Extract data from SpiGes XML files using R programming.
Installation
# install from the r-universe
install.packages("SpiGesXML", repos = "https://swissstatsr.r-universe.dev")
# install from GitHub
remotes::install_github("SwissStatsR/SpiGesXML")Examples
Using spiges_get_df(), you can get the data from any SpiGes XML file using the x argument. The x argument can be an URL or the path of a give XML file.
library(SpiGesXML)
# SpiGes XML file example
# https://www.bfs.admin.ch/bfs/de/home/statistiken/gesundheit/gesundheitswesen/projekt-spiges.assetdetail.27905035.html
xml_example <- "https://dam-api.bfs.admin.ch/hub/api/dam/assets/32129227/master"
spiges_get_df(x = xml_example, node = "Administratives")## ✔ Format correctly validated using spiges-data v.1.4.
## # A tibble: 13 × 34
## ent_id burnr fall_id burnr…¹ abc_f…² gesch…³ alter alter…⁴ wohno…⁵ wohnk…⁶
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 100000012 1000… 1 712978… A 2 97 <NA> GE03 GE
## 2 100000012 1000… 2 712879… A 1 49 <NA> AG52 AG
## 3 100000012 1000… 3 712934… A 2 101 <NA> BE76 BE
## 4 100000012 1000… 4 712879… A 1 62 <NA> AG52 AG
## 5 100000012 1000… 5 712879… A 2 61 <NA> AG52 AG
## 6 100000012 1000… 6 712978… A 2 84 <NA> VD39 VD
## 7 100000012 1000… 7 712879… A 1 75 <NA> BE48 BE
## 8 100000012 1000… 8 711791… A 2 91 <NA> BE52 BE
## 9 100000012 1000… 9 712879… A 1 65 <NA> BE48 BE
## 10 100000012 1000… 10 712934… A 2 105 <NA> ZH29 ZH
## 11 100000012 1000… 11 711791… A 1 67 <NA> ZH23 ZH
## 12 100000012 1000… 12 712934… A 1 55 <NA> BS09 BS
## 13 100000012 1000… 13 712879… A 2 67 <NA> TI30 TI
## # … with 24 more variables: wohnland <chr>, nationalitaet <chr>,
## # eintrittsdatum <chr>, eintritt_aufenthalt <chr>, eintrittsart <chr>,
## # einw_instanz <chr>, liegeklasse <chr>, versicherungsklasse <chr>,
## # admin_urlaub <chr>, chlz <chr>, aufenthalt_ips <chr>, beatmung <chr>,
## # schwere_score <chr>, art_score <chr>, nems <chr>, aufenthalt_imc <chr>,
## # aufwand_imc <chr>, hauptleistungsstelle <chr>, grundversicherung <chr>,
## # tarif <chr>, austrittsdatum <chr>, austrittsentscheid <chr>, …If for some reasons there is no data for a given node, spiges_get_df() will return an error with suggestions of existing nodes in the SpiGes file.
spiges_get_df(x = xml_example, node = "Admin")Error in `spiges_get_df()`:
! `node` must be one of "Administratives", "Diagnose", "KostentraegerFall", "Behandlung", or "Rechnung", not "Admin".
ℹ Did you mean "Administratives"?The spiges_get_df() function validate internally the XML file. If correctly validated, it returns the data with a success message in the console. If the validation is incorrect, only an error message is returned. To return the data even with an incorrect validation, you can add use the force argument as TRUE.
Here an example of an incorrect format with an “INCORRECT VALUE” for “burnr”:
xml_file_incorrect <- system.file(
"example_incorrect_format.xml",
package = "SpiGesXML"
)
library(xml2) # install.packages("xml2")
# for example burnr="INCORRECT VALUE"
xml2::read_xml(xml_file_incorrect)## {xml_document}
## <Unternehmen ent_id="100000012" version="1.4" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.bfs.admin.ch/xmlns/gvs/spiges-data/1.4">
## [1] <Standort burnr="INCORRECT VALUE">\n <Fall fall_id="1">\n <Administra ...If you use this incorrect XML file, spiges_get_df() will return an error message (but the function can return the data anyway using force = TRUE):
spiges_get_df(
x = xml_file_incorrect,
node = "Administratives",
force = FALSE # TO RETURN DATA, USE "TRUE"
)## ✖ Incorrect format using spiges-data v.1.4.
##
## Element '{http://www.bfs.admin.ch/xmlns/gvs/spiges-data/1.4}Standort', attribute 'burnr': 'INCORRECT VALUE' is not a valid value of the local atomic type.Variables can be individually selected using the variables argument:
spiges_get_df(x = xml_example, node = "Administratives", variables = c("abc_fall", "geschlecht"))## ✔ Format correctly validated using spiges-data v.1.4.
## # A tibble: 13 × 5
## ent_id burnr fall_id abc_fall geschlecht
## <chr> <chr> <chr> <chr> <chr>
## 1 100000012 10000012 1 A 2
## 2 100000012 10000012 2 A 1
## 3 100000012 10000012 3 A 2
## 4 100000012 10000012 4 A 1
## 5 100000012 10000012 5 A 2
## 6 100000012 10000012 6 A 2
## 7 100000012 10000012 7 A 1
## 8 100000012 10000012 8 A 2
## 9 100000012 10000012 9 A 1
## 10 100000012 10000012 10 A 2
## 11 100000012 10000012 11 A 1
## 12 100000012 10000012 12 A 1
## 13 100000012 10000012 13 A 2If the variable name in variables doesn’t exist in the file, will return an error message. When multiple variable names are provided, only correct variable names will be returned (with no error messages if a variable name is correct).
spiges_get_df(x = xml_example, node = "Administratives", variables = "Geschlecht")Error in `spiges_get_df()`:
! `variables` must be one of "burnr_gesv", "abc_fall", "geschlecht", "alter", "alter_U1", "wohnort_medstat", "wohnkanton",
"wohnland", "nationalitaet", "eintrittsdatum", "eintritt_aufenthalt", "eintrittsart", "einw_instanz", "liegeklasse",
"versicherungsklasse", "admin_urlaub", "chlz", "aufenthalt_ips", "beatmung", "schwere_score", "art_score", "nems", "aufenthalt_imc",
"aufwand_imc", "hauptleistungsstelle", "grundversicherung", "tarif", "austrittsdatum", "austrittsentscheid", "austritt_aufenthalt", or
"austritt_behandlung", not "Geschlecht".
ℹ Did you mean "geschlecht"?Get IDs data
You can also access “Personenidentifikatoren” data using spiges_get_df(). Under the hood the function is using the spiges-ids format validation (while other available nodes are using the spiges-data validation format).
id_example <- "https://dam-api.bfs.admin.ch/hub/api/dam/assets/32129180/master"
spiges_get_df(x = id_example, node = "Personenidentifikatoren")Change format validation version
You can change the version of the XSD schema validation using the schema_xsd argument (by default “latest”). Note that you might encounter issues with custom schema validation as SpigGesXML aims to work with the latest schema version available.
Here an example for schema version “1.3”:
# SpiGes format version 1.3
spiges_get_df(
x = "https://dam-api.bfs.admin.ch/hub/api/dam/assets/27905035/master",
node = "Diagnose",
schema_xsd = "https://dam-api.bfs.admin.ch/hub/api/dam/assets/27905037/master"
)## ✔ Format correctly validated using spiges-data v.1.3.
## # A tibble: 2 × 8
## ent_id burnr fall_id diagnose_id diagnose_kode diagnos…¹ diagn…² diagn…³
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 845724581 71548624 5443546 1 Z380 <NA> <NA> <NA>
## 2 845724581 71548624 5443547 1 F29 <NA> 1 <NA>
## # … with abbreviated variable names ¹diagnose_seitigkeit, ²diagnose_poa,
## # ³diagnose_zusatzHere another example of version 1.3 for “Personenidentifikatoren” node:
spiges_get_df(
x = "https://dam-api.bfs.admin.ch/hub/api/dam/assets/27905038/master",
node = "Personenidentifikatoren",
schema_xsd = "https://dam-api.bfs.admin.ch/hub/api/dam/assets/27905036/master"
)Get available node names
Show node names available for data extraction in XML SpiGes:
spiges_get_name_nodes(x = xml_example)Get available variable names
Get list of variable names available by SpiGes node names of any SpiGes Schema XSD file:
spiges_get_name_variables(
schema_xsd = "https://dam-api.bfs.admin.ch/hub/api/dam/assets/32129184/master"
) |>
str()