Check SEFRA data inputs

Tom Peatman and Charles Edwards

06-Apr-2025

Set up an R session for data preparation

Load packages required for data preparation and visualisation:

library(sefraInputs)

Test that sefra_data.R works

Return list of available data

sefra_data()

## Available SEFRA data:

##                       name                        description
## 1                inputsBio                     2024_CCSBT_SRA
## 2                inputsBio                          reference
## 3 cryptic_capture_longline                          reference
## 4             density_maps                     2024_CCSBT_SRA
## 5             density_maps 2024_CCSBT_SRA_combined_range_maps
## 6             density_maps                          reference
## 7             density_maps      reference_combined_range_maps
##               created                version id
## 1 2025-03-27 12:25:55 20250327T112555Z-1dd6f  1
## 2 2025-03-27 12:25:55 20250327T112555Z-ed41c  2
## 3 2025-03-27 12:25:55 20250327T112555Z-240cc  1
## 4 2025-03-27 12:26:01 20250327T112601Z-e6ac4  1
## 5 2025-03-27 12:26:02 20250327T112602Z-80743  2
## 6 2025-03-27 12:26:03 20250327T112603Z-92e7d  3
## 7 2025-03-27 12:26:04 20250327T112604Z-a6ad2  4

Load density maps into global environment:

sefra_data("density_maps", description = "reference")

## Loaded data:

## 
## 
## |name         |description |created             |version                | id|
## |:------------|:-----------|:-------------------|:----------------------|--:|
## |density_maps |reference   |2025-03-27 12:26:03 |20250327T112603Z-92e7d |  3|

stopifnot("dam" %in% names(density_maps), length(density_maps) == 25)

Load biological inputs into global environment and assign:

inputs_bio_ref <- sefra_data("inputsBio", description = "reference")

## Loaded data:

## 
## 
## |name      |description |created             |version                | id|
## |:---------|:-----------|:-------------------|:----------------------|--:|
## |inputsBio |reference   |2025-03-27 12:25:55 |20250327T112555Z-ed41c |  2|

stopifnot("N_BP" %in% names(inputs_bio_ref))

Note that loading another set of biological inputs will overwrite inputsBio object in global environment (and similarly for the other data objects):

attr(inputsBio, "description")

## [1] "current inputs for 2025 CCSBT risk assessment"

attr(inputs_bio_ref, "description")

## [1] "current inputs for 2025 CCSBT risk assessment"

inputs_bio_prev <- sefra_data("inputsBio", description = "2024_CCSBT_SRA")

## Loaded data:

## 
## 
## |name      |description    |created             |version                | id|
## |:---------|:--------------|:-------------------|:----------------------|--:|
## |inputsBio |2024_CCSBT_SRA |2025-03-27 12:25:55 |20250327T112555Z-1dd6f |  1|

attr(inputsBio, "description")

## [1] "inputs for 2024 CCSBT risk assessment"

attr(inputs_bio_prev, "description")

## [1] "inputs for 2024 CCSBT risk assessment"

## the original inputsBio object in global environment was overwritten
## when reloading inputsBio and assigning to inputs_bio_prev

Examine structure of data objects:

str(density_maps)

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##   ..- attr(*, "agr")= Factor w/ 3 levels "constant","aggregate",..: NA NA
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##   ..- attr(*, "agr")= Factor w/ 3 levels "constant","aggregate",..: NA NA
##   .. ..- attr(*, "names")= chr [1:2] "month" "value"
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##   .. ..- attr(*, "class")= chr [1:3] "XY" "POLYGON" "sfg"
##   ..$ month   : Factor w/ 12 levels "Jan","Feb","Mar",..: 1 2 3 4 5 6 7 8 9 10 ...
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##   ..- attr(*, "agr")= Factor w/ 3 levels "constant","aggregate",..: NA NA
##   .. ..- attr(*, "names")= chr [1:2] "month" "value"
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##   .. ..- attr(*, "class")= chr [1:3] "XY" "POLYGON" "sfg"
##   ..$ month   : Factor w/ 12 levels "Jan","Feb","Mar",..: 1 2 3 4 5 6 7 8 9 10 ...
##   ..$ value   : num [1:15552] 0 0 0 0 0 0 0 0 0 0 ...
##   ..- attr(*, "sf_column")= chr "geometry"
##   ..- attr(*, "agr")= Factor w/ 3 levels "constant","aggregate",..: NA NA
##   .. ..- attr(*, "names")= chr [1:2] "month" "value"
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##   ..$ geometry:sfc_POLYGON of length 15552; first list element: List of 1
##   .. ..$ : num [1:5, 1:2] 1564564 2331950 2228485 1495146 1564564 ...
##   .. ..- attr(*, "class")= chr [1:3] "XY" "POLYGON" "sfg"
##   ..$ month   : Factor w/ 12 levels "Jan","Feb","Mar",..: 1 2 3 4 5 6 7 8 9 10 ...
##   ..$ value   : num [1:15552] 0 0 0 0 0 0 0 0 0 0 ...
##   ..- attr(*, "sf_column")= chr "geometry"
##   ..- attr(*, "agr")= Factor w/ 3 levels "constant","aggregate",..: NA NA
##   .. ..- attr(*, "names")= chr [1:2] "month" "value"
##  - attr(*, "date")= chr "27-Mar-2025"
##  - attr(*, "description")= chr "current density maps for 2025 CCSBT risk assessment"

str(inputs_bio_ref)

