,
Agroscope [cph]| Title: | The Swiss Register of Plant Protection Products as an R Package |
|---|---|
| Description: | Functions to generate data objects from XML versions of the Swiss Register of Plant Protection Products 'SRPPP'. An online version of the register can be accessed at <https://www.psm.admin.ch/de/produkte>. There is no guarantee of correspondence of the data read in using this package with that online version, or with the original registration documents. Also, the Federal Food Safety and Veterinary Office, coordinating the authorisation of plant protection products in Switzerland, does not answer requests regarding this package. |
| Authors: | Marcel Mathis [ctb, rev],
Romualdus Kasteel [rev] (Provided feedback to version 0.3.4),
Daniel Baumgartner [ctb] (Provided feedback, explanations and
background information),
Johannes Ranke [aut, cre] ,
Agroscope [cph] |
| Maintainer: | Johannes Ranke <[email protected]> |
| License: | GPL (>= 3) |
| Version: | 0.99.3 |
| Built: | 2024-09-10 18:18:37 UTC |
| Source: | https://github.com/agroscope-ch/srppp |
This function searches for uses of a given list of active substances and reports either a table of uses with the number of available alternative products for each use, a detailed table of the alternative product uses, a table of uses without alternatives, or a list containing these three tables.
alternative_products( srppp, active_ingredients, details = FALSE, missing = FALSE, list = FALSE, lang = c("de", "fr", "it") )alternative_products( srppp, active_ingredients, details = FALSE, missing = FALSE, list = FALSE, lang = c("de", "fr", "it") )
srppp |
A srppp_dm object. |
active_ingredients |
Character vector of active ingredient names that will be matched against the column 'substances_de' in the srppp table 'substances'. |
details |
Should a table of alternative uses with 'wNbr' 'use_nr' be returned? |
missing |
If this is set to TRUE, uses without alternative product registrations are listed. |
list |
If TRUE, a list of three tables is returned, a table of uses without alternative products ("Lückenindikationen"), a table of the number of alternative products for each use, if any, and a detailed table of all the alternative uses. This argument overrides the arguments 'details' and 'missing'. |
lang |
The language used for the active ingredient names and the returned tables. |
A use is defined as a combination of an application area, a crop ('culture') and a pathogen ('pest').
## Not run: sr <- srppp_dm() actives_de <- c("Lambda-Cyhalothrin", "Deltamethrin") alternative_products(sr, actives_de) alternative_products(sr, actives_de, missing = TRUE) alternative_products(sr, actives_de, details = TRUE) alternative_products(sr, actives_de, list = TRUE) # Example in Italian actives_it <- c("Lambda-Cialotrina", "Deltametrina") alternative_products(sr, actives_it, lang = "it") ## End(Not run)## Not run: sr <- srppp_dm() actives_de <- c("Lambda-Cyhalothrin", "Deltamethrin") alternative_products(sr, actives_de) alternative_products(sr, actives_de, missing = TRUE) alternative_products(sr, actives_de, details = TRUE) alternative_products(sr, actives_de, list = TRUE) # Example in Italian actives_it <- c("Lambda-Cialotrina", "Deltametrina") alternative_products(sr, actives_it, lang = "it") ## End(Not run)
An application rate in g active substance/ha is calculated from information on dosage (product concentration in the application solution), application volume, or directly from the product application rate. This is complicated by the fact that a rate ("expenditure" in the XML file) with units l/ha can refer to the application solution or to the liquid product.
application_rate_g_per_ha( product_uses, aggregation = c("max", "mean", "min"), dosage_units = c("percent_ww", "percent_vv", "state_of_matter"), skip_l_per_ha_without_g_per_L = TRUE, fix_l_per_ha = TRUE )application_rate_g_per_ha( product_uses, aggregation = c("max", "mean", "min"), dosage_units = c("percent_ww", "percent_vv", "state_of_matter"), skip_l_per_ha_without_g_per_L = TRUE, fix_l_per_ha = TRUE )
product_uses |
A tibble containing the columns 'pNbr', 'use_nr', 'application_area_de', 'min_dosage', 'max_dosage', 'min_rate', 'max_rate', from the 'uses' table in a srppp_dm object, as well as the columns 'percent' and 'g_per_L' from the 'ingredients' table in a srppp_dm object. |
aggregation |
How to represent a range if present, e.g. "max" (default) or "mean". |
dosage_units |
If no units are given, or units are "%", then the applied amount in g/ha is calculated using a reference application volume and the dosage. As the dosage units are not explicitly given, we can specify our assumptions about these using this argument (currently not implemented, i.e. specifying the argument has no effect). |
skip_l_per_ha_without_g_per_L |
Per default, uses where the use rate has units of l/ha are skipped, if there is not product concentration in g/L. This was also done in the 2023 indicator project. |
fix_l_per_ha |
During the review of the 2023 indicator project calculations, a number of cases were identified where the unit l/ha specifies a water volume, and not a product volume. If TRUE (default), these cases are corrected, if FALSE, these cases are discarded. |
In some cases (currently one), external information was found, indicating that the "expenditure" is an application volume l_per_ha_is_water_volume.
