srppp (version 2.0.2)

resolve_cultures: Resolve culture specifications to their lowest hierarchical level

Description

Resolves culture levels in a dataset to their lowest hierarchical level (leaf nodes) using a parent-child relationship dataset derived from a culture tree using the German culture names. Only German culture names are supported. If no match is found, the function assigns NA to the leaf_culture_de column. If correct_culture_names is set to TRUE, the function corrects variations in the naming of aggregated culture groups with "allg.".

Usage

resolve_cultures(
  dataset,
  srppp,
  culture_column = "culture_de",
  application_area_column = "application_area_de",
  correct_culture_names = TRUE,
  resolve_culture_allg = TRUE
)

Value

A data frame or tibble with the same structure as the input dataset, but with an additional column "leaf_culture_de" that contains the resolved leaf culture levels. For cultures, that are not defined in the register, the leaf culture is set to NA.

Arguments

dataset

A data frame or tibble containing the data to be processed. It should include a column that represents the culture information to be resolved.

srppp

An srppp_dm object. From this object the relations from each culture to the leaf cultures (lowest level in the hierarchical tree) are used, which are stored as attribute 'culture_leaf_df' of the culture tree, which is itself stored as an attribute of the object.

culture_column

(Optional) A character string specifying the column in the dataset that contains the culture information to be resolved. Defaults to "culture_de".

application_area_column

(Optional). A character string specifing the name of the column in dataset containing application area information. Default is "application_area_de".

correct_culture_names

If this argument is set to TRUE, the following corrections will be applied: In the culture_tree, and consequently in the culture_leaf_df, there are variations in the naming of aggregated culture groups with "allg.". For example, both "Obstbau allg." and "allg. Obstbau" exist. The information about the leaf nodes is only available in one of these terms. Therefore, the information from the term containing the leaf nodes is transferred to the corresponding "allg. ..." term.

resolve_culture_allg

If this argument is set to TRUE, the culture "allg." is resolved to their lowest hierarchical level. The information on the application area is additionally used to resolve the culture "allg." to the lowest hierarchical level. For example if the culture "allg." is used in the application area "Obstbau", only the leaf cultures of the culture "Obstbau" are used to resolve the culture "allg.". If the application area is not found in the culture tree, all leaf cultures are used to resolve the culture "allg.".

Details

The resolve_cultures function processes the input dataset as follows

Leaf Node Resolution: The cultures in the specified column of the dataset are resolved to their lowest hierarchical level (leaf nodes) based on the culture_leaf_df mapping.

The result is an expanded dataset that includes an additional column (leaf_culture_de) containing the resolved cultures at their lowest level.

Examples

# \donttest{
library(srppp)
sr <- try(srppp_dm())

if (inherits(sr, "try-error")) {
  sr <- system.file("testdata/Daten_Pflanzenschutzmittelverzeichnis_2024-12-16.zip",
      package = "srppp") |>
    srppp_xml_get_from_path(from = "2024-12-16") |>
    srppp_dm()
}

example_dataset_1 <- data.frame(
  substance_de = c("Spirotetramat", "Spirotetramat", "Spirotetramat", "Spirotetramat"),
  pNbr = c(7839, 7839, 7839, 7839),
  use_nr = c(5, 7, 18, 22),
  application_area_de = c("Obstbau", "Obstbau", "Obstbau", "Obstbau"),
  culture_de = c("Birne", "Kirsche", "Steinobst", "Kernobst"),
    pest_de = c("Birnblattsauger", "Kirschenfliege", "Blattläuse (Röhrenläuse)", "Spinnmilben"))

# Same as above, but with culture name "Kirschen" instead of "Kirsche"
example_dataset_2 <- data.frame(
  substance_de = c("Spirotetramat", "Spirotetramat", "Spirotetramat", "Spirotetramat"),
  pNbr = c(7839, 7839, 7839, 7839),
  use_nr = c(5, 7, 18, 22),
  application_area_de = c("Obstbau", "Obstbau", "Obstbau", "Obstbau"),
  culture_de = c("Birne", "Kirschen", "Steinobst", "Kernobst"),
  pest_de = c("Birnblattsauger", "Kirschenfliege", "Blattläuse (Röhrenläuse)", "Spinnmilben"))

resolve_cultures(example_dataset_1, sr)

# Here we get NA for the leaf culture of "Kirschen"
resolve_cultures(example_dataset_2, sr)

# Example showing how cereals "Getreide" are resolved
example_dataset_3 <- data.frame(
  substance_de = c("Pirimicarb"),
  pNbr = c(2210),
  use_nr = c(3),
  application_area_de = c("Feldbau"),
  culture_de = c("Getreide"),
  pest_de = c("Blattläuse (Röhrenläuse)") )

resolve_cultures(example_dataset_3, sr)

# Example resolving ornamental plants ("Zierpflanzen")
example_dataset_4 <- data.frame(substance_de = c("Metaldehyd"),
 pNbr = 6142, use_nr = 1, application_area_de = c("Zierpflanzen"),
 culture_de = c("Zierpflanzen allg."), pest_de = c("Ackerschnecken/Deroceras Arten") )

resolve_cultures(example_dataset_4, sr)

# Illustrate the resolution of the culture "allg."
example_dataset_5 <- data.frame(
  substance_de = c("Kupfer (als Oxychlorid)","Metaldehyd","Metaldehyd","Schwefel"),
  pNbr = c(585,1090,1090,38),
  use_nr = c(12,4,4,1),
  application_area_de = c("Weinbau","Obstbau","Obstbau","Beerenbau"),
  culture_de = c("allg.","allg.","allg.","Brombeere"),
  pest_de = c("Graufäule (Botrytis cinerea)","Wegschnecken/Arion Arten",
    "Wegschnecken/Arion Arten","Gallmilben"))

 resolve_cultures(example_dataset_5, sr, resolve_culture_allg = FALSE)
 resolve_cultures(example_dataset_5, sr)

# Illustrate the resolution of "Obstbau allg.", which does not have children in
# the XML files, but which should have children, because Obstbau allg. is
# not a leaf culture.
example_dataset_6 <- data.frame(
  substance_de = c("Schwefel"),
  pNbr = c(3561),
  use_nr = c(4),
  application_area_de = c("Obstbau"),
  culture_de = c("Obstbau allg."),
  pest_de = c("Wühl- oder Schermaus") )

 resolve_cultures(example_dataset_6, sr,
   correct_culture_names = FALSE)
 resolve_cultures(example_dataset_6, sr,
   correct_culture_names = TRUE)
# }