## List of 12
##  $ sp_codes          :'data.frame':  25 obs. of  3 variables:
##   ..$ id_species : int [1:25] 1 2 3 4 5 6 7 8 9 10 ...
##   ..$ code       : chr [1:25] "DIW" "DQS" "DIX" "DBN" ...
##   ..$ common_name: chr [1:25] "Gibson's albatross" "Antipodean albatross" "Wandering albatross" "Tristan albatross" ...
##  $ sp_groups         :'data.frame':  40 obs. of  15 variables:
##   ..$ common_name         : chr [1:40] "Gibson's albatross" "Antipodean albatross" "Wandering albatross" "Tristan albatross" ...
##   ..$ scientific_name     : chr [1:40] "Diomedea antipodensis gibsoni" "Diomedea antipodensis antipodensis" "Diomedea exulans" "Diomedea dabbenena" ...
##   ..$ genus               : chr [1:40] "Diomedea" "Diomedea" "Diomedea" "Diomedea" ...
##   ..$ family              : chr [1:40] "Diomedeidae" "Diomedeidae" "Diomedeidae" "Diomedeidae" ...
##   ..$ species_group       : chr [1:40] "Wandering albatross" "Wandering albatross" "Wandering albatross" "Wandering albatross" ...
##   ..$ catchability_group  : chr [1:40] "Wandering albatross" "Wandering albatross" "Wandering albatross" "Wandering albatross" ...
##   ..$ capture_group       : chr [1:40] "Great albatross" "Great albatross" "Great albatross" "Great albatross" ...
##   ..$ id_code             : int [1:40] 1 2 3 4 5 6 7 8 9 10 ...
##   ..$ id_genus            : num [1:40] 1 1 1 1 1 1 1 2 2 2 ...
##   ..$ id_family           : int [1:40] 1 1 1 1 1 1 1 1 1 1 ...
##   ..$ code                : chr [1:40] "DIW" "DQS" "DIX" "DBN" ...
##   ..$ taxonomic_resolution: chr [1:40] "species" "species" "species" "species" ...
##   ..$ fao_code            : logi [1:40] TRUE TRUE TRUE TRUE TRUE TRUE ...
##   ..$ id_species          : int [1:40] 1 2 3 4 5 6 7 8 9 10 ...
##   ..$ id_species_group    : num [1:40] 1 1 1 1 1 2 2 3 3 3 ...
##  $ breeding_season   :'data.frame':  25 obs. of  6 variables:
##   ..$ id_species  : int [1:25] 1 2 3 4 5 6 7 8 9 10 ...
##   ..$ code        : chr [1:25] "DIW" "DQS" "DIX" "DBN" ...
##   ..$ common_name : chr [1:25] "Gibson's albatross" "Antipodean albatross" "Wandering albatross" "Tristan albatross" ...
##   ..$ breeding    : chr [1:25] "1,2,3,4,5,6,7,8,9,10,11,12" "1,2,3,4,5,6,7,8,9,10,11,12" "1,2,3,4,5,6,7,8,9,10,11,12" "1,2,3,4,5,6,7,8,9,10,11,12" ...
##   ..$ nonbreeding : chr [1:25] NA NA NA NA ...
##   ..$ breeding_str: chr [1:25] "All year" "All year" "All year" "All year" ...
##  $ p_nest            : num [1:25, 1:12] 0.5 0.4 0.5 0.6 0.05 0.5 0.5 0.3 0.2 0.2 ...
##   ..- attr(*, "dimnames")=List of 2
##   .. ..$ : chr [1:25] "DIW" "DQS" "DIX" "DBN" ...
##   .. ..$ : chr [1:12] "Jan" "Feb" "Mar" "Apr" ...
##  $ breeding_phenology: chr [1:25, 1:12] "IN" "IN" "IN" "IN" ...
##   ..- attr(*, "dimnames")=List of 2
##   .. ..$ : chr [1:25] "DIW" "DQS" "DIX" "DBN" ...
##   .. ..$ : chr [1:12] "Jan" "Feb" "Mar" "Apr" ...
##  $ p_southern        : num [1:25, 1:12] 1 1 1 1 1 1 1 1 1 1 ...
##   ..- attr(*, "dimnames")=List of 2
##   .. ..$ : chr [1:25] "DIW" "DQS" "DIX" "DBN" ...
##   .. ..$ : chr [1:12] "Jan" "Feb" "Mar" "Apr" ...
##  $ N_BP              :'data.frame':  25 obs. of  6 variables:
##   ..$ id_species  : int [1:25] 1 2 3 4 5 6 7 8 9 10 ...
##   ..$ code        : chr [1:25] "DIW" "DQS" "DIX" "DBN" ...
##   ..