', colnames(recordsTable))] <- 'colection'
#mongoConectRec <- mongo(db = "records", collection = "records", url = "mongodb://192.168.11.81:27017", verbose = FALSE)
mongoConectRec$insert(recordsTable)
}
## Insert record in species table v2
updateSpeciesTable2 <- function(rec){
taxCols <- c("species" ,"taxonomicStatus", "acceptedNameUsage", "scientificNameAuthorship",
"kingdom", "phylum", "class", "order",
"family", "genus", "specificEpithet", "nameAccordingTo",
"TaxVerifSource", "sppInCol", "speciesInCountry", "validName",
"bmClass", "invasive", "endemic", "iucn",
"cites", "taxID", "migratoryType")
speciesTable <- rec[, taxCols]
speciesTable[1, is.na(speciesTable[1, ]) | speciesTable[1, ] == ''] <- 'NULL'
mongoConectSpe$insert(speciesTable)
}
## Insert record in records table v2
updateRecordsTable2 <- function(rec){
excCols <- c("taxonomicStatus", "scientificNameAuthorship",
"specificEpithet", "nameAccordingTo", "TaxVerifSource",
"kingdom", "phylum", "class", "order", "family", "genus",
"sppInCol", "speciesInCountry", "validName",
"bmClass", "invasive", "endemic", "iucn", "cites", "migratoryType",
"consecutivoID", "otherID", "withLat", "withLon", "recSizeBytes", "bigSizeRecord",
"hasTaxDoubt", "privateDataset", "tmpTax", "tmpGeo")
recordsTable <- rec[, setdiff(colnames(rec), excCols)]
recordsTable[1, is.na(recordsTable[1, ]) | recordsTable[1, ] == ''] <- 'NULL'
colnames(recordsTable)[grep('collection', colnames(recordsTable))] <- 'colection'
mongoConectRec$insert(recordsTable)
}
## Chek if the species alredy exists in mongoDB
specAlreadyInDb <- function(rec){
dbTaxFields <- c('species', 'originalGenus', 'originalSpecificEpithet',
'taxonomicStatus', 'originalScientificNameID',
'scientificNameID', 'acceptedNameUsage', 'scientificNameAuthorship',
'kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'specificEpithet',
'nameAccordingTo', 'TaxVerifSource', 'sppInCol', 'speciesInCountry', 'validName')
mongoQ <- paste0('{"$or":[{"species":"', rec$species, '"}, {"acceptedNameUsage":"', rec$species,
'"}, {"species":"', rec$acceptedNameUsage, '", "acceptedNameUsage":"', rec$acceptedNameUsage, '"}]}')
mongoCount <- mongoConectSpe$count(mongoQ)
if (mongoCount == 0){
return(FALSE)
} else if (mongoCount != 0){
return(mongoConectSpe$find(mongoQ)$taxID)
}
}
## Format the original record
formatRecord <- function(rec, aoi, .privateData = .privateData, .override = FALSE, .url = '', fr.onlySp = FALSE,
.visualizationPrivileges = 0, .privateDataset = 0,
.tmpTax = 1, .tmpGeo = 1, .contributedRecord = FALSE){
#.privateData = 0; .override = 0; .url = ''; .visualizationPrivileges = 0; .privateDataset = 0; .tmpTax = 1; .tmpGeo = 1; .contributedRecord = FALSE
# fr.onlySp = TRUE
# rec <- .recT <- origRec <- record
# Taxonomic and requierd Cols for script. NA is given if is absent
taxCols <- c('kingdom', 'phylum', 'class', 'order', 'family')
reqCols <- c("source", "occurrenceID", "species", "speciesOriginal", "continent",
"country", "adm1", "adm2", "locality","lat",
"lon","coordUncertaintyM", "alt","institution", "collection",
"catalogNumber", "basisOfRecord", "collector", "earliestDateCollected",
"latestDateCollected", "downloadDate", "resourceName", "resourceFolder","resourceIncorporationDate",
"privateData", "otherID")
## Create new formated record
if (is.null(rec$speciesOriginal)) rec$speciesOriginal <- rec$species
nwRec <- nwRecFun(.rec = rec, .reqCols = reqCols)
nwRec[, c('lat', 'lon')] <- sapply(nwRec[, c('lat', 'lon')], as.numeric)
# 1 Incomplet coords ----
if(is.na(nwRec$lat) | is.na(nwRec$lon)) {
message('Incomplete coordinates!')
nwRec$lon <- nwRec$lat <- 0
stop('Incomplete coordinates!')
} else {
# 2 Coords in aoi ----
if(!(nwRec$lon > extent(aoi)@xmin & nwRec$lon < extent(aoi)@xmax &
nwRec$lat > extent(aoi)@ymin & nwRec$lat < extent(aoi)@ymax)){
message('Coordinates outside region of interest!')
stop('Coordinates outside region of interest!')
