awkHelper: subset helper function for use reading in large data, called...

In pcvr: Plant Phenotyping and Bayesian Statistics

subset helper function for use reading in large data, called in pcv.sub.read

Description

subset helper function for use reading in large data, called in pcv.sub.read

Usage

awkHelper(inputFile, filters, awk = NULL)

Arguments

inputFile	Path to csv file of plantCV output, should be provided internally in read.pcv
filters	filtering conditions, see read.pcv for details. Format as list("trait in area, perimeter", "other contains stringToMatch")
awk	Optional awk command to use instead.

Details

awkHelper attempts to make awk commands from human readable input. Currently when filters are supplied the input file has quotes removed by 'sed' then is piped into awk, so an equivalent command line statement may be: sed 's/\"//g' pcvrTest2.csv | awk -F ',' '{ if (NR==1 || $18=="area") { print } }'

Value

Returns a character string representing a unix style awk statement which is typically passed to pipe or used as a connection in data.table::fread.

Examples

tryCatch(
  { # in case offline
    link1 <- "https://gist.githubusercontent.com/seankross/"
    link2 <- "a412dfbd88b3db70b74b/raw/5f23f993cd87c283ce766e7ac6b329ee7cc2e1d1/mtcars.csv"
    file <- paste0(link1, link2)
    awkHelper(file, list("gear in 4, 3"), awk = NULL)
    awkHelper(file, "gear contains 3", awk = NULL)
    # note that to be filtered the file has to exist on your local system, this example only shows
    # the output of awkHelper, which would then be executed by read.pcv on a unix system
    awkHelper(file, list("gear in 4, 3"), awk = "existing_command")
  },
  error = function(e) {
    message(e)
  }
)

pcvr documentation built on April 16, 2025, 5:12 p.m.