summarizeData: summarizeData

In SOLV-Code/sdsynopsis: Salmon data extraction and summary

Description

Function to generate various data summaries (number of records by DB, input for heatmap of tag recoveries) Target folders are generated if they don't exist. Uses files generated with matchRecords().

Usage

summarizeData(
  nuseds.rds.file = "DATA/RDSFiles/nuSEDS_mod.RDS",
 
    nuseds.pop.info = "DATA/LookupFiles/aopen-data-portaljanuary-2019conservation_unit_system_sites.csv",
  epad.rds.file = "DATA/RDSFiles/EPAD_mod.RDS",
  mrp.rds.file = "DATA/RDSFiles/MRP_mod.RDS",
  mrp.rds.details.file = "DATA/RDSFiles/MRP_Details_mod.RDS",
  rosetta.cu = read.csv("DATA/LookupFiles/Generated_RosettaFile_CU.csv",
    stringsAsFactors = FALSE),
  rosetta.pop = read.csv("DATA/LookupFiles/Generated_RosettaFile_Pop.csv",
    stringsAsFactors = FALSE),
  cu.summary = read.csv("OUTPUT/Summary_CU.csv", stringsAsFactors = FALSE),
  out.folder = "OUTPUT/Summaries",
  tracking.folder = "DATA/TrackingFiles"
)

Arguments

nuseds.rds.file	path to the modified nuSEDS input file (in RDS format).
nuseds.pop.info	path to the pop/site info file from nuSEDS (in csv format)
epad.rds.file	path to the modified EPAD input file (in RDS format)
mrp.rds.file	path to the modified MRP summary input file (in RDS format)
out.folder	path for storing output (CU summary stored there)
tracking.folder	path for storing tracking files (site mismatches etc. stored there)
epad.rds.details.file	path to the modified EPAD details input file (in RDS format)

Examples

## Not run: summarizeData( nuseds.rds.file = "DATA/RDSFiles/nuSEDS_mod.RDS",
        nuseds.pop.info = "DATA/LookupFiles/aopen-data-portaljanuary-2019conservation_unit_system_sites.csv",
        epad.rds.file =  "DATA/RDSFiles/EPAD_mod.RDS",
        mrp.rds.file =  "DATA/RDSFiles/MRP_mod.RDS",
        mrp.rds.details.file =  "DATA/RDSFiles/MRP_Details_mod.RDS",
        rosetta.cu = read.csv("DATA/LookupFiles/Generated_RosettaFile_CU.csv",stringsAsFactors = FALSE),
        rosetta.pop = read.csv("DATA/LookupFiles/Generated_RosettaFile_Pop.csv",stringsAsFactors = FALSE),
        cu.summary = read.csv("OUTPUT/Summary_CU.csv", stringsAsFactors =  FALSE), 
        out.folder = "OUTPUT/Summaries",
        tracking.folder = "DATA/TrackingFiles")
	
## End(Not run)

SOLV-Code/sdsynopsis documentation built on April 29, 2020, 5:20 p.m.