}
}
# Taxonomic validation ----
nwRec$species <- cleanSciNames(y = nwRec$species)
nwRec <- taxValidation(.recT = nwRec, origRec = rec) # .recT = nwRec; origRec = rec
if (fr.onlySp == FALSE ){
# Geographical validation ----
#nwRec <- withCoords(.recG = nwRec)
validCountry <- geoValidationCountry(.recG = nwRec)
nwRec <- validCountry$nwRec
validState <- geoValidationState(.recG = nwRec)
nwRec <- validState$nwRec
validCounty <- geoValidationCounty(.recG = nwRec)
nwRec <- validCounty$nwRec
nwRec$sourceLayer <- paste0(validCountry$sourceLayer, ' - ', validState$sourceLayer, ' - ',
validCounty$sourceLayer) #32
nwRec <- geoValidationMunicipality(.recG = nwRec)
}
# Spp in Colombia
nwRec <- sppInCol(.rec = nwRec)
nwRec <- speciesInCountry(.rec = nwRec)
# Record size
nwRec <- sizeBytes(.rec = nwRec)
if (fr.onlySp == FALSE ){
# db Duplicated
nwRec <- dbDuplicate(.rec = nwRec)
if (nwRec$dbDuplicate == TRUE){
message('Record duplicated inside the current data base. Catalog number and collection code values already registered')
}
# Uncertanity
nwRec <- uncertanity(.rec = nwRec, thresh = 5000)
}
# Valid name
nwRec <- validName(.rec = nwRec)
# Taxonomic doubt
nwRec <- hasTaxDoubt(.rec = nwRec)
if (fr.onlySp == FALSE ){
# Has locality
nwRec <- hasLocality(.rec = nwRec)
# Record in urban area
nwRec <- inUrbanArea(.rec = nwRec)
# Pixel ID y spatial duplicated
nwRec <- cellID(.rec = nwRec)
nwRec <- spatialDuplicated(.rec = nwRec)
# URL
nwRec <- url(.rec = nwRec, origRec = rec)
# Dates
nwRec <- dates(.rec = nwRec)
# Override
nwRec$override <- .override
# Visualization privileges in Biomodelos
nwRec$visualizationPrivileges <- .visualizationPrivileges
# contributedRecord
nwRec$contributedRecord <- .contributedRecord
# Inside known distribution of IUCN
nwRec <- insideKnownDistribution(.rec = nwRec)
# Get elevation from coordinates and google API
nwRec <- demAltitude(.rec = nwRec)
nwRec <- interpretedElevation(.rec = nwRec, .rule = 'mean')
nwRec$altitudinalOutlier <- nwRec$consistentAltitude <- nwRec$diferenceInAltitude <- nwRec$environmentalOutlier <- NA
# nwRec <- altitudinalOutlier(.rec = nwRec)
# nwRec <- environmentalOutlier(.rec = nwRec)
# nwRec <- consistentAltitude(.rec = nwRec)
# nwRec <- diferenceInAltitude(.rec = nwRec)
nwRec$privateDataset <- .privateDataset
nwRec <- tmpTax(.rec = nwRec, tmpTax = .tmpTax)
nwRec <- tmpGeo(.rec = nwRec, tmpGeo = .tmpGeo)
nwRec <- Use(.rec = nwRec)
}
nwRec <- sppCateg(.rec = nwRec)
return(nwRec)
}
# <- function(.rec){
# return(nwRec = .rec)
# }
sppCateg <- function(.rec){
.rec$bmClass <- .rec$iucn <- .rec$cites <- ''
.rec$invasive <- .rec$endemic <- FALSE
.rec$bmClass[grep('Mammalia', .rec$class)] <- 'Mamíferos'
.rec$bmClass[grep('Amphibia', .rec$class)] <- 'Anfibios'
.rec$bmClass[grep('Reptilia', .rec$class)] <- 'Reptiles'
.rec$bmClass[grep('Aves', .rec$class)] <- 'Aves'
.rec$bmClass[
grep('Actinopterygii|Myxini|^Characiformes$|^Siluriformes$|^Perciformes$|^Gymnotiformes$|^Cyprinodontiformes$|^Clupeiformes$|^Myliobatiformes$|^Pleuronectiformes$|^Beloniformes$|^Batrachoidiformes$|^Osteoglossiformes$|^Lepidosireniformes$|^Synbranchiformes$|^Tetraodontiformes$',
.rec$class)] <- 'Peces'
.rec$bmClass[grep('Plantae', .rec$kingdom)] <- 'Plantas'
.rec$bmClass[grep('Arthropoda|Mollusca', .rec$phylum)] <- 'Invertebrados'
# Invasive
.rec$invasive[.rec$acceptedNameUsage %in% inv] <- TRUE
if (.rec$invasive == FALSE){
.rec$invasive[.rec$species %in% inv] <- TRUE
}
.rec$endemic[.rec$acceptedNameUsage %in% end] <- TRUE
if (.rec$endemic == FALSE){
.rec$endemic[.rec$species %in% end] <- TRUE
}
iuPos <- any(.rec$acceptedNameUsage %in% iuc$acceptedNameUsage)
if (iuPos){
