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read_proc_reports_abund_cross: Read in report(s) generated by Matlab biomass estimation/kriging process

read_proc_reports_abund_cross.Rd

Read in report(s) from Matlab kriged abundance estimation from a directory and calculate the total survey abundance estimate and abundance by age. Uses readxl Is able to read in with separate method (age-1 or age-2+ method) and hakeflag.

Usage

read_proc_reports_abund_cross(
  SurveyName,
  DirNameFile,
  sheet = NULL,
  hakeflag = 2,
  method = 1,
  ...
)

Arguments

SurveyName

- name of survey

DirNameFile

excel file - contains paths and locations of files. Uses Export_dir as the directory that the exported files are in.

sheet

is an optional argument to denote which sheet of the DirNameFile want to use. This defaults to the first sheet if not set.

hakeflag:

adult hake (hakeflag=2), not filtering for hake (hakeflag=-1), age-0 hake (hakeflag=0), age-1 hake only(hakeflag=1), all hake (hakeflag=3), age-1+ (hakeflag=4). set to 1 if want age1+ numbers, set to 0 (or other number) if want age2+. Defaults to age2+

method:

Can read in age-2+ biomass for either age-1+ method () or age-2+ method. Cannot read in age-1 biomass for age-2+ method. Method = 1 is for age-1+ method, method = 2 is for the age-2+ method.

Examples

if (FALSE) { # \dontrun{
temp<-read_proc_reports_cross(SurveyName, DirNameFile,sheet,hakeflag, method)
} # }