library(knitr)
library(icesVMS)

icesVMS

icesVMS Functions to support the creation of ICES Fisheries Overviews, ….

icesVMS is implemented as an R package

and available on GitHub and our CRAN-like repository

Installation

icesVMS can be installed from our CRAN-like repository using the standard install.packages() command

install.packages("icesVMS", repos = 'https://ices-tools-prod.r-universe.dev')

Usage

For a summary of the package:

library(icesVMS)
?icesVMS

Examples

Download c square information

All of the VMS data submitted to ICES is at the c square level (concise spatial query and representation system, (Rees 2003)), and to aid in the exploration of display of data summaries extracted from the ICES VMS/Logbook database there is a service to extract information related to a C square. For example, the following code returns a table of all the c squares in the Celtic Seas ecoregion (see https://ices.dk/community/advisory-process/Pages/ICES-ecosystems-and-advisory-areas.aspx):

## celtic <- get_csquare(ecoregion = "Celtic Seas")
## sr_32D5 <- get_csquare(stat_rec="32D5")
get_csquare(c_square = "7501:114:383:4")

##   csquare_area
## 1     19.08342
##                                                                                                                                                                                                            wkt
## 1 POLYGON ((-14.400000000000002 51.849999999999994,-14.400000000000002 51.89999999999999,-14.350000000000001 51.89999999999999,-14.350000000000001 51.849999999999994,-14.400000000000002 51.849999999999994))
##   id       c_square stat_rec ices_area   ecoregion    lat     lon
## 1  3 7501:114:383:4     32D5       7k2 Celtic Seas 51.875 -14.375

These can be plotted by parsing the WKT (Well Known Text, https://en.wikipedia.org/wiki/Well-known_text_representation_of_geometry) field (here using the sf package) and then plotting using ggplot2, for example:

ukwest <- get_csquare(ices_area = "6a")
ukwest <- sf::st_as_sf(ukwest, wkt = "wkt", crs = 4326)

ggplot2::ggplot() +
  ggplot2::geom_sf(data = ukwest, color = "lightblue", fill = "transparent")

Download bottom contact model parameters (BENTHIS)

To calculate swept area ratio by c_square, ICES uses methods developed by the BENTHIS project and within the WGSFD in which gear codes are used to imply the area swept by the gear for a given fishing speed. The parameters are available via:

benthis <- get_benthis_parameters()

id	benthisMet	avKw	avLoa	avFspeed	subsurfaceProp	gearWidth	firstFactor	secondFactor	gearModel	gearCoefficient	contactModel
1	OT_SPF	883.8421	34.38526	2.9	2.8	0.1015789	0.9652	68.3890	linear	avg_oal	trawl_contact
2	SDN_DMF	167.6765	18.91915	0	0	6.5366439	1948.8347	0.2363	power	avg_kw	danish_seine_contact
3	OT_DMF	441.6667	19.8	3.064286	7.8	0.1054698	9.6054	0.4337	power	avg_kw	trawl_contact
4	OT_MIX_DMF_BEN	691.0217	24.36896	2.911111	8.6	0.1563055	3.2141	77.9812	linear	avg_oal	trawl_contact
5	SSC_DMF	481.795	23.1175	0	5	6.4542120	4461.2700	0.1176	power	avg_oal	scottish_seine_contact
6	OT_MIX	400.6089	20.13774	2.788636	14.7	0.0613659	10.6608	0.2921	power	avg_kw	trawl_contact
7	OT_MIX_DMF_PEL	690.3574	23.745	3.410385	22	0.0762053	6.6371	0.7706	power	avg_oal	trawl_contact
8	OT_MIX_CRU_DMF	473.097	19.89515	2.629	22.9	0.1139591	3.9273	35.8254	linear	avg_oal	trawl_contact
9	OT_MIX_CRU	681	21.685	3.008889	29.2	0.1051172	37.5272	0.1490	power	avg_kw	trawl_contact
10	OT_CRU	345.5205	18.67739	2.47963	32.1	0.0789228	5.1039	0.4690	power	avg_kw	trawl_contact
11	TBB_CRU	210.625	20.765	2.975	52.2	0.0171507	1.4812	0.4578	power	avg_kw	trawl_contact
12	TBB_DMF	822.1667	33.8866	5.230851	100	0.0202760	0.6601	0.5078	power	avg_kw	trawl_contact
13	TBB_MOL	107.1773	10.14545	2.428571	100	0.0049306	0.9530	0.7094	power	avg_oal	trawl_contact
14	DRB_MOL	382.4375	24.59848	2.5	100	0.0169653	0.3142	1.2454	power	avg_oal	trawl_contact