A tibble containing one additional column 'rate_g_per_ha'
A reference application volume is used if there is no 'expenditure'. It is selected only based on the product application area. This is not correct if hops ('Hopfen') is the culture, as it has a unique reference application volume of 3000 L/ha.
Applications to hops were excluded for calculating mean use rates in the indicator project (Korkaric 2023), arguing that it is not grown in large areas in Switzerland.
## Not run: library(srppp) library(dplyr, warn.conflicts = FALSE) library(dm, warn.conflicts = FALSE) sr <- srppp_dm() product_uses_with_ingredients <- sr$substances |> filter(substance_de %in% c("Halauxifen-methyl", "Kupfer (als Kalkpr\u00E4parat)")) |> left_join(sr$ingredients, by = "pk") |> left_join(sr$uses, by = "pNbr") |> left_join(sr$products, by = "pNbr") |> select(pNbr, name, use_nr, min_dosage, max_dosage, min_rate, max_rate, units_de, application_area_de, substance_de, percent, g_per_L) application_rate_g_per_ha(product_uses_with_ingredients) |> filter(name %in% c("Cerelex", "Pixxaro EC", "Bordeaux S")) |> select(ai = substance_de, app_area = application_area_de, min_d = min_dosage, max_d = max_dosage, min_r = min_rate, max_r = max_rate, units_de, rate = rate_g_per_ha) |> print(n = Inf) ## End(Not run)## Not run: library(srppp) library(dplyr, warn.conflicts = FALSE) library(dm, warn.conflicts = FALSE) sr <- srppp_dm() product_uses_with_ingredients <- sr$substances |> filter(substance_de %in% c("Halauxifen-methyl", "Kupfer (als Kalkpr\u00E4parat)")) |> left_join(sr$ingredients, by = "pk") |> left_join(sr$uses, by = "pNbr") |> left_join(sr$products, by = "pNbr") |> select(pNbr, name, use_nr, min_dosage, max_dosage, min_rate, max_rate, units_de, application_area_de, substance_de, percent, g_per_L) application_rate_g_per_ha(product_uses_with_ingredients) |> filter(name %in% c("Cerelex", "Pixxaro EC", "Bordeaux S")) |> select(ai = substance_de, app_area = application_area_de, min_d = min_dosage, max_d = max_dosage, min_r = min_rate, max_r = max_rate, units_de, rate = rate_g_per_ha) |> print(n = Inf) ## End(Not run)
Use definitions where the rate in l/ha refers to the volume of the spraying solution
l_per_ha_is_water_volumel_per_ha_is_water_volume
An object of class tbl_df (inherits from tbl, data.frame) with 1 rows and 4 columns.
library(srppp) l_per_ha_is_water_volumelibrary(srppp) l_per_ha_is_water_volume
While reading in the data, the information obtained from the XML file is
left unchanged, with the exceptions listed in the section 'Details'.
An overview of the contents of the most important tables in the resulting
data object is given in vignette("srppp").
srppp_dm(from = srppp_xml_url, remove_duplicates = TRUE) ## S3 method for class 'srppp_dm' print(x, ...)srppp_dm(from = srppp_xml_url, remove_duplicates = TRUE) ## S3 method for class 'srppp_dm' print(x, ...)
from |
A specification of the way to retrieve the XML |
remove_duplicates |
Should duplicates based on wNbrs be removed? |
x |
A srppp_dm object |
... |
Not used |
In the following case, the product composition is corrected while reading in the data: The active substance content of Dormex (W-3066) is not 667 g/L, but 520 g/L This was confirmed by a visit to the Wädenswil archive by Johannes Ranke and Daniel Baumgartner, 2024-03-27.
Information on products that has been duplicated across several products sharing the same P-Number has been associated directly with this P-Number, in order to avoid duplications. While reading in the XML file, it is checked that the resulting deduplication does not remove any data.
In very few cases of historical XML files, there are two <Product>
sections sharing the same W-Number. In these cases, one of these has apparently
been included in error and an informed decision is taken while reading in
the data which one of these sections is discarded. The details of this
procedure can be found in the source code of the function
srppp_xml_get_products.