$ common_name : chr [1:25] "Gibson's albatross" "Antipodean albatross" "Wandering albatross" "Tristan albatross" ...
##   ..$ distribution: chr [1:25] "log-normal" "log-normal" "log-normal" "weibull" ...
##   ..$ par1        : num [1:25] 4425 3383 10130 9.25 60 ...
##   ..$ par2        : num [1:25] 0.05 0.05 0.05 1710 0.1 0.07 0.11 0.1 0.1 0.05 ...
##  $ P_B               :'data.frame':  25 obs. of  6 variables:
##   ..$ id_species  : int [1:25] 1 2 3 4 5 6 7 8 9 10 ...
##   ..$ code        : chr [1:25] "DIW" "DQS" "DIX" "DBN" ...
##   ..$ common_name : chr [1:25] "Gibson's albatross" "Antipodean albatross" "Wandering albatross" "Tristan albatross" ...
##   ..$ distribution: chr [1:25] "beta" "beta" "logit-normal" "beta" ...
##   ..$ par1        : num [1:25] 0.595 0.45 0.494 0.349 0.6 0.531 0.531 0.596 0.596 0.844 ...
##   ..$ par2        : num [1:25] 170 91.3 0.05 51.3 0.05 22.2 22.2 4100 0.05 174 ...
##  $ S_curr            :'data.frame':  25 obs. of  6 variables:
##   ..$ id_species  : int [1:25] 1 2 3 4 5 6 7 8 9 10 ...
##   ..$ code        : chr [1:25] "DIW" "DQS" "DIX" "DBN" ...
##   ..$ common_name : chr [1:25] "Gibson's albatross" "Antipodean albatross" "Wandering albatross" "Tristan albatross" ...
##   ..$ distribution: chr [1:25] "beta" "beta" "beta" "beta" ...
##   ..$ par1        : num [1:25] 0.912 0.907 0.918 0.948 0.971 0.92 0.95 0.923 0.902 0.931 ...
##   ..$ par2        : num [1:25] 59.9 138 159 1230 0.001 138 2260 1470 0.02 147 ...
##  $ S_opt             :'data.frame':  25 obs. of  6 variables:
##   ..$ id_species  : int [1:25] 1 2 3 4 5 6 7 8 9 10 ...
##   ..$ code        : chr [1:25] "DIW" "DQS" "DIX" "DBN" ...
##   ..$ common_name : chr [1:25] "Gibson's albatross" "Antipodean albatross" "Wandering albatross" "Tristan albatross" ...
##   ..$ distribution: chr [1:25] "uniform" "uniform" "uniform" "uniform" ...
##   ..$ par1        : num [1:25] 0.95 0.95 0.95 0.95 0.95 0.95 0.95 0.93 0.93 0.93 ...
##   ..$ par2        : num [1:25] 0.98 0.98 0.98 0.98 0.98 0.98 0.98 0.97 0.97 0.97 ...
##  $ A_curr            :'data.frame':  25 obs. of  6 variables:
##   ..$ id_species  : int [1:25] 1 2 3 4 5 6 7 8 9 10 ...
##   ..$ code        : chr [1:25] "DIW" "DQS" "DIX" "DBN" ...
##   ..$ common_name : chr [1:25] "Gibson's albatross" "Antipodean albatross" "Wandering albatross" "Tristan albatross" ...
##   ..$ distribution: chr [1:25] "log-normal" "log-normal" "log-normal" "log-normal" ...
##   ..$ par1        : num [1:25] 11.9 13.9 9.91 9.18 9.91 9.19 8.9 8.9 8.9 9.91 ...
##   ..$ par2        : num [1:25] 0.165 0.142 0.15 0.177 0.15 0.189 0.023 0.165 0.165 0.15 ...
##  $ A_opt             :'data.frame':  25 obs. of  6 variables:
##   ..$ id_species  : int [1:25] 1 2 3 4 5 6 7 8 9 10 ...
##   ..$ code        : chr [1:25] "DIW" "DQS" "DIX" "DBN" ...
##   ..$ common_name : chr [1:25] "Gibson's albatross" "Antipodean albatross" "Wandering albatross" "Tristan albatross" ...
##   ..$ distribution: chr [1:25] "log-normal" "log-normal" "log-normal" "log-normal" ...
##   ..$ par1        : num [1:25] 11.9 13.9 9.91 9.18 9.91 9.19 8.9 8.9 8.9 9.91 ...
##   ..$ par2        : num [1:25] 0.165 0.142 0.15 0.177 0.15 0.189 0.023 0.165 0.165 0.15 ...
##  - attr(*, "date")= chr "27-Mar-2025"
##  - attr(*, "description")= chr "current inputs for 2025 CCSBT risk assessment"