Development

.Rbuildignore

@@ -8,3 +8,4 @@
 ^doc$
 ^Meta$
 ^README\.Rmd$
+^CITATION\.cff$

CITATION.cff

@@ -0,0 +1,33 @@
+# --------------------------------------------
+# CITATION file created with {cffr} R package
+# See also: https://docs.ropensci.org/cffr/
+# --------------------------------------------
+
+cff-version: 1.2.0
+message: 'To cite package "furdeb" in publications use:'
+type: software
+license: GPL-3.0-only
+title: 'furdeb: FUnctions for R DEvelopment and Beyond!'
+version: 1.0.0
+abstract: Functions and processes for R development and beyond!
+authors:
+- family-names: Depetris
+  given-names: Mathieu
+  email: [email protected]
+  orcid: https://orcid.org/0000-0001-8080-0531
+- family-names: Bouhineau
+  given-names: Oceane
+  email: [email protected]
+  orcid: https://orcid.org/0000-0001-7418-2925
+- family-names: Lerebourg
+  given-names: Clara
+  email: [email protected]
+  orcid: https://orcid.org/0000-0003-0589-8932
+repository-code: https://github.com/OB7-IRD/furdeb
+url: https://github.com/OB7-IRD/furdeb
+contact:
+- family-names: Depetris
+  given-names: Mathieu
+  email: [email protected]
+  orcid: https://orcid.org/0000-0001-8080-0531
+

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: furdeb
 Type: Package
 Title: FUnctions for R DEvelopment and Beyond!
-Version: 0.0.0.9000
+Version: 1.0.0
 Authors@R:
     c(person(given = "Mathieu",
             family = "Depetris",
@@ -27,6 +27,11 @@ Authors@R:
               email = "[email protected]",
               role = c("ctb"),
               comment = c(ORCID = "0000-0001-6135-9015")),
+       person(given = "Jeanne",
+           family = "Clément",
+           email = "[email protected]",
+           role = c("ctb"),
+           comment = c(ORCID = "0000-0002-5228-5015")),
        person(given = "IRD - Ob7",
               family = "Observatory of Exploited Tropical Pelagic Ecosystems",
               email = "[email protected]",

NEWS.md

@@ -1,3 +1,14 @@
+# furdeb 1.0.0 - 2024.11.29
+
+## Added
+* time_allocation_activity_code_ref.csv : reference table for allocating fishing time and time at sea according to activity code
+
+## Changed
+* Update vignettes
+* Update control functions 
+* Update function data extraction
+* Update marine_area_overlay.R
+
 # furdeb 0.0.0.9000 - 2023.10.12
 
 ## Added

inst/time_allocation_activity_code_ref.csv

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+activity_code_avdth;activity_code_observe;set_success_status_code_observe;objectoperation_code_observe;schooltype_code_observe;time_at_sea;fishing_time;set_duration;activity_label_observe;activity_label_avdth; objectoperation_label_observe;schooltype_label_observe;status_active_observe;comment
+15;0;;;;0;0;0;At port;At port;;;1;
+4;1;;;;1;0;0;Transit (steaming without searching);Transit (steaming without searching);;;1;If no DCP delared in AVDTH database. (In AVDTH database, there are DCPs declared for activities that are not compatible with the use of a DCP in ObServe database).
+3;2;;;;1;1;0;Searching (in general);Searching;;;1;If no DCP delared in AVDTH database. (In AVDTH database, there are DCPs declared for activities that are not compatible with the use of a DCP in ObServe database).
+3;3;;;;1;1;0;Searching for floating objects (logs or FADs);Searching;;;0;
+3;4;;;;1;1;0;Steaming towards observed system associated to the tuna school;Searching;;;1;
+3;5;;;;0;0;0;Arrival of vessel at the observed system;Searching;;;1;
+0;6;0;99;1;1;1;1;Fishing (skiff is deployed);Null set ;Unknown;Object school type;1;fishing_time=set_duration
+0;6;0;;2;1;1;1;Fishing (skiff is deployed);Null set ;;Free school type;1;fishing_time=set_duration
+1;6;1;99;1;1;1;1;Fishing (skiff is deployed);Positive set;Unknown;Object school type;1;fishing_time=set_duration
+1;6;1;;2;1;1;1;Fishing (skiff is deployed);Positive set;;Free school type;1;fishing_time=set_duration
+2;6;2;99;1;1;1;1;Fishing (skiff is deployed);Unknown set;Unknown;Object school type;1;fishing_time=set_duration
+2;6;2;;2;1;1;1;Fishing (skiff is deployed);Unknown set;;Free school type;1;fishing_time=set_duration
+14;6;2;99;1;1;1;1;Fishing (skiff is deployed);Pocket capsizing;Unknown;Object school type;1;fishing_time=set_duration
+14;6;2;;2;1;1;1;Fishing (skiff is deployed);Pocket capsizing;;Free school type;1;fishing_time=set_duration
+99;7;;;;0;0;0;End of fishing (skiff is brought on board);Other non-fishing activities;;;0;
+3;8;;;;1;1;0;Drifting during the day near a tuna school, a log or a FAD;Searching;;;1;
+10;9;;;;1;0;0;Drifting during the night (engine stopped);Waiting;;;1;
+8;10;;;;1;0;0;Drifting due to bad weather;Heaving to ;;;1;
+7;11;;;;1;0;0;Drifting due to mechanical problems;Damage;;;1;
+11;12;;;;1;1;0;Transshipping at sea (equipment, FADs, crew member);Transshipping at sea ;;;1;
+1;13;;3;;0;0;0;Operation on FOB only (visit, deployment, modification, retrieval);Fishing on FOB;Fishing;;0;The time_at_sea, set_duration and fishing_time of fishing on FOB activity have already been taken into account via corresponding fishing activity (code 6 in observe and 0,1,2, or 14 in avdth database) and elementary catches associated.
+5;13;;1;;1;1;0;Operation on FOB only (visit, deployment, modification, retrieval);Deployment of FOB;Deployment;;1;
+6;13;;4;;1;1;0;Operation on FOB only (visit, deployment, modification, retrieval);Recovery of FOB;Removal;;1;
+6;13;;6;;1;1;0;Operation on FOB only (visit, deployment, modification, retrieval);Recovery of FOB;Destruction;;1;
+23;13;;9;;1;1;0;Operation on FOB only (visit, deployment, modification, retrieval);Redeployment of FOB with beacon;Replacement;;1;
+29;13;;2;;1;1;0;Operation on FOB only (visit, deployment, modification, retrieval);Visit to FOB equipped with beacon;Visit;;1;
+32;13;;8;;1;1;0;Operation on FOB only (visit, deployment, modification, retrieval);Reinforced of a FOB with beacon;Modified or reinforced;;1;
+33;13;;5;;0;0;0;Operation on FOB only (visit, deployment, modification, retrieval);Loss, end or controlled shutdown of FOB transmission;Abandonment (without beacon, not destroyed, not sunk);;1;
+33;13;;7;;0;0;0;Operation on FOB only (visit, deployment, modification, retrieval);Loss, end or controlled shutdown of FOB transmission;Sinking;;1;
+40;13;;11;;0;0;0;Operation on FOB only (visit, deployment, modification, retrieval);Loss of FOB;Loss;;1;
+98;13;;99;;0;0;0;Operation on FOB only (visit, deployment, modification, retrieval);Unknown operation on FOB;Unknown;;0;
+99;13;;10;;0;0;0;Operation on FOB only (visit, deployment, modification, retrieval);Unknown operation on FOB;Other (to be precised);;1;
+;13;;12;;0;0;0;Operation on FOB only (visit, deployment, modification, retrieval);;Stranding;;1;
+6;14;;;;1;1;0;Recovering a floating object (log or FAD) belonging to the vessel;Recovery of FOB;;;0;
+6;15;;;;1;1;0;Recovering a floating object (log or FAD) that does not belong to the vessel;Recovery of FOB;;;0;
+3;16;;;;0;0;0;End of searching;Searching;;;1;
+10;17;;;;1;1;0;Anchorage on top of a seamount;Waiting;;;0;
+4;18;;;;1;0;0;Steaming at night towards a floating object;Transit (steaming without searching);;;1;
+3;19;;;;1;1;0;Continue steaming towards observed system associated to the tuna school;Searching;;;0;
+6;20;;;;1;1;0;Recovery of a floating object;Recovery of FOB;;;0;
+42;21;;;;0;0;0;FPA zone change;FPA zone change;;;1;
+7;22;;;;1;0;0;Damage;Damage;;;0;
+9;23;;;;1;1;0;Bait fishing;Bait ;;;1;
+10;24;;;;1;0;0;Waiting;Waiting;;;1;
+11;25;;;;1;1;0;Offshore transshipment (details unknown);Transshipping at sea ;;;1;
+12;26;;;;1;1;0;Transshipment from a purse seiner;Transshipment from a purse seiner;;;1;
+13;27;;;;1;1;0;Transshipment to a purse seiner;Transshipment to a purse seiner;;;1;
+19;29;;;;1;1;0;Transshipment to a bait boat;Transshipment to a bait boat;;;1;
+20;30;;;;1;1;0;Transshipment from a bait boat;Transshipment from a bait boat;;;1;
+35;31;;;;1;1;0;Fish discard;Discard;;;1;
+2;32;;;;1;0;1;Activity/set created from the well plan;Unknown set;;;0;fishing_time=set_duration
+36;36;;;;1;0;0;Refueling;Refueling;;;1;
+37;37;;;;1;0;0;Medical evacuation;Medical evacuation;;;1;
+38;38;;;;1;0;0;This vessel towed;Vessel towed;;;1;
+39;39;;;;1;0;0;Towing another vessel;Towing another vessel;;;1;
+99;50;;;;1;0;0;Training on board (priracy, fire, abandonment, etc);Other non-fishing activities;;;1;
+15;51;;;;0;0;0;Transfert at port of a crew member;At port;;;1;
+52;52;;;;0;0;0;Fake set, for hosting historical samples;Fake set, for hosting historical samples;;;0;
+99;99;;;;1;0;0;Other (to detail in the comments);Other non-fishing activities;;;1;
+4;101;;99;;1;0;0;[deprecated] Transit (steaming without searching);Transit (steaming without searching);;;0;If DCP delared in AVDTH database. (In AVDTH database, there are DCPs declared for activities that are not compatible with the use of a DCP in ObServe database).
+3;102;;99;;1;1;0;[deprecated] Searching (in general);Searching;;;0;If DCP delared in AVDTH database. (In AVDTH database, there are DCPs declared for activities that are not compatible with the use of a DCP in ObServe database).
+4;103;;;;1;0;0;Day without activity;Transit (steaming without searching);;;1;
+4;101;;;;1;0;0;[deprecated] Transit (steaming without searching);Transit (steaming without searching);;;0;
+3;102;;;;1;1;0;[deprecated] Searching (in general);Searching;;;0;
+;104;;;;1;0;0;Transit (added by t3R);;;;0;Activity added by t3R to allocate time at sea when no activity allows the time at sea declared on a given date to be allocated.
+;105;;;;1;1;0;Searching  (added by t3R);;;;0;Activity added by t3R to allocate fishing time when no activity allows the fishing time on a given date to be allocated.