Issue 273

.Rbuildignore

@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^data-raw$
@@ -17,3 +19,5 @@ package_overview.Rmd
 ^.pptx$
 ^_pkgdown\.yml$
 ^pkgdown$
+^\.positai$
+^\.claude$

.gitignore

@@ -33,14 +33,17 @@ FishNCo/testData/RegionalTestData/*
 ~$*
 /doc/
 /Meta/
-<<<<<<< Updated upstream
 .vscode/
 docs
-=======
 # Data to develop fun
 /NLdata/
->>>>>>> Stashed changes
 package_overview.tex
 package_overview.html
 package_overview.pptx
 package_overview.md
+
+# add renv stuff
+/renv/
+.Rprofile
+renv.lock
+.positai

DESCRIPTION

@@ -1,124 +1,124 @@
 Package: RDBEScore
 Type: Package
 Title: Functions for the ICES Regional Database and Estimation System (RDBES)
-Version: 0.3.5
+Version: 0.4.0
 Author: c(
-    person(given = "David", 
-           family = "Currie", 
-           role = c("aut"), 
+    person(given = "David",
+           family = "Currie",
+           role = c("aut"),
            comment = c(ORCID = "0000-0002-3523-6895")),
     person(given = "Richard",
            family = "Meitern",
            role =  c("aut"),
            email = "richard.meitern@ut.ee",
            comment = c(ORCID = "0000-0002-2600-3002")),
-    person(given = "Nuno", 
-           family = "Prista", 
-           role = c("aut"), 
-		   email = "nuno.prista@slu.se", 
+    person(given = "Nuno",
+           family = "Prista",
+           role = c("aut"),
+		   email = "nuno.prista@slu.se",
 		   comment = c(ORCID = "0000-0002-5145-7241")),
-    person(given = "Nicholas", 
-           family = "Carey", 
+    person(given = "Nicholas",
+           family = "Carey",
            role = c("aut"),
            email = "nicholas.carey@gov.scot"),
-    person(given = "Petri", 
-           family = "Sarvamaa", 
-           role = c("aut"), 
+    person(given = "Petri",
+           family = "Sarvamaa",
+           role = c("aut"),
            email = "Petri.Sarvamaa@luke.fi"),
-    person(given = "Kirsten", 
-           family = "Birch Håkansson", 
-           role = c("aut"), 
+    person(given = "Kirsten",
+           family = "Birch Håkansson",
+           role = c("aut"),
            email = "kih@aqua.dtu.dk"),
-    person(given = "Karolina", 
-           family = "Molla Gazi", 
-           role = c("aut"), 
-           email = "karolina.mollagazi@wur.nl"),	
-    person(given = "Julia", 
-           family = "Wischnewski", 
-           role = c("aut"), 
-           email = "julia.wischnewski@thuenen.de"),			   
-    person(given = "Ana Cláudia", 
-           family = "Fernandes", 
-           role = c("aut"), 
+    person(given = "Karolina",
+           family = "Molla Gazi",
+           role = c("aut"),
+           email = "karolina.mollagazi@wur.nl"),
+    person(given = "Julia",
+           family = "Wischnewski",
+           role = c("aut"),
+           email = "julia.wischnewski@thuenen.de"),
+    person(given = "Ana Cláudia",
+           family = "Fernandes",
+           role = c("aut"),
            email = "acfernandes@ipma.pt"),
-    person(given = "Katarzyna", 
-           family = "Krakówka", 
-           role = c("aut"), 
+    person(given = "Katarzyna",
+           family = "Krakówka",
+           role = c("aut"),
            email = "kkrakowka@mir.gdynia.pl"),
-    person(given = "Marta", 
-           family = "Szymańska", 
-           role = c("aut"), 
-           email = "msuska@mir.gdynia.pl"),	 
-	person(given = "Nicolas", 
-           family = "Goñi", 
-           role = c("aut"), 
-           email = "nicolas.goni@luke.fi"),	
-	person(given = "Annica", 
-           family = "de Groote", 
-           role = c("ctb"), 
-           email = "annica.isaksson.de.groote@slu.se"),		   
-	person(given = "Jonathan", 
-           family = "Ball", 
-           role = c("ctb"), 
+    person(given = "Marta",
+           family = "Szymańska",
+           role = c("aut"),
+           email = "msuska@mir.gdynia.pl"),
