odb_organize_dataset: Organize ODBio datasets

In adalardo/Rppsp: R functions to manage permanent plot data (short line)

Organize ODBio datasets

Description

Organize data object from exported opendatabio datasets.

OpenDataBio datasets are exported as zip file containing several tabular data compressed files, with basic information about individuos (Organisms.csv), identification (Taxons.csv) and mapping (Locations.csv). If there is any measurements associated with the individual there is a file (MeasurementsOrFacts.csv) containing those measurements. This function organize those mesaruments in an format that is used by CTFS/FoestGEO network.

Usage

odb_organize_dataset(path = getwd())

Arguments

dirPath

directory address with the uncompressed files exported from openDataBio datasets.

Value

'odbData' returns a data frame organized as CTFS\/ForestGEO format.and a

Author(s)

Alexandre Adalardo de Oliveira [e-mail]

See Also

data.frame http://labtrop.ib.usp.br

Examples

## Not run: 
dir.create(".Rtmp")
species <- paste("species", 1:10, sep = "_")
family <-  paste("family", 1:10, sep = "_")
spOrder <- sample(1:10, size = 100, replace = TRUE)
x <- sample(seq(0.1, 19.9, by =0.1), size = 100, replace = TRUE)
y <- sample(seq(0.1, 19.9, by =0.1), size = 100, replace = TRUE)
quads <- subplotXY(xcode = LETTERS[1:3], ycode = paste("0", 0:2, sep = "")) 
locationName <- sample(quads$subplot, size =100, replace= TRUE)
ordLoc <- match(locationName, quads$subplot)
gx <- x + quads$xlim[ordLoc] 
gy <- y + quads$ylim[ordLoc]
recordNumber = sample(1:10000, size = 100)

write.table(x = data.frame(id = 1:100,
                           recordNumber,  
                           organismID = paste(recordNumber,"-USER-", locationName, sep = ""),
                           scientificName = species[spOrder],
                           family = family[spOrder],
                           locationName = locationName,
                           locationParentName = "paradisePlot",
                           decimalLatitude =NA,
                           decimalLongitude = NA,
                           x = x,
                           y = y,
                           gx = gx,
                           gy = gy,
                           datasetName = "imaginationPlot"),
            file =".Rtmp/.testOrganisms.csv", sep = ",", row.names = FALSE)
dap <- exp(rnorm(100, mean = 3.68, sd = 0.91))
dap[dap > 10100]<- 64
dap[dap < 10]<- 10
dap <- round(dap)
alt <- exp(-0.73 + 0.63* log(dap) + rnorm(100, 0, 0.35))
alt <- round(alt, 1)

write.table(data.frame(id = 1:200,
                       measured_id = c(1:100, 1:100),
                       measurementType = rep(c("dbh", "height"), each = 100),
                       measurementValue = c(dap, alt),
                       measurementDeterminedDate = "2019-01-10",
                       resourceRelationshipID = paste(recordNumber,"-USER-", locationName, sep = ""),
                       datasetName = "imaginationPlot" ),
            ".Rtmp/.testMeasurementsOrFacts.csv", sep = ",", row.names = FALSE)
dataForestGEO <- odb_organize_dataset(path = ".Rtmp")
str(dataForestGeo)
unlink(""

## End(Not run)

adalardo/Rppsp documentation built on Sept. 17, 2022, 3:42 a.m.