age1_indx_comp.R
age1_indx_comp.Rd
Function to compare the age-1 abundance estimate from cases to that from the original age-1 index.
Usage
age1_indx_comp(
SurveyNamein,
DirNameFilein,
imagedirin,
casesin,
hakeflagin,
yearin,
age1indfnamein,
...
)
Arguments
- hakeflagin
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). Passing this although assuming this will be hakeflag=1
- yearin
is the year that is being investigated
- 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.
- imagedir
- the directory for the images files to be placed in
- cases
- is the set of cases to be compared
- age1indfname
is the directory the age-1 index file is found in (file needs to be named 'Age1_Full_Time_Series'