R/getNIdata.R
In NINAnor/NIcalc: Functions to Calculate a Nature Index
Defines functions
getScalingModelData
getRefYearData
getIndicatorValues2
getIndicatorEcosystemData
getIndicators2
getICunitBSunit
getICunits
getFunctionalGroupData
getEcosystemBSunitData
getEcosystems
getBSunits
Documented in
getBSunits
getEcosystemBSunitData
getEcosystems
getFunctionalGroupData
getICunitBSunit
getICunits
getIndicatorEcosystemData
getIndicators2
getIndicatorValues2
getRefYearData
getScalingModelData
#' Read a Table in the NI Database
#'
#' Functions that reads data from tables in the NI database via
#' [The Nature Index Application Programming Interface](https://www8.nina.no/NaturindeksNiCalc/index.html)
#' and imports the content as a data.frame.
#'
#' Each function reads one table in the database:
#' \tabular{llll}{
#' Function \tab Table in NI database \tab Content
#' \tab Column names in returned dataframe\cr
#' \code{getBSunits} \tab \code{Kommune}
#' \tab Characteristics for all BSunits.
#' \tab \code{[,1]} \code{"id"},\cr
#' \tab \tab \tab \code{[,2]} \code{"name"},\cr
#' \tab \tab \tab \code{[,3]} \code{"area"},\cr
#' \tab \tab \tab \code{[,4]} \code{"terrestrial"},\cr
#' \tab \tab \tab \code{[,5]} \code{"marine"},\cr
#' \tab \tab \tab \code{[,6]} \code{"county"},\cr
#' \tab \tab \tab \code{[,7]} \code{"part"},\cr
#' \tab \tab \tab \code{[,8]} \code{"centerLat"},\cr
#' \tab \tab \tab \code{[,9]} \code{"centerLong"}\cr\cr
#' \code{getEcosystems} \tab \code{T_Okosystem}
#' \tab Ecosystem names and ids.\tab \code{[,1]} \code{"id"},\cr
#' \tab \tab \tab \code{[,2]} \code{"name"},\cr
#' \tab \tab \tab \code{[,3]} \code{"nameEnglish"}.\cr\cr
#' \code{getEcosystemBSunitData} \tab \code{Kommune_Okosystem}
#' \tab Area of major ecosystems
#' \tab \code{[,1]} \code{"ecosystemId"},\cr
#' \tab \tab per BSunit \tab \code{[,2]} \code{"municipalityId"},\cr
#' \tab \tab \tab \code{[,3]} \code{"area"}.\cr\cr
#' \code{getFunctionalGroupData} \tab \code{T_FunksjonellGruppe}
#' \tab names of functional groups
#' \tab \code{[,1]} \code{"id"},\cr
#' \tab \tab \tab \code{[,2]} \code{"name"},\cr
#' \tab \tab \tab \code{[,3]} \code{"nameEnglish"}.\cr\cr
#' \code{getICunits} \tab \code{Omraade} \tab ICunit for each indicator
#' \tab \code{[,1]} \code{"id"},\cr
#' \tab \tab \tab \code{[,2]} \code{"name"},\cr
#' \tab \tab \tab \code{[,3]} \code{"indicatorId"}.\cr\cr
#' \code{getICunitBSunit} \tab \code{Omraade_Kommune} \tab BSunits within each ICunit.
#' \tab \code{[,1]} \code{"areaId"},\cr
#' \tab \tab \tab \code{[,2]} \code{"municipalityId"}.\cr\cr
#' \code{getIndicators2} \tab \code{Indikator} \tab Characteristics for all indicators
#' \tab \code{[, 1]} \code{"id"},\cr
#' \tab \tab \tab \code{[, 2]} \code{"active"},\cr
#' \tab \tab \tab \code{[, 3]} \code{"name"},\cr
#' \tab \tab \tab \code{[, 4]} \code{"nameEnglish"},\cr
#' \tab \tab \tab \code{[, 5]} \code{"nameLatin"},\cr
#' \tab \tab \tab \code{[, 6]} \code{"indicatorTypeId"},\cr
#' \tab \tab \tab \code{[, 7]} \code{"taxaDetailId"},\cr
#' \tab \tab \tab \code{[, 8]} \code{"functionalGroupId"},\cr
#' \tab \tab \tab \code{[, 9]} \code{"scalingModel"},\cr
#' \tab \tab \tab \code{[,10]} \code{"taxaKingdomId"},\cr
#' \tab \tab \tab \code{[,11]} \code{"keyElement"},\cr
#' \tab \tab \tab \code{[,12]} \code{"referenceStateId"}.\cr\cr
#' \code{getIndicatorEcosystemData} \tab \code{Indikator_Okosystem}
#' \tab Fidelity of indicators
#' \tab \code{[,1]} \code{"indicatorId"},\cr
#' \tab \tab per major ecosystem \tab \code{[,2]} \code{"ecosystemId"},\cr
#' \tab \tab \tab \code{[,3]} \code{"percent"}.\cr\cr
#' \code{getIndicatorValues2} \tab \code{Verdier}
#' \tab Reference values and
#' \tab \code{[, 1]} \code{"indicatorId"},\cr
#' \tab \tab indicator observations \tab \code{[, 2]} \code{"indicatorName"},\cr
#' \tab \tab \tab \code{[, 3]} \code{"areaId"},\cr
#' \tab \tab \tab \code{[, 4]} \code{"areaName"},\cr
#' \tab \tab \tab \code{[, 5]} \code{"yearId"},\cr
#' \tab \tab \tab \code{[, 6]} \code{"yearName"},\cr
#' \tab \tab \tab \code{[, 7]} \code{"verdi"},\cr
#' \tab \tab \tab \code{[, 8]} \code{"nedre_Kvartil"},\cr
#' \tab \tab \tab \code{[, 9]} \code{"ovre_Kvartil"},\cr
#' \tab \tab \tab \code{[,10]} \code{"datatypeId"},\cr
#' \tab \tab \tab \code{[,11]} \code{"datatypeName"},\cr
#' \tab \tab \tab \code{[,12]} \code{"unitOfMeasurement"},\cr
#' \tab \tab \tab \code{[,13]} \code{"customDistributionUUID"},\cr
#' \tab \tab \tab \code{[,14]} \code{"distributionName"},\cr
#' \tab \tab \tab \code{[,15]} \code{"distributionId"},\cr
#' \tab \tab \tab \code{[,16]} \code{"distParam1"},\cr
#' \tab \tab \tab \code{[,17]} \code{"distParam2"}.\cr\cr
#' \code{getRefYearData} \tab \code{T_RefAar}
#' \tab Ids for observation years and
#' \tab \code{[,1]} \code{"id"},\cr
#' \tab \tab the reference value category\tab \code{[,2]} \code{"name"},\cr
#' \tab \tab \tab \code{[,3]} \code{"nameEnglish"}.\cr\cr
#' \code{getScalingModelData} \tab \code{T_Skaleringsmodell}
#' \tab names of scaling models
#' \tab \code{[,1]} \code{"id"},\cr
#' \tab \tab \tab \code{[,2]} \code{"name"}.
#' }
#'
#' @seealso \code{\link{getToken}} for retrieving tokens from the Nature Index API,
#' \code{\link{extractContentFromNiapi}}, a general purpose utility function called
#' by the functions described here that retrieves data from the specified tables
#' in the Nature Index database, and \code{\link{importDatasetApi}} for importing
#' from the database all required data for calculating the Nature Index for an
#' ecosystem.
#'
#' @encoding UTF-8
#' @author Bård Pedersen
#' @name getNIdata
#'
#' @importFrom plyr ldply
#'
#' @param BSunitIds integer, optional.
#' \cr\code{getBSunits}: Data for specified BSunits will be retrieved from the
#' \code{Kommune} table. The default (\code{NULL}) is to retrieve data for all BSunits.
#' @param ecosystemIds integer, optional.
#' \cr\code{getIndicatorEcosystemData}: Fidelity of all indicators (or of
#' those specified in \code{indicatorIds}) to the specified ecosystems, will
#' be retrieved from the \code{Indikator_Okosystem} table. The default
#' (\code{ecosystemIds = NULL}) is to retrieve fidelity of all indicators
#' to all ecosystems.
#' @param indicatorIds integer, optional. \cr\code{getIndicators2}: Data for specified indicators
#' will be retrieved from the \code{Indikator} table. The default (\code{NULL}) is to
#' retrieve data for all indicators.
#' \cr\code{getIndicatorEcosystemData}: Fidelity of specified indicators to all
#' ecosystems or those given in \code{ecosystemIds}, will be retrieved from the
#' \code{Indikator_Okosystem} table.
#' \cr\code{getICunits}: ICunits for specified indicators will be retrieved from
#' \code{Omraade}. The default (\code{NULL}) is to retrieve all ICunits.
#' \cr\code{getIndicatorValues2}: Observations for specified indicators will be
#' retrieved from \code{Verdier}. The default (\code{NULL}) \emph{is to retrieve no