Example got-to script

Example Script Using R Package `GAPsurvey`

Last updated April 2024

Open Rstudio script example_script.R. This should already be located on desktop, otherwise find it using the link below.

system.file("r/example_script.R", package = "GAPsurvey")
#> [1] "C:/Users/sean.rohan/AppData/Local/Temp/RtmpWSLcfB/temp_libpath15cc58f34baf/GAPsurvey/r/example_script.R"

Install R package

Rerun this only when there is a new version of the package to install. The user may install from GitHub:

devtools::install_github("afsc-gap-products/GAPsurvey")

or install from local file .tar.gz:

# example, the user may have a different path
install.packages('C:/Users/User/Downloads/GAPsurvey_2023.04.04.tar.gz',
                 repos=NULL, type='source')

Load libraries

library(GAPsurvey)

Now we can use functions from GAPSurvey!

What have we historically caught at this station?

Learn more about and find examples using…

?get_catch_haul_history

get_catch_haul_history(
  years = 2021:2023, # optional; if you only want to see a specific year, not the last 10
  species_codes = c(21720, 21740), # optional; pacific cod and walleye pollock ONLY
  survey = "EBS", # for example
  station = "I-13") # for example
#> $catch
#> $catch$`2021`
#>   station     scientific_name     common_name count weight_kg cpue_kgkm2
#> 5    I-13 Gadus chalcogrammus walleye pollock   793   550.359 11529.7821
#> 6    I-13 Gadus macrocephalus     Pacific cod    91    31.140   652.3695
#>   cpue_nokm2
#> 5   16613.01
#> 6    1906.41
#> 
#> $catch$`2022`
#>   station     scientific_name     common_name count weight_kg cpue_kgkm2
#> 3    I-13 Gadus chalcogrammus walleye pollock   135   140.138   3252.886
#> 4    I-13 Gadus macrocephalus     Pacific cod   173   104.016   2414.421
#>   cpue_nokm2
#> 3   3133.623
#> 4   4015.679
#> 
#> $catch$`2023`
#>   station     scientific_name     common_name count weight_kg cpue_kgkm2
#> 1    I-13 Gadus chalcogrammus walleye pollock    70    41.744    898.023
#> 2    I-13 Gadus macrocephalus     Pacific cod    31     9.190    197.701
#>   cpue_nokm2
#> 1  1505.8837
#> 2   666.8913
#> 
#> 
#> $catch_means
#>       scientific_name     common_name station count weight_kg cpue_kgkm2
#> 1 Gadus chalcogrammus walleye pollock    I-13 332.7    244.08    5226.90
#> 2 Gadus macrocephalus     Pacific cod    I-13  98.3     48.12    1088.16
#>   cpue_nokm2 Freq
#> 1    7084.17    3
#> 2    2196.33    3
#> 
#> $haul
#>   year station haul stratum        vessel_name           date_time
#> 1 2021    I-13    7      31      ALASKA KNIGHT 2021-06-02 12:05:29
#> 2 2022    I-13   12      31        VESTERAALEN 2022-06-01 16:20:20
#> 3 2023    I-13   16      31 NORTHWEST EXPLORER 2023-05-30 13:43:02
#>   latitude_dd_start longitude_dd_start bottom_temperature_c
#> 1          57.65493          -160.2535                  4.4
#> 2          57.65502          -160.2754                  3.6
#> 3          57.66505          -160.2725                  3.4
#>   surface_temperature_c depth_m distance_fished_km net_width_m net_height_m
#> 1                   4.7      55              2.954      16.159        1.794
#> 2                   7.6      54              2.854      15.095        2.566
#> 3                   3.4      55              2.879      16.146        2.175
#>   area_swept_km2 duration_hr total_weight_kg
#> 1       0.047734       0.522            1220
#> 2       0.043081       0.531            1190
#> 3       0.046484       0.516             812

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