In the table of obligations, the following information on mitigation measures is extracted from the ones relevant for the environment (SPe 3).
"sw_drift_dist": Unsprayed buffer towards surface waters to mitigate spray drift in meters
"sw_runoff_dist": Vegetated buffer towards surface waters to mitigate runoff in meters
"sw_runoff_points": Required runoff mitigation points to mitigate runoff
"biotope_drift_dist": Unsprayed buffer towards biotopes (as defined in articles 18a and 18b of the Federal Act on the Protection of Nature and Cultural Heritage) to mitigate spray drift in meters
A dm::dm object with tables linked by foreign keys pointing to primary keys, i.e. with referential integrity.
library(dplyr, warn.conflicts = FALSE) library(dm, warn.conflicts = FALSE) sr <- srppp_dm() dm_examine_constraints(sr) ## Not run: dm_draw(sr) ## End(Not run) # Show ingredients for products named 'Boxer' sr$products |> filter(name == "Boxer") |> left_join(sr$ingredients, by = "pNbr") |> left_join(sr$substances, by = "pk") |> select(wNbr, name, pNbr, isSalePermission, substance_de, g_per_L) # Show authorised uses of the original product boxer_uses <- sr$products |> filter(name == "Boxer", !isSalePermission) |> left_join(sr$uses, by = "pNbr") |> select(pNbr, use_nr, min_dosage, max_dosage, min_rate, max_rate, units_de, waiting_period, time_units_de, application_area_de) print(boxer_uses) # Show crop for use number 1 boxer_uses |> filter(use_nr == 1) |> left_join(sr$cultures, join_by(pNbr, use_nr)) |> select(use_nr, culture_de) # Show target pests for use number 1 boxer_uses |> filter(use_nr == 1) |> left_join(sr$pests, join_by(pNbr, use_nr)) |> select(use_nr, pest_de) # Show obligations for use number 1 boxer_uses |> filter(use_nr == 1) |> left_join(sr$obligations, join_by(pNbr, use_nr)) |> select(use_nr, sw_runoff_points, obligation_de) |> knitr::kable() |> print() # Show application comments for use number 1 boxer_uses |> filter(use_nr == 1) |> left_join(sr$application_comments, join_by(pNbr, use_nr)) |> select(use_nr, application_comment_de)library(dplyr, warn.conflicts = FALSE) library(dm, warn.conflicts = FALSE) sr <- srppp_dm() dm_examine_constraints(sr) ## Not run: dm_draw(sr) ## End(Not run) # Show ingredients for products named 'Boxer' sr$products |> filter(name == "Boxer") |> left_join(sr$ingredients, by = "pNbr") |> left_join(sr$substances, by = "pk") |> select(wNbr, name, pNbr, isSalePermission, substance_de, g_per_L) # Show authorised uses of the original product boxer_uses <- sr$products |> filter(name == "Boxer", !isSalePermission) |> left_join(sr$uses, by = "pNbr") |> select(pNbr, use_nr, min_dosage, max_dosage, min_rate, max_rate, units_de, waiting_period, time_units_de, application_area_de) print(boxer_uses) # Show crop for use number 1 boxer_uses |> filter(use_nr == 1) |> left_join(sr$cultures, join_by(pNbr, use_nr)) |> select(use_nr, culture_de) # Show target pests for use number 1 boxer_uses |> filter(use_nr == 1) |> left_join(sr$pests, join_by(pNbr, use_nr)) |> select(use_nr, pest_de) # Show obligations for use number 1 boxer_uses |> filter(use_nr == 1) |> left_join(sr$obligations, join_by(pNbr, use_nr)) |> select(use_nr, sw_runoff_points, obligation_de) |> knitr::kable() |> print() # Show application comments for use number 1 boxer_uses |> filter(use_nr == 1) |> left_join(sr$application_comments, join_by(pNbr, use_nr)) |> select(use_nr, application_comment_de)
Clean product names
srppp_xml_clean_product_names(names)srppp_xml_clean_product_names(names)
names |
The product names that should be cleaned from comments |
Define use identification numbers in an SRPPP read in from an XML file
srppp_xml_define_use_numbers(srppp_xml = srppp_xml_get())srppp_xml_define_use_numbers(srppp_xml = srppp_xml_get())
srppp_xml |
An object as returned by 'srppp_xml_get' |
An srppp_xml object with use_nr added as an attribute of 'Indication' nodes.
srppp_xml_define_use_numbers()srppp_xml_define_use_numbers()
Read an XML version of the Swiss Register of Plant Protection Products
srppp_xml_get(from, ...) ## S3 method for class ''NULL'' srppp_xml_get(from, ...) ## S3 method for class 'character' srppp_xml_get(from, ...) srppp_xml_get_from_path(path, from)srppp_xml_get(from, ...) ## S3 method for class ''NULL'' srppp_xml_get(from, ...) ## S3 method for class 'character' srppp_xml_get(from, ...) srppp_xml_get_from_path(path, from)
from |
A specification of the way to retrieve the XML |
... |
Unused argument introduced to facilitate future extensions |
path |
A path to a zipped SRPPP XML file |
An object inheriting from 'srppp_xml', 'xml_document', 'xml_node'
# The current SRPPP as available from the FOAG website srppp_cur <- srppp_xml_get() # The current SRPPP as available from the FOAG website srppp_cur <- srppp_xml_get(srppp_xml_url)# The current SRPPP as available from the FOAG website srppp_cur <- srppp_xml_get() # The current SRPPP as available from the FOAG website srppp_cur <- srppp_xml_get(srppp_xml_url)
Get ingredients for all products described in an XML version of the Swiss Register of Plant Protection Products
srppp_xml_get_ingredients(srppp_xml = srppp_xml_get())srppp_xml_get_ingredients(srppp_xml = srppp_xml_get())
srppp_xml |
An object as returned by 'srppp_xml_get' |
srppp_xml_get_ingredients()srppp_xml_get_ingredients()
Get Parallel Imports from an XML version of the Swiss Register of Plant Protection Products
srppp_xml_get_parallel_imports(srppp_xml = srppp_xml_get())srppp_xml_get_parallel_imports(srppp_xml = srppp_xml_get())
srppp_xml |
An object as returned by 'srppp_xml_get' |
A tibble::tibble with a row for each parallel import section in the XML file.
# Get current list of parallel_imports srppp_xml_get_parallel_imports()# Get current list of parallel_imports srppp_xml_get_parallel_imports()
Get Products from an XML version of the Swiss Register of Plant Protection Products
srppp_xml_get_products( srppp_xml = srppp_xml_get(), verbose = TRUE, remove_duplicates = TRUE )srppp_xml_get_products( srppp_xml = srppp_xml_get(), verbose = TRUE, remove_duplicates = TRUE )
srppp_xml |
An object as returned by 'srppp_xml_get' |
verbose |
Should we give some feedback? |
remove_duplicates |
Should duplicates based on wNbrs be removed? If set to 'TRUE', one of the two entries with identical wNbrs is removed, based on an investigation of background information carried out by the package authors. In all cases except for one, one of the product sections with duplicate wNbrs has information about an expiry of the registration, and the other doesn't. In these cases the registration without expiry is kept, and the expiring registration is discarded. In the remaining case (wNbr 5945), the second entry is selected, as it contains more indications which were apparently intended to be published as well. |
A tibble::tibble with a row for each product section in the XML file. An attribute 'duplicated_wNbrs' is also returned, containing duplicated W-Numbers, if applicable, or NULL.
# Get current list of products srppp_xml_get_products()# Get current list of products srppp_xml_get_products()
Get substances from an XML version of the Swiss Register of Plant Protection Products
srppp_xml_get_substances(srppp_xml = srppp_xml_get())srppp_xml_get_substances(srppp_xml = srppp_xml_get())
srppp_xml |
An object as returned by 'srppp_xml_get' |
srppp_xml_get_substances()srppp_xml_get_substances()
Get uses ('indications') for all products described in an XML version of the Swiss Register of Plant Protection Products
srppp_xml_get_uses(srppp_xml = srppp_xml_get())srppp_xml_get_uses(srppp_xml = srppp_xml_get())
srppp_xml |
An object as returned by srppp_xml_get with use numbers defined by srppp_xml_define_use_numbers |
srppp_xml <- srppp_xml_get() srppp_xml <- srppp_xml_define_use_numbers(srppp_xml) srppp_xml_get_uses(srppp_xml)srppp_xml <- srppp_xml_get() srppp_xml <- srppp_xml_define_use_numbers(srppp_xml) srppp_xml_get_uses(srppp_xml)
URL of the XML version of the Swiss Register of Plant Protection Products
srppp_xml_urlsrppp_xml_url
length one character string
print(srppp_xml_url)print(srppp_xml_url)
Product application rate units convertible to grams active substance per hectare
units_convertible_to_g_per_haunits_convertible_to_g_per_ha
An object of class character of length 7.
library(srppp) library(dplyr) # These are the convertible units units_convertible_to_g_per_halibrary(srppp) library(dplyr) # These are the convertible units units_convertible_to_g_per_ha