+	person(given = "Nicolas",
+           family = "Goñi",
+           role = c("aut"),
+           email = "nicolas.goni@luke.fi"),
+	person(given = "Annica",
+           family = "de Groote",
+           role = c("ctb"),
+           email = "annica.isaksson.de.groote@slu.se"),
+	person(given = "Jonathan",
+           family = "Ball",
+           role = c("ctb"),
            email = "johnathan.ball@cefas.co.uk"),
-	person(given = "Jonathan", 
-           family = "Rault", 
-           role = c("ctb"), 
+	person(given = "Jonathan",
+           family = "Rault",
+           role = c("ctb"),
            email = "Jonathan.Rault@ifremer.fr"),
-	person(given = "Antti", 
-           family = "Sykkö", 
-           role = c("ctb"), 
+	person(given = "Antti",
+           family = "Sykkö",
+           role = c("ctb"),
            email = "antti.sykko@luke.fi"),
-	person(given = "Liz", 
-           family = "Clarke", 
-           role = c("ctb"), 
+	person(given = "Liz",
+           family = "Clarke",
+           role = c("ctb"),
            email = "Liz.Clarke@gov.scot"),
-	person(given = "Chun", 
-           family = "Chen", 
-           role = c("ctb"), 
+	person(given = "Chun",
+           family = "Chen",
+           role = c("ctb"),
            email = "chun.chen@wur.nl"),
-	person(given = "Hongru", 
-           family = "Zhai", 
-           role = c("ctb"), 
+	person(given = "Hongru",
+           family = "Zhai",
+           role = c("ctb"),
            email = "hongru.zhai@slu.se"),
-	person(given = "Eros", 
-           family = "Quesada", 
-           role = c("ctb"), 
+	person(given = "Eros",
+           family = "Quesada",
+           role = c("ctb"),
            email = "eros.quesada@slu.se"),
-	person(given = "Jonathan", 
-           family = "Stounberg", 
-           role = c("ctb"), 
+	person(given = "Jonathan",
+           family = "Stounberg",
+           role = c("ctb"),
            email = "jostou@aqua.dtu.dk"),
-		   person(given = "Ana", 
-           family = "Ribeiro Santos", 
-           role = c("ctb"), 
+		   person(given = "Ana",
+           family = "Ribeiro Santos",
+           role = c("ctb"),
            email = "ana.ribeirosantos@cefas.co.uk"),
-	person(given = "Jose", 
-           family = "Castro", 
-           role = c("ctb"), 
-           email = "jose.castro@ieo.es"),		   
-	person(given = "Jessica", 
-           family = "Craig", 
-           role = c("ctb"), 
-           email = "Jessica.Craig@gov.scot")		   
-           )
-Maintainer: Colin Millar <colin.millar@ices.dk>
-Description: The RDBEScore package provides functions to import and work with  
-    fisheries data downloaded from the ICES RDBES database. It also contains 
-    functions to perform estimation analysis using the resulting objects. 
+	person(given = "Jose",
+           family = "Castro",
+           role = c("ctb"),
+           email = "jose.castro@ieo.es"),
+	person(given = "Jessica",
+           family = "Craig",
+           role = c("ctb"),
+           email = "Jessica.Craig@gov.scot"),
+  person(given = "Colin", family = "Millar", role = "ctb"),
+  person(given = "Ejaz", family = "Muhammad", role = "ctb"))
+Maintainer: Richard Meitern <richard.meitern@ut.ee>
+Description: The RDBEScore package provides functions to import and work with
+    fisheries data downloaded from the ICES RDBES database. It also contains
+    functions to perform estimation analysis using the resulting objects.
 URL: https://github.com/ices-tools-dev/RDBEScore, https://rdbes.ices.dk, https://ices-tools-dev.github.io/RDBEScore/
 License: GPL-3 + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
-Suggests: 
+Suggests:
     knitr,
     rmarkdown,
     testthat
-Depends: 
+Depends:
     R (>= 4.1)
-Imports: 
-    dplyr (>= 1.1.3), 
+Imports:
     data.table
 VignetteBuilder: knitr
+Config/roxygen2/version: 8.1.1

