getting linked table subsets function exported

R/getLinkedDataFromLevel.R

@@ -0,0 +1,69 @@
+#' Retrieve Linked Data Between RDBES Tables at a Specified Level
+#'
+#' The `getLinkedDataFromLevel` function facilitates the retrieval of linked data between different levels of RDBES tables. Depending on the relative positions of the source and target tables within the `RDBESDataObject`, the function determines whether to traverse "up" or "down" the data hierarchy to obtain the desired linked data.
+#'
+#' @param field A character string specifying the field name from which to retrieve linked data. The first two characters of this field indicate the source table.
+#' @param values A vector of values corresponding to the specified `field` for which linked data is to be retrieved.
+#' @param rdbesTables An `RDBESDataObject` containing the relevant RDBES tables. This object should include all tables that may be linked based on the provided `field` and `level`.
+#' @param level A character string specifying the target table level from which to retrieve linked data. This must be one of the names within the `rdbesTables` object.
+#' @param verbose Logical flag indicating whether to print detailed information about the data retrieval process. Default is `FALSE`.
+#'
+#' @return  The subset of the table at the specified `level`.
+#'
+#' @examples
+#' \dontrun{
+#' # Example 1: Going up in the table hierarchy to retrieve data from the DE table
+#' # Retrieve data from the DE level based on BVid from the BV table
+#' # This returns 1 row from the DE table
+#' getLinkedDataFromLevel("BVid", c(1), H8ExampleEE1, "DE", TRUE)
+#'
+#' # Example 2: Going down in the table hierarchy to retrieve data from the SA table
+#' # Retrieve data from the SA level based on DEid from the DE table
+#' # This returns 15 rows from the SA table
+#' getLinkedDataFromLevel("DEid", c(1), H8ExampleEE1, "SA", TRUE)
+#'
+#' # Example 3: Going up in the table hierarchy to see the Vessel that caught a specific fish
+#' # Retrieve data from the VS level based on BVfishId from the BV table
+#' getLinkedDataFromLevel("BVfishId", c("410472143", "410472144"), H8ExampleEE1, "VS", TRUE)
+#' }
+#' @export
+getLinkedDataFromLevel <- function(field, values, rdbesTables, level, verbose = FALSE){
+
+  # Check if rdbesTables is of class "RDBESDataObject"
+  if(inherits(rdbesTables, "RDBESDataObject")) {
+    rdbesTables <- sort(rdbesTables)
+  } else {
+    stop("rdbesTables must be of class RDBESDataObject")
+  }
+
+  # Check if the specified level exists within rdbesTables
+  if(!level %in% names(rdbesTables)){
+    stop("Table ", level, " not found in the RDBESDataObject")
+  }
+
+  # Extract the source table abbreviation from the field name
+  sourceTbl <- substr(field, 1, 2)
+
+  # Get the list of table names
+  tblNames <- names(rdbesTables)
+
+  # Determine the positions of sourceTbl and target level in the table list
+  sourcePos <- which(tblNames == sourceTbl)
+  targetPos <- which(tblNames == level)
+
+  # Determine traversal direction based on table positions
+  res <- NULL
+  if(sourcePos > targetPos){
+    if(verbose){
+      cat("Traversing upwards in the table hierarchy from", sourceTbl, "to", level, "\n")
+    }
+    res <- upperTblData(field, values, rdbesTables, level, verbose)
+  } else {
+    if(verbose){
+      cat("Traversing downwards in the table hierarchy from", sourceTbl, "to", level, "\n")
+    }
+    res <- lowerTblData(field, values, rdbesTables, level, verbose)
+  }
+
+  return(res)
+}

R/getLowerTableSubsets.R

@@ -22,24 +22,10 @@
 #' based on the ID column of the target table.
 #'
 getLowerTableSubsets <- function(subsets, tblName, rdbesTables, combineStrata = TRUE, verbose = FALSE) {
-  # Check if rdbesTables is of class "RDBESDataObject"
-  if(inherits(rdbesTables, "RDBESDataObject")) {
-    tableNames <- names(summary(rdbesTables)$data)
-    # Select only the relevant hierarchy table names
-    rdbesTables <- rdbesTables[tableNames]
-  } else {
-    stop("rdbesTables must be of class RDBESDataObject")
-  }
-  if(!tblName %in% names(rdbesTables)){
-    stop("Table ", tblName, " not found in the RDBESData object")
-  }
-
   res <- list()
-  if(verbose) print("Getting lower table data")
-
   # Process each subset
   for(ss in names(subsets)){
-    res[[ss]] <- lowerTblData(ss, subsets[[ss]], rdbesTables, tblName, verbose)
+    res[[ss]] <- getLinkedDataFromLevel(ss, subsets[[ss]], rdbesTables, tblName, verbose)
   }
 
   # Function to get the intersection of IDs

R/lowerTblData.R

@@ -27,7 +27,6 @@
 #' tblsSprat <- list( DE = DE ,SD = SD, TE = TE, VS = VS, LE = LE )
 #'
 #' lowerTblData("TEid", c(4), tblsSprat, "LE", T)
-#'@export
 lowerTblData <- function(field, values, tbls, level, verbose = FALSE) {
   #check if tables are of correct type
   if(!is.list(tbls)) stop("tbls must be a list")