These high level gear categories referred to as BenthisMet are connected to lower level metiers via a lookup table maintained by the WGSFD and available via:

metiers <- get_metier_lookup()

leMetLevel6	benthisMetiers	metierLevel5	metierLevel4	fishingCategoryFo
FPO_FWS_110-156_0_0	NA	FPO_FWS	FPO	Static
FPO_FWS_31-49_0_0	NA	FPO_FWS	FPO	Static
FPO_FWS_>0_0_0	NA	FPO_FWS	FPO	Static
FPO_MCF_0-0_0_0	NA	FPO_MCF	FPO	Static
FPO_MOL_0-0_0_0	NA	FPO_MOL	FPO	Static
FPO_MOL_0_0_0	NA	FPO_MOL	FPO	Static
FPO_MOL_>0_0_0	NA	FPO_MOL	FPO	Static
FPO_MOL_>=29_0_0	NA	FPO_MOL	FPO	Static
FPO_NOC_0_0_0	NA	FPO_MOL	FPO	Static
FPO_SPF_0-0_0_0	NA	FPO_SPF	FPO	Static

Total landings by country

The VMS/Logbook database also gives access to total landings by country and year. This information is used in the ICES Fisheries Overviews. All data used in the Fisheries Overviews is published where possible, so this function provides open access to the aggregated landings weights.

benthis <- get_benthis_parameters()

id	benthisMet	avKw	avLoa	avFspeed	subsurfaceProp	gearWidth	firstFactor	secondFactor	gearModel	gearCoefficient	contactModel
1	OT_SPF	883.8421	34.38526	2.9	2.8	0.1015789	0.9652	68.3890	linear	avg_oal	trawl_contact
2	SDN_DMF	167.6765	18.91915	0	0	6.5366439	1948.8347	0.2363	power	avg_kw	danish_seine_contact
3	OT_DMF	441.6667	19.8	3.064286	7.8	0.1054698	9.6054	0.4337	power	avg_kw	trawl_contact
4	OT_MIX_DMF_BEN	691.0217	24.36896	2.911111	8.6	0.1563055	3.2141	77.9812	linear	avg_oal	trawl_contact
5	SSC_DMF	481.795	23.1175	0	5	6.4542120	4461.2700	0.1176	power	avg_oal	scottish_seine_contact
6	OT_MIX	400.6089	20.13774	2.788636	14.7	0.0613659	10.6608	0.2921	power	avg_kw	trawl_contact
7	OT_MIX_DMF_PEL	690.3574	23.745	3.410385	22	0.0762053	6.6371	0.7706	power	avg_oal	trawl_contact
8	OT_MIX_CRU_DMF	473.097	19.89515	2.629	22.9	0.1139591	3.9273	35.8254	linear	avg_oal	trawl_contact
9	OT_MIX_CRU	681	21.685	3.008889	29.2	0.1051172	37.5272	0.1490	power	avg_kw	trawl_contact
10	OT_CRU	345.5205	18.67739	2.47963	32.1	0.0789228	5.1039	0.4690	power	avg_kw	trawl_contact
11	TBB_CRU	210.625	20.765	2.975	52.2	0.0171507	1.4812	0.4578	power	avg_kw	trawl_contact
12	TBB_DMF	822.1667	33.8866	5.230851	100	0.0202760	0.6601	0.5078	power	avg_kw	trawl_contact
13	TBB_MOL	107.1773	10.14545	2.428571	100	0.0049306	0.9530	0.7094	power	avg_oal	trawl_contact
14	DRB_MOL	382.4375	24.59848	2.5	100	0.0169653	0.3142	1.2454	power	avg_oal	trawl_contact

References

Rees, Tony. 2003. “C-Squares, a New Spatial Indexing System and Its Applicability to the Description of Oceanographic Datasets.” Oceanography 16 (1): 11–19. https://doi.org/10.5670/oceanog.2003.52.