NAMESPACE

@@ -11,6 +11,7 @@ export(createRDBESDataObject)
 export(createRDBESEstObject)
 export(doBVestimCANUM)
 export(doEstimationForAllStrata)
+export(doEstimationRatio)
 export(estim)
 export(estimMC)
 export(exportEstimationResultsToInterCatchFormat)
@@ -34,10 +35,14 @@ export(updateSAwithTaxonFromSL)
 export(validateRDBESDataObject)
 export(validateRDBESEstObject)
 import(data.table)
-importFrom(stats,formula)
-importFrom(stats,na.omit)
-importFrom(stats,rnorm)
-importFrom(stats,setNames)
-importFrom(utils,file_test)
-importFrom(utils,packageDescription)
-importFrom(utils,tail)
+importFrom(stats,
+  formula,
+  na.omit,
+  rnorm,
+  setNames
+)
+importFrom(utils,
+  file_test,
+  packageDescription,
+  tail
+)

NEWS.md

@@ -1,3 +1,9 @@
+# RDBEScore 0.4.0
+- Breaking: `getLinkedDataFromLevel()` now returns the requested field and target-table columns in both directions, without adding intermediate hierarchy ids (#268). Non-id requested fields are retained when going down the hierarchy. `getLowerTableSubsets()` avoids duplicated requested-field columns.
+- Package README updated with AI usage guidelines
+- Dependencies: removed `dplyr` from Imports. Joins now use the internal `data.table` helper `joinDT()`, which keeps dplyr's row order, column order and `.x`/`.y` suffixes, so results are unchanged; `filterRDBESEstObject()` and the vignette use base R/`data.table` instead of dplyr.
+- Bug fix: addressed [#259](https://github.com/ices-tools-dev/RDBEScore/issues/259) selecting multiple strata with `addCLtoLowerCS()`
+
 # RDBEScore 0.3.5
 
 - Bug fix: addressed [#251](https://github.com/ices-tools-dev/RDBEScore/issues/251).

R/addCLtoLowerCS.R

@@ -47,7 +47,7 @@ addCLtoLowerCS <- function(rdbes, strataListCS, strataListCL, combineStrata =T,
   # Function to subset data.table based on criteria list
   subset_dt <- function(dt, criteria) {
     for (field in names(criteria)) {
-      dt <- dt[get(field) == criteria[[field]], ]
+      dt <- dt[get(field) %in% criteria[[field]], ]
     }
     return(dt)
   }

R/combineRDBESDataObjects.R

@@ -22,15 +22,12 @@
 #'
 #' @examples
 #' \dontrun{
-#'
-#' myH1RawObject <-
-#'     importRDBESDataCSV(rdbesExtractPath = "tests\\testthat\\h1_v_1_19")
-#' myH5RawObject <-
-#'     importRDBESDataCSV(rdbesExtractPath = "tests\\testthat\\h5_v_1_19")
-#'
-#' myCombinedRawObject <- combineRDBESDataObjects(RDBESDataObject1=myH1RawObject,
-#'                                              RDBESDataObject2=myH5RawObject)
-#' }
+#' myH1DataObject <- H1Example
+#' myH5DataObject <- H5Example
+#' myCombinedRawObject <- combineRDBESDataObjects(RDBESDataObject1=myH1DataObject,
+#'                                              RDBESDataObject2=myH5DataObject)
+#' myCombinedRawObject <- combineRDBESDataObjects(RDBESDataObject1=myH1DataObject,
+#'                                              RDBESDataObject2=myH5DataObject, strict=F)}                                              RDBESDataObject2=myH5RawObject)
 combineRDBESDataObjects <- function(RDBESDataObject1,
                                     RDBESDataObject2,
                                     verbose = FALSE,

R/createDBEPrepObj.R

@@ -12,7 +12,7 @@
 #' input <- "WKRDB-EST2/testData/output/DBErawObj/"
 #' output <- "WKRDB-EST2/subGroup1/personal/John/PreparedOutputs/"
 #'
-#' createDBEPrepObj(input = input, output = output)
+#' RDBEScore:::createDBEPrepObj(input = input, output = output)
 #' }
 createDBEPrepObj <- function(input, output) {