.rec$iucn <- iuc$Red.List.status[iuc$acceptedNameUsage %in% .rec$acceptedNameUsage][1]
} else {
iuPos <- any(.rec$acceptedNameUsage %in% iuc$sciName)
if (iuPos){
.rec$iucn <- iuc$Red.List.status[iuc$sciName %in% .rec$acceptedNameUsage][1]
} else {
iuPos <- any(.rec$species %in% iuc$acceptedNameUsage)
if (iuPos){
.rec$iucn <- iuc$Red.List.status[iuc$acceptedNameUsage %in% .rec$species][1]
} else {
iuPos <- any(.rec$species %in% iuc$sciName)
if (iuPos){
.rec$iucn <- iuc$Red.List.status[iuc$sciName %in% .rec$species][1]
}
}
}
}
citPos <- any(.rec$acceptedNameUsage %in% na.omit(cit$acceptedNameUsage))
if (citPos){
.rec$cites <- cit$CurrentListing[cit$acceptedNameUsage %in% .rec$acceptedNameUsage][1]
} else {
citPos <- any(.rec$acceptedNameUsage %in% cit$FullName)
if (citPos){
.rec$cites <- cit$CurrentListing[cit$FullName %in% .rec$acceptedNameUsage][1]
} else {
citPos <- any(.rec$species %in% cit$acceptedNameUsage)
if (citPos){
.rec$cites <- cit$CurrentListing[cit$acceptedNameUsage %in% .rec$species][1]
} else {
citPos <- any(.rec$species %in% cit$FullName)
if (citPos){
.rec$cites <- cit$CurrentListing[cit$FullName %in% .rec$species][1]
}
}
}
}
.rec$migratoryType <- NA
return(nwRec = .rec)
}
dates <- function(.rec){
.rec$earliestDateCollected <- ifelse(.rec$earliestDateCollected == '', NA, .rec$earliestDateCollected)
.rec$latestDateCollected <- ifelse(.rec$latestDateCollected == '', NA, .rec$latestDateCollected)
nwDate <- na.omit(c(.rec$earliestDateCollected, .rec$latestDateCollected))[1]
nwDate <- parse_date_time(nwDate, c("Y-m-d HMS", "dbY HMS", "dmyHMS", "BdY H", 'y', "Ymd", "mdY", 'dmY'))
.rec$yyyy <- year(nwDate)
.rec$mm <- month(nwDate)
.rec$dd <- day(nwDate)
return(nwRec = .rec)
}
tmpGeo <- function(.rec, tmpGeo){
.rec$tmpGeo <- tmpGeo
return(nwRec = .rec)
}
tmpTax <- function(.rec, tmpTax){
.rec$tmpTax <- tmpTax
return(nwRec = .rec)
}
altitudinalOutlier <- function(.rec){
.rec$altitudinalOutlier <- FALSE
return(nwRec = .rec)
}
environmentalOutlier <- function(.rec){
.rec$environmentalOutlier <- NA
mongoQ <- ifelse(is.na(.rec$acceptedNameUsage),
paste0('{"$or":[{"species":"', .rec$species, '"}, {"acceptedNameUsage":"', .rec$species, '"}]}'),
paste0('{"$or":[{"species":"', .rec$species, '"}, {"acceptedNameUsage":"', .rec$species,
'"}, {"species":"', .rec$acceptedNameUsage, '", "acceptedNameUsage":"', .rec$acceptedNameUsage, '"}]}'))
mongoTable <- mongoConectRec$find(mongoQ, fields = '{"_id" : 0, "lat" : 1, "lon" : 1, "dbDuplicate" : 1}')
head(mongoTable)
if (nrow(mongoTable) >= 9){
dat <- rbind(mongoTable, .rec[, c('lat', 'lon', 'dbDuplicate')])
coordSpatial <- SpatialPoints(dat[, c(2:1)], proj4string = CRS("+proj=longlat +datum=WGS84"))
extVals <- raster::extract(layNE, coordSpatial)
envOut <- apply(extVals, 2, FUN = function(x) {
apply(outliersIG(rid = 1:nrow(dat), species = rep('SP', nrow(dat)), dups = dat[, 3], ev = x), 1, function(x) any(x) * 1)
})
.rec$environmentalOutlierLayer <- NA
if( any(tail(envOut, 1) == 1)) {
.rec$environmentalOutlier <- TRUE
.rec$environmentalOutlierLayer <- paste0(colnames(envOut)[which(tail(envOut, 1) == 1)], collapse = '-')
}
}
return(nwRec = .rec)
}
outliersIG <- function(rid, species, dups, ev){
# rid = .datenv$ID; species = .datenv$Species; dups = rep(0, nrow(.datenv)); ev = x
# rid = rid; species = cid2$Species; dups = cid2$dups; ev = env[, i]
uspp <- unique(species)
nr <- length(species)
ee <- rep(0, nr)
ee2 <- rep(0, nr)
for (j in 1:length(uspp)) {
spp <- uspp[j]
fsp <- which(species == spp & dups == 0 & !is.na(ev))
if (length(fsp) >= 10) {
xc <- ev[fsp] # datos seleccionados para especie
ri <- rid[fsp] # ids de los datos