R/upperTblData.R

@@ -29,7 +29,6 @@
 #' VS <- data.table(VSid = c(1, 2),SDid =c(1,2),  value = c(10, 20))
 #' tbls <- list(DE = DE, SD = SD, VS = VS)
 #' upperTblData("VSid", c(1), tbls, "DE")
-#'@export
 upperTblData <- function(field, values, tbls, level, verbose = FALSE){
   #check if tables are of correct type
   if(!is.list(tbls)) stop("tbls must be a list")

tests/testthat/test-getLinkedDataFromLevel.R

@@ -0,0 +1,63 @@
+
+# Test for Example 1: Going up in the table hierarchy to retrieve data from the DE table
+test_that("Retrieve data from DE based on BVid", {
+  result <- getLinkedDataFromLevel("BVid", c(1), H8ExampleEE1, "DE")
+
+  # Check that the result is a data.table (or other expected data structure)
+  expect_s3_class(result, "data.table")
+
+  # Check that the result has 1 row, as expected
+  expect_equal(nrow(result), 1)
+
+})
+
+# Test for Example 2: Going down in the table hierarchy to retrieve data from the SA table
+test_that("Retrieve data from SA based on DEid", {
+  result <- getLinkedDataFromLevel("DEid", c(1), H8ExampleEE1, "SA")
+
+  # Check that the result is a data.table (or other expected data structure)
+  expect_s3_class(result, "data.table")
+
+  # Check that the result has 15 rows, as expected
+  expect_equal(nrow(result), 15)
+
+})
+
+# Test for Example 3: Going up in the table hierarchy to retrieve data from the VS table based on BVfishId
+test_that("Retrieve data from VS based on BVfishId", {
+  result <- getLinkedDataFromLevel("BVfishId", c("410472143", "410472144"), H8ExampleEE1, "VS")
+
+  # Check that the result is a data.table (or other expected data structure)
+  expect_s3_class(result, "data.table")
+
+  # Check that the result contains data (you can adjust this depending on known expected results)
+  expect_equal(nrow(result), 1)
+
+  # Optionally, check for specific values in the result
+
+})
+
+test_that("Error when rdbesTables is not of class RDBESDataObject", {
+  # Pass an invalid class (e.g., a list) instead of RDBESDataObject
+  invalid_rdbesTables <- list()
+
+  # Expect the function to throw an error
+  expect_error(
+    getLinkedDataFromLevel("BVid", c(1), invalid_rdbesTables, "DE"),
+    "rdbesTables must be of class RDBESDataObject"
+  )
+})
+
+test_that("Error when level is not found in rdbesTables", {
+  # Assume H8ExampleEE1 is a valid RDBESDataObject, but "XX" is not a valid level
+  expect_error(
+    getLinkedDataFromLevel("BVid", c(1), H8ExampleEE1, "XX"),
+    "Table XX not found in the RDBESDataObject"
+  )
+})
+
+
+
+
+
+

tests/testthat/test-getLowerTableSubsets.R

@@ -21,7 +21,7 @@ test_that("Function throws error for missing table name", {
   subsets <- list(TEid = c(4))
 
   expect_error(getLowerTableSubsets(subsets, "XYZ", H8ExampleEE1),
-               "Table XYZ not found in the RDBESData object")
+               "Table XYZ not found in the RDBESDataObject")
 })
 
 test_that("Function returns correct data with valid inputs", {

vignettes/manipulating-rdbesdataobjects.Rmd

@@ -186,7 +186,35 @@ validateRDBESDataObject(myFilteredObjectValidSpeciesLinks, verbose = FALSE)
 
 ```
 
+## Getting Subsets of RDBESDataObject Tables
 
+Sometimes it we want to see how a field or values in the **RDBESDataObject** are connected to otther tables.
+One use case would be e.g. to see when a specific Landing Event (LE) occured.For this we can use the **getLinkedDataFromLevel()** function. 
+
+```{r}
+#get the TE table corresponding to the first LEid in the H8ExampleEE1 object
+getLinkedDataFromLevel("LEid", c(1), H8ExampleEE1, "TE", verbose = TRUE)
+```
+Similarly we can get the subset of the LE table corresponding to a specific value in the TE table. This does not have to be the *id* field, but can be any field in the table.
+
+```{r}
+#get the TE table corresponding to the first LEid in the H8ExampleEE1 object
+getLinkedDataFromLevel("TEstratumName", c("November"), H8ExampleEE1, "LE", verbose = TRUE)
+```
+Several values can be used to get a subset of the table. 
+
+```{r}
+#get the SA table corresponding to the first 2 TEids in the H8ExampleEE1 object
+getLinkedDataFromLevel("TEid", c(1,2), H8ExampleEE1, "SA", verbose = TRUE)
+```
+Also lower hierarchy tables can be used to get the subset of the higher hierarchy tables.
+
+```{r}
+#which vessel caught those fish?
+getLinkedDataFromLevel("BVfishId", c("410472143", "410472144"), H8ExampleEE1, "VS", TRUE)
+```
+
+If some table is missing it is skipped if possible. If it is not possible to skip it, the function will return an error.
 
 See also other package vignettes: