ReconstructProbDup: Reconstruct an object of class ProbDup

In PGRdup: Discover Probable Duplicates in Plant Genetic Resources Collections

Reconstruct an object of class ProbDup

Description

ReconstructProbDup reconstructs a data frame of probable duplicate sets created using the function ReviewProbDup and subjected to manual clerical review, back into an object of class ProbDup.

Usage

ReconstructProbDup(rev)

Arguments

rev	A data frame with the the core columns(fields) SET_NO, TYPE, K, PRIM_ID, DEL, SPLIT, COUNT and IDKW

Details

A data frame created using the function ReviewProbDup from an object of class ProbDup for manual clerical review of identified probable duplicate sets can be reconstituted back to the same object after the review using this function. The instructions for modifying the sets entered in the appropriate format in the columns DEL and SPLIT during clerical review are taken into account for reconstituting the probable duplicate sets.

Any records with Y in column DEL are deleted and records with identical integers in the column SPLIT other than the default 0 are reassembled into a new set.

Value

An object of class ProbDup with the modified fuzzy, phonetic and semantic probable duplicate sets according to the instructions specified under clerical review.

See Also

ProbDup, ReviewProbDup

Examples

## Not run: 

# Load PGR passport database
GN <- GN1000

# Specify as a vector the database fields to be used
GNfields <- c("NationalID", "CollNo", "DonorID", "OtherID1", "OtherID2")

# Clean the data
GN[GNfields] <- lapply(GN[GNfields], function(x) DataClean(x))
y1 <- list(c("Gujarat", "Dwarf"), c("Castle", "Cary"), c("Small", "Japan"),
c("Big", "Japan"), c("Mani", "Blanco"), c("Uganda", "Erect"),
c("Mota", "Company"))
y2 <- c("Dark", "Light", "Small", "Improved", "Punjab", "SAM")
y3 <- c("Local", "Bold", "Cary", "Mutant", "Runner", "Giant", "No.",
        "Bunch", "Peanut")
GN[GNfields] <- lapply(GN[GNfields], function(x) MergeKW(x, y1, delim = c("space", "dash")))
GN[GNfields] <- lapply(GN[GNfields], function(x) MergePrefix(x, y2, delim = c("space", "dash")))
GN[GNfields] <- lapply(GN[GNfields], function(x) MergeSuffix(x, y3, delim = c("space", "dash")))

# Generate KWIC index
GNKWIC <- KWIC(GN, GNfields)

# Specify the exceptions as a vector
exep <- c("A", "B", "BIG", "BOLD", "BUNCH", "C", "COMPANY", "CULTURE", 
         "DARK", "E", "EARLY", "EC", "ERECT", "EXOTIC", "FLESH", "GROUNDNUT", 
         "GUTHUKAI", "IMPROVED", "K", "KUTHUKADAL", "KUTHUKAI", "LARGE", 
         "LIGHT", "LOCAL", "OF", "OVERO", "P", "PEANUT", "PURPLE", "R", 
         "RED", "RUNNER", "S1", "SAM", "SMALL", "SPANISH", "TAN", "TYPE", 
         "U", "VALENCIA", "VIRGINIA", "WHITE")
          
# Specify the synsets as a list
syn <- list(c("CHANDRA", "AH114"), c("TG1", "VIKRAM"))

# Fetch probable duplicate sets
GNdup <- ProbDup(kwic1 = GNKWIC, method = "a", excep = exep, fuzzy = TRUE,
                 phonetic = TRUE, encoding = "primary", 
                 semantic = TRUE, syn = syn)

# Get disjoint probable duplicate sets of each kind
disGNdup <- DisProbDup(GNdup, combine = NULL)

# Get the data frame for reviewing the duplicate sets identified
RevGNdup <- ReviewProbDup(pdup = disGNdup, db1 = GN1000,
                          extra.db1 = c("SourceCountry", "TransferYear"), 
                          max.count = 30, insert.blanks = TRUE)
# Examine and review the duplicate sets using edit function
RevGNdup <- edit(RevGNdup)

# Examine and make changes to a set
subset(RevGNdup, SET_NO==12 & TYPE=="P", select= c(IDKW, DEL, SPLIT))
RevGNdup[c(110, 112, 114, 118, 121, 122, 124), 6] <- "Y"
RevGNdup[c(111, 115, 128), 7] <- 1
RevGNdup[c(113, 117, 120), 7] <- 2
RevGNdup[c(116, 119), 7] <- 3
RevGNdup[c(123, 125), 7] <- 4
RevGNdup[c(126, 127), 7] <- 5
subset(RevGNdup, SET_NO==12 & TYPE=="P", select= c(IDKW, DEL, SPLIT))

# Reconstruct ProDup object
GNdup2 <- ReconstructProbDup(RevGNdup)
lapply(disGNdup, nrow)
lapply(GNdup2, nrow)


## End(Not run)

PGRdup documentation built on Sept. 1, 2023, 1:05 a.m.