b1 <- boxplot.stats(xc, coef = 1.5)
xr <- range(b1$stats)
fe <- which(xc > xr[2] | xc < xr[1]) # posicion de datos y ID fuera de rango m1
fe2 <- rjackIG(d = xc) # posicion de datos y ID fuera de rango m2
ff1 <- which(rid %in% ri[fe])
ff2 <- which(rid %in% ri[fe2])
if (any(ff1)) ee[ff1] <- 1
if (any(ff2)) ee2[ff2] <- 1
}
}
out <- cbind(ee, ee2)
return(out)
}
rjackIG <- function (d) {
xx <- d
d <- unique(d)
mx <- mean(d)
n <- length(d)
n1 <- n - 1
t1 <- (0.95 * sqrt(n)) + 0.2
x <- sort(d)
y <- rep(0, n1)
for (i in 1:n1) {
x1 <- x[i + 1]
if (x[i] < mx) {
y[i] <- (x1 - x[i]) * (mx - x[i])
}
else {
y[i] <- (x1 - x[i]) * (x1 - mx)
}
}
my <- mean(y)
z <- y/(sqrt(sum((y - my)^2)/n1))
out <- rep(0, length(xx))
if (any(z > t1)) {
f <- which(z > t1)
v <- x[f]
if (v < median(x)) {
xa <- (xx <= v) * 1
out <- out + xa
}
if (v > median(x)) {
xb <- (xx >= v) * 1
out <- out + xb
}
} else {
out <- out
}
#return(out)
return(which(out == 1))
}
demAltitude <- function(.rec){
.rec$demAltitude <- NA
latOk <- ifelse(abs(.rec$lat) > 90 | is.na(.rec$lat) | .rec$lat == 0, 0, 1)
lonOk <- ifelse(abs(.rec$lon) > 180 | is.na(.rec$lon) | .rec$lon == 0, 0, 1)
if(latOk & lonOk){
url <- paste0("https://maps.googleapis.com/maps/api/elevation/json?locations=",
.rec$lat, ',', .rec$lon, "&key=AIzaSyAz6sPnMLuIJrOWvNKnn6-PWYK56PDGa30")
elev <- GET(url)
elevChar <- as.character(elev)
if(any(grep('You have exceeded your daily', elevChar))){
.rec$demAltitude <- -9999
} else{
elev2 <- strsplit(elevChar, ' ')[[1]]
elev3 <- elev2[grep('elev', elev2) + 2]
finPos <- regexec(pattern = '\\,', elev3)[[1]]
elev <- substr(elev3, 0, finPos - 1)
.rec$demAltitude <- as.numeric(elev)
}
return(nwRec = .rec)
}
}
Use <- function(.rec){
toUse <- which(.rec$withLat== 1 & .rec$withLon == 1,
.rec$sppInCol == 1 & .rec$speciesInCountry == TRUE &
.rec$tmpTax == 1 & .rec$tmpGeo == 1 &
.rec$bigSizeRecord == 0 &
.rec$dbDuplicate == FALSE & .rec$spatialDuplicated == FALSE &
.rec$lowUncertainty == 0 &
.rec$hasLocality == TRUE &
.rec$hasTaxDoubt == 0 &
.rec$override == FALSE )
.rec$use <- ifelse(length(toUse) == 0, 0, 1)
return (nwRec = .rec)
}
url <- function(.rec, origRec){
origRec$url <- ifelse(is.null(origRec$url), NA, as.character(origRec$url))
if (origRec$url == '' | is.na(origRec$url)){
.rec$url <- NA
} else {
if(!any(grep('@', origRec$url)) ){
.rec$url <- ifelse(GET(origRec$url)$status == 200, origRec$url, NA)
}
}
return (nwRec = .rec)
}
consistentAltitude <- function(.rec){
.rec$consistentAltitude <- FALSE
return(nwRec = .rec)
}
diferenceInAltitude <- function(.rec){
.rec$diferenceInAltitude <- NA
return(nwRec = .rec)
}
#oSpec <- .rec$species; .rec$species <- 'Ateles hybridus'
insideKnownDistribution <- function(.rec){
.rec$insideKnownDistribution <- FALSE
.rec$dist2KnowRange <- NA
#return(nwRec = .rec) # comment when uncoment the other
if(.rec$lat != 0 & .rec$lon != 0 & !is.na(.rec$lat) & !is.na(.rec$lon)){
availableMap <- c(.rec$species, .rec$acceptedNameUsage) %in%
unique(na.omit(c(iucnShapes$iucnShapes, iucnShapes$acceptedNameUsage)))
if (any(availableMap)){
spIucn <- which(iucnShapes$acceptedNameUsage %in% c(.rec$species, .rec$acceptedNameUsage))
spIucn2 <- which(iucnShapes$iucnShapes %in% c(.rec$species, .rec$acceptedNameUsage))
if (any(spIucn)){
field2Load <- c(.rec$acceptedNameUsage, .rec$species) %in% iucnShapes$iucnShapes[spIucn]
field2Load2 <- c(.rec$acceptedNameUsage, .rec$species)[field2Load][1]
iucnShape <- readOGR(iucnShapesPath, field2Load2, verbose = FALSE)
} else if(!any(spIucn) & any(spIucn2)) {
field2Load <- c(.rec$acceptedNameUsage, .rec$species) %in% iucnShapes$acceptedNameUsage[spIucn]
