auditing_tools
auditing_tools.Rmd
library(framrsquared)
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#> framrsquared 0.5.0
#> Auditing Tools
We have built a series functions in framrsquared to compare two runs and identify differences; these can be useful for QAQC.
Input specific:
-
compare_fishery_inputs()compares fishery inputscompare_fishery_input_flags()is a variant to compare flags -
compare_recruits()compares recruits between two runs -
compare_non_retention_inputs()compares non-retention inputscompare_non_retention_input_flags()is a variant to compare flags -
compare_stock_fishery_rate_scalers()compares the stock fishery rate scalers
Reporting to console:
-
compare_runs()Generates a report to the console with all of the outputs from the functions above
FRAM development QAQC
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compare_databases()compares all relevant tables of two FRAM databases and generates diagnostics list of differences and their magnitude. This can be used when developing modifications to the FRAM software: after running the original version of the software and the modified version of the software on the runs of two initially identical databases,compare_databases()will identify how the outputs were affected by the modifications in the FRAM software.
Example
Most commonly we will use compare_runs() during the NOF
process when developing a new run to confirm that we only have intended
changes to the database.
fram_db <- connect_fram_db('<path_to_coho_database>')
fram_db |>
compare_runs(c(56:57))
── Comparing run bc-Coho2423_STT_NOF to bc-Coho2424_NOF ─────────────────────────────────────────────────────────────────────────────────
ℹ bc-Coho2423_STT_NOF was run at 2024-04-09 10:41:30 PM, bc-Coho2424_NOF was run at 2024-04-10 12:40:07 PM
── Non-Retention Inputs ──
── Checking for changes in non-retention flagging
ℹ Changes detected in non-retention flagging, below is a table outlining them
# A tibble: 4 × 5
fishery_id time_step fishery_name `bc-Coho2423_STT_NOF` `bc-Coho2424_NOF`
<int> <int> <chr> <int> <int>
1 154 4 1212BNetTR 1 NA
2 36 4 Area2TrlTR NA 1
3 39 4 Area3TrlTR NA 1
4 43 4 A4/4BTrlTR NA 1
── Checking for changes in non-retention inputs
ℹ Changes detected in non-retention inputs, below is a table outlining them
# A tibble: 7 × 6
fishery_id time_step name fishery_name `bc-Coho2423_STT_NOF` `bc-Coho2424_NOF`
<int> <int> <chr> <chr> <dbl> <dbl>
1 154 3 cnr_input1 1212BNetTR 71.4 36.7
2 154 4 cnr_input1 1212BNetTR 28.4 0
3 154 5 cnr_input1 1212BNetTR 7 8
4 156 5 cnr_input1 A9-9ANetTR 15 18
5 36 4 cnr_input1 Area2TrlTR 0 52
6 39 4 cnr_input1 Area3TrlTR 0 52
7 43 4 cnr_input1 A4/4BTrlTR 0 52
── Recruit Inputs ──
── Checking for changes to recruits
✔ No changes detected in recruit inputs
── Fishery Inputs ──
── Checking for changes to fishery flags
✔ No changes detected in fishery flag inputs
── Checking for changes to fishery inputs
ℹ Detection tolerance set to: 1%
ℹ Changes detected in fishery inputs, below is a table outlining them
# A tibble: 12 × 6
fishery_id fishery_name time_step name `bc-Coho2423_STT_NOF` `bc-Coho2424_NOF`
<int> <chr> <int> <chr> <dbl> <dbl>
1 47 WlpaBT Net 4 quota 26427 25411
2 48 GryHbr Spt 4 quota 2489 2285
3 49 SGryHb Spt 5 quota 79 73
4 50 GryHbr Net 5 quota 5873 4751
5 51 Hump R Spt 5 quota 1551 1505
6 52 LwCheh Net 5 quota 24219 26299
7 54 Chehal Spt 5 quota 14723 14553
8 55 Hump R Net 5 quota 4485 4372
9 56 UpCheh Net 5 quota 4267 3844
10 63 Quin R Net 4 quota 10166 9860
11 68 Queets Net 4 quota 7486 8079
12 68 Queets Net 5 quota 2358 170
── Checking for changes to stock fishery rate scalers
✔ No changes detected in fishery inputs