field2Load2 <- c(.rec$acceptedNameUsage, .rec$species)[field2Load][1]
iucnShape <- readOGR(iucnShapesPath, field2Load2, verbose = FALSE)
}
coords <- .rec
coordinates(coords) =~ lon + lat
coords@proj4string@projargs <- "+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0"
coords <- spTransform(coords, CRSobj = CRS(prjUTM))
if(iucnShape@proj4string@projargs != prjUTM){
iucnShape <- spTransform(iucnShape, CRSobj = CRS(prjUTM))
}
over <- over(coords, iucnShape)
if (is.na(over$id_no)){
.rec$dist2KnowRange <- gDistance(iucnShape, coords)
return(nwRec = .rec)
} else if(!is.na(over$id_no)){
.rec$insideKnownDistribution <- TRUE
.rec$dist2KnowRange <- 0
return(nwRec = .rec)
}
} else {
return(nwRec = .rec)
}
} else {
return(nwRec = .rec)
}
}
spatialDuplicated <- function(.rec){
## Reemplazar 'speciesOriginal' por 'species'
#mongoConectRec <- mongo(db = 'records', collection = 'records', url='mongodb://192.168.11.81:27017', verbose = FALSE)
.rec$spatialDuplicated <- FALSE
latOk <- ifelse(abs(.rec$lat > 180) | is.na(.rec$lat) | .rec$lat == 0, 0, 1)
lonOk <- ifelse(abs(.rec$lon > 180) | is.na(.rec$lon) | .rec$lon == 0, 0, 1)
if(latOk & lonOk){
mongoQ <- ifelse(is.na(.rec$acceptedNameUsage),
paste0('{"$or":[{"species":"', .rec$species, '"}, {"acceptedNameUsage":"', .rec$species, '"}]}'),
paste0('{"$or":[{"species":"', .rec$species, '"}, {"acceptedNameUsage":"', .rec$species,
'"}, {"species":"', .rec$acceptedNameUsage, '", "acceptedNameUsage":"', .rec$acceptedNameUsage, '"}]}'))
mongoTable <- mongoConectRec$find(mongoQ)
#mongoConectRec$count(mongoQ)
#mongoTable$catalogNumber
if (nrow(mongoTable) != 0){
recInDb <- mongoTable[, c('cellID', 'species', 'acceptedNameUsage', 'correctCounty')]
indDup <- paste0(recInDb$acceptedNameUsage, '-', recInDb$cellID, '_', recInDb$correctCounty)
indDup2 <- paste0(recInDb$species, '-', recInDb$cellID, '_', recInDb$correctCounty)
isSpatialDup <- ifelse(is.na(.rec$acceptedNameUsage),
paste0(.rec$species, '-', .rec$cellID, '_', .rec$correctCounty) %in% indDup2,
paste0(.rec$acceptedNameUsage, '-', .rec$cellID, '_', .rec$correctCounty) %in% indDup)
.rec$spatialDuplicated <- ifelse(isSpatialDup == TRUE, TRUE, FALSE)
}
}
return(nwRec = .rec)
}
cellID <- function(.rec){
.rec$cellID <- 0
latOk <- ifelse(abs(.rec$lat > 180) | is.na(.rec$lat) | .rec$lat == 0, 0, 1)
lonOk <- ifelse(abs(.rec$lon > 180) | is.na(.rec$lon) | .rec$lon == 0, 0, 1)
if(latOk & lonOk){
coords <- .rec
coordinates(coords) =~ lon + lat
.rec$cellID <- raster::extract(id, coords)
}
return(nwRec = .rec)
}
inUrbanArea <- function(.rec){
.rec$inUrbanArea <- ifelse(is.na(.rec$suggestedMunicipality), FALSE, TRUE)
return(nwRec = .rec)
}
hasLocality <- function(.rec){
.rec$hasLocality <- ifelse(is.na(.rec$locality) | .rec$locality == '', FALSE, TRUE)
return(nwRec = .rec)
}
hasTaxDoubt<- function(.rec){
.rec$hasTaxDoubt <- 0
taxDoubdt <- grep(" cf\\. | cf |\\?| aff | sp\\.| sp\\. | sp | aff\\. | affin\\. | aff | affin | sp$",
.rec$speciesOriginal)
.rec$hasTaxDoubt[taxDoubdt] <- 1
return(nwRec = .rec)
}
validName <- function(.rec){
binom <- grep(' ', .rec$species)
.rec$validName <- ifelse(is.na(.rec$acceptedNameUsage) | length(binom) == 0, FALSE, TRUE)
return(nwRec = .rec)
}
interpretedElevation <- function(.rec, .rule = 'mean'){
sep <- grep('-|/', .rec$alt)
if (any(sep)){
sepAlts <- as.numeric(strsplit(.rec$alt, '-|/')[[1]])
if(.rule == 'mean') .rec$interpretedElevation <- mean(sepAlts)
if(.rule == 'max') .rec$interpretedElevation <- max(sepAlts)
if(.rule == 'min') .rec$interpretedElevation <- min(sepAlts)
} else {
.rec$interpretedElevation <- as.numeric(gsub('[[:alpha:]]', '', .rec$alt))
}
return(nwRec = .rec)
}
uncertanity <- function(.rec, thresh = 5000){
numUnc <- as.numeric(gsub('[[:alpha:]]', '', .rec$coordUncertaintyM))
feet <- grep('f', .rec$coordUncertaintyM)
if (any(feet)){
.rec$numUnc[feet] <- .rec$numUnc[feet] * .3048
}
.rec$lowUncertainty <- ifelse(numUnc >= 5000, TRUE, FALSE)
#.rec$lowUncertainty <- ifelse(is.na(numUnc), FALSE, .rec$lowUncertainty)
return(nwRec = .rec)
}
dbDuplicate <- function(.rec){
.rec$dbDuplicate <- FALSE
# .rec$collection <- 'IAvH-M'
# .rec$catalogNumber <- 421
#mongoConectRec <- mongo(db = 'records', collection= 'records', url='mongodb://192.168.11.81:27017', verbose = FALSE)
dup <- paste0(.rec$acceptedNameUsage, '__', .rec$collection, '--', .rec$catalogNumber)
naCases <- '^NA
02__|^__|__NA--|__--|--$|--NA$'
naValue <- grep(naCases, dup)
if(!any(naValue)){
mongoQ <- ifelse(is.na(.rec$acceptedNameUsage) | .rec$acceptedNameUsage == '',
paste0('{"species":"', .rec$species, '", "acceptedNameUsage":"', .rec$species, '"}'),
paste0('{"species":"', .rec$acceptedNameUsage, '", "acceptedNameUsage":"', .rec$acceptedNameUsage, '"}'))
mongoTable <- mongoConectRec$find(mongoQ)
if (nrow(mongoTable) != 0){
recSppInDb <- mongoTable[, c('colection', 'catalogNumber')]
indDup <- paste(recSppInDb$colection, recSppInDb$catalogNumber, sep ="-")
indDup <- gsub("^NA-NA$|^-$|^-NA$|^NA-$", '', indDup)
dup <- paste0(.rec$colection, '-', .rec$catalogNumber)
dupInd <- which(dup %in% indDup)
.rec$dbDuplicate[dupInd] <- TRUE
}
}
return(nwRec = .rec)
}
sizeBytes <- function(.rec){
.rec$recSizeBytes <- as.numeric(object.size(.rec))
.rec$bigSizeRecord <- ifelse(.rec$recSizeBytes > 16000000, 1, 0)
return(nwRec = .rec)
}
speciesInCountry <- function(.rec){
.rec$speciesInCountry <- TRUE
return(nwRec = .rec)
}
sppInCol <- function(.rec){
.rec$sppInCol <- FALSE
#mongoConectSpe <- mongo(db = "records", collection = "species", url = "mongodb://192.168.11.81:27017", verbose = FALSE)
# Desde las coordenadas
sugg <- grep('Colombia', .rec$suggestedCountry)
validMun <- grep('CO', .rec$sourceLayer)
.rec$sppInCol[unique(c(sugg, validMun))] <- TRUE
rm(sugg, validMun)
# Desde el listado de especies (TAX de DINAVIS)
if(.rec$sppInCol == FALSE){
sp.Mongo <- mongoConectSpe$find('{"sppInCol":1}')
if(nrow(sp.Mongo) != 0){
mongoNames <- gsub(' ', '', na.omit(unique(c(sp.Mongo$species, sp.Mongo$acceptedNameUsage))))
sp.Mongo1 <- which(gsub(' ', '', .rec$species) %in% mongoNames)
sp.Mongo2 <- which(gsub(' ', '', .rec$speciesOriginal) %in% mongoNames)
sp.Mongo3 <- which(gsub(' ', '', .rec$acceptedNameUsage) %in% mongoNames)
sp.TAX1 <- which(gsub(' ', '', .rec$species) %in% TAXNames)
sp.TAX2 <- which(gsub(' ', '', .rec$speciesOriginal) %in% TAXNames)
sp.TAX3 <- which(gsub(' ', '', .rec$acceptedNameUsage) %in% TAXNames)
posSppTAX <- unique(c(sp.TAX1, sp.TAX2, sp.TAX3, sp.Mongo1, sp.Mongo2, sp.Mongo3))
.rec$sppInCol[posSppTAX] <- TRUE
}
}
return(nwRec = .rec)
}
geoValidationMunicipality <- function(.recG, .scriptMaxchar = .2){
coords <- .recG
coordinates(coords) =~ lon + lat
coords@proj4string@projargs <- "+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0"
ovMunicipality <- over(coords, casco)
.recG$suggestedMunicipality <- ovMunicipality$NOMBRE_GEO
return(nwRec = .recG)
}
nwRecFun <- function(.rec, .reqCols){
.nw <- data.frame(matrix(rep(NA, length(.reqCols)), ncol = length(.reqCols)), stringsAsFactors = FALSE)
colnames(.nw) <- .reqCols
commCols <- base::intersect(colnames(.nw), colnames(.rec))
.nw[, commCols] <- .rec[, commCols]
return(.nw)
}
taxValidation <- function(.recT, origRec){
#origRec$acceptedNameUsage <- .recT$species # for test
#mongoConectSpe <- mongo(db = "records", collection = "species", url = "mongodb://192.168.11.81:27017", verbose = FALSE)
mongoQ <- paste0('{"$or":[{"species":"', .recT$species, '"}, {"acceptedNameUsage":"', .recT$species, '"}]}')
mongoCount <- mongoConectSpe$count(mongoQ)
if(mongoCount != 0){
currentTax <- mongoConectSpe$find(mongoQ)[1, ]
#deleteMe <- mongoConectSpe$find()
.recT$originalGenus <- currentTax$originalGenus
.recT$originalSpecificEpithet <- currentTax$originalSpecificEpithet
.recT$taxonomicStatus <- currentTax$taxonomicStatus
.recT$originalScientificNameID <- currentTax$originalScientificNameID
.recT$scientificNameID <- currentTax$scientificNameID
.recT$acceptedNameUsage <- currentTax$acceptedNameUsage
.recT$scientificNameAuthorship <- currentTax$scientificNameAuthorship
.recT$kingdom <- currentTax$kingdom
.recT$phylum <- currentTax$phylum
.recT$class <- currentTax$class
.recT$order <- currentTax$order
.recT$family <- currentTax$family
.recT$genus <- currentTax$genus
.recT$specificEpithet <- currentTax$specificEpithet
.recT$nameAccordingTo <- currentTax$nameAccordingTo
.recT$TaxVerifSource <- currentTax$TaxVerifSource
} else if(mongoCount == 0){
#taxCols <- c('kingdom', 'phylum', 'class', 'order', 'family')
taxCols <- c('acceptedNameUsage')
haveAllTaxFields <- all(taxCols %in% colnames(origRec))
haveAllTaxFieldsFilled <- ifelse(haveAllTaxFields == TRUE,
all(origRec[, taxCols] != '' & !is.na(origRec[, taxCols])),
FALSE)
if(haveAllTaxFields & haveAllTaxFieldsFilled){
set1 <- data.frame(id = 1, nombre = .recT$species,
genero = strsplit(.recT$species, ' ')[[1]][1],
epiteto_especifico = strsplit(.recT$species, ' ')[[1]][2],
stringsAsFactors = FALSE)
set1 <- nameValidationGenus(con = conMSQ, inTable = set1) # 1.98 sec
set1$specificEpithet <- strsplit(.recT$species, ' ')[[1]][2]
set1$originalNameUsage <- NULL
.recT <- cbind(.recT, set1[, -c(1)])
.recT$TaxVerifSource <- ifelse(is.na(set1$acceptedNameUsage), NA, "Catalogue of Life 2015")
# .recT$originalGenus <- strsplit(.recT$species, ' ')[[1]][1]
# .recT$originalSpecificEpithet <- strsplit(.recT$species, ' ')[[1]][2]
.recT$originalSpecificEpithet <- strsplit(.recT$species, ' ')[[1]][2]
.recT$taxonomicStatus <- 'pending'
.recT$acceptedNameUsage <- origRec$acceptedNameUsage
# .recT$originalScientificNameID <- .recT$scientificNameID <- ''
# .recT$acceptedNameUsage <- .recT$species
# .recT$scientificNameAuthorship <- ''
# .recT$kingdom <- origRec$kingdom
# .recT$phylum <- origRec$phylum
# .recT$class <- origRec$class
# .recT$order <- origRec$order
# .recT$family <- origRec$family
# .recT$genus <- .recT$originalGenus
# .recT$specificEpithet <- .recT$originalSpecificEpithet
.recT$nameAccordingTo <- 'Record author'
.recT$TaxVerifSource <- 'Record author'
} else {
set1 <- data.frame(id = 1, nombre = .recT$species,
genero = strsplit(.recT$species, ' ')[[1]][1],
epiteto_especifico = strsplit(.recT$species, ' ')[[1]][2],
stringsAsFactors = FALSE)
set1 <- nameValidation2(con = conMSQ, inTable = set1) # 1.98 sec
set1$originalNameUsage <- NULL
.recT <- cbind(.recT, set1[, -c(1)])
.recT$TaxVerifSource <- ifelse(is.na(set1$acceptedNameUsage), NA, "Catalogue of Life 2015")
## Taxize
# if(is.na(set1$acceptedNameUsage)){
# require(taxize)
# dbs <- c("itis", "col", "tropicos", "eol", "ncbi")
# db <- 2
# for (db in 1:length(dbs)){
# class.db <- classification(nwRec$species, db = dbs[db])
# if (!is.logical(class.db[[1]])){
# taxize <- class.db[[1]]
# taxize <- taxize[taxize$rank %in% c("family", "order", "class", "phylum", "kingdom"), ]
# rankT <- taxize$rank
# taxize <- t(taxize$name)
# colnames(taxize) <- rankT
# .recT[, colnames(taxize)] <- taxize[, colnames(taxize)]
# .recT$TaxVerifSource <- dbs[db]
# .recT$acceptedNameUsage <- nwRec$species
# break
# }
# }
# }
#
## COL RST API | http://api.cybertaxonomy.org/col/name_catalogue/fuzzy.json?accuracy=0.1&hits=1&query=Ateles%2520hybridus
#
# if(is.na(set1$acceptedNameUsage)){
#
# .recT$originalGenus <- strsplit(.recT$species, ' ')[[1]][1]
# .recT$originalSpecificEpithet <- strsplit(.recT$species, ' ')[[1]][2]
# .recT$taxonomicStatus <- 'pending'
# .recT$originalScientificNameID <- .recT$scientificNameID <- ''
# .recT$acceptedNameUsage <- .recT$species
# .recT$scientificNameAuthorship <- ''
# .recT$kingdom <- origRec$kingdom
# .recT$phylum <- origRec$phylum
# .recT$class <- origRec$class
# .recT$order <- origRec$order
# .recT$family <- origRec$family
# .recT$genus <- .recT$originalGenus
# .recT$specificEpithet <- .recT$originalSpecificEpithet
# .recT$nameAccordingTo <- 'Record author'
# .recT$TaxVerifSource <- 'Record author'
# }
## The plant list
# taxVal <- TPL(.recT$species, corr=TRUE)
}
}
return(.recT)
}
withCoords <- function(.recG){
.recG$withLat <- ifelse(is.na(.recG$lat) | .recG$lat == 0, 0, 1)
.recG$withLon <- ifelse(is.na(.recG$lon) | .recG$lon == 0, 0, 1)
return(.recG)
}
geoValidationCountry <- function(.recG, .scriptMaxchar = .2){
validCou <- ifelse(.recG$country == '' |.recG$country == ' ' | is.na(.recG$country) , FALSE, TRUE)
if (!(validCou)){
.recG$correctCountry <- 0
.recG$suggestedCountry <- NA
return(list(nwRec = .recG, sourceLayer = NA))
} else {
coords <- .recG
coordinates(coords) =~ lon + lat
coords@proj4string@projargs <- "+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0"
over <- over(coords, paises)
corPai <- corroboracion(overPointsField = over$PAIS, dataField = .recG$country,
dataID = 1, maxchar = .scriptMaxchar)
if (corPai[[1]] == 0){
corPai[[1]] <- (.recG$country %in% c(over$ISO3, over$ISO2)) * 1
}
sourceLayer <- 'southAmerica'
suggCountry <- corPai[[3]]
if (corPai[[1]] == 0){
over <- over(coords, mpios2014)
corPai <- corroboracion(overPointsField = over$PAIS, dataField = .recG$country,
dataID = 1, maxchar = .scriptMaxchar)
if (corPai[[1]] == 0){
corPai[[1]] <- (.recG$country %in% c(over$ISO3, over$ISO2)) * 1
}
sourceLayer <- 'mpiosCol2014'
suggCountry <- corPai[[3]]
if (corPai[[1]] == 0){
over <- over(coords, mpios2011)
corPai <- corroboracion(overPointsField = over$PAIS, dataField = .recG$country,
dataID = 1, maxchar = .scriptMaxchar)
sourceLayer <- 'mpiosCol2011'
if (corPai[[1]] == 0){
corPai[[1]] <- (.recG$country %in% c(over$ISO3, over$ISO2)) * 1
}
if (corPai[[1]] == 0){
over <- over(coords, mpios2003)
corPai <- corroboracion(overPointsField = over$PAIS, dataField = .recG$country,
dataID = 1, maxchar = .scriptMaxchar)
sourceLayer <- 'mpiosCol2003'
if (corPai[[1]] == 0){
corPai[[1]] <- (.recG$country %in% c(over$ISO3, over$ISO2)) * 1
}
if (corPai[[1]] == 0){
over <- over(coords, mpios1993)
corPai <- corroboracion(overPointsField = over$PAIS, dataField = .recG$country,
dataID = 1, maxchar = .scriptMaxchar)
sourceLayer <- 'mpiosCol1993'
if (corPai[[1]] == 0){
corPai[[1]] <- (.recG$country %in% c(over$ISO3, over$ISO2)) * 1
}
if (corPai[[1]] == 0){
over <- over(coords, mpios1985)
corPai <- corroboracion(overPointsField = over$PAIS, dataField = .recG$country,
dataID = 1, maxchar = .scriptMaxchar)
sourceLayer <- 'mpiosCol1985'
if (corPai[[1]] == 0){
corPai[[1]] <- (.recG$country %in% c(over$ISO3, over$ISO2)) * 1
}
if (corPai[[1]] == 0){
over <- over(coords, mpios1973)
corPai <- corroboracion(overPointsField = over$PAIS, dataField = .recG$country,
dataID = 1, maxchar = .scriptMaxchar)
sourceLayer <- 'mpiosCol1973'
if (corPai[[1]] == 0){
corPai[[1]] <- (.recG$country %in% c(over$ISO3, over$ISO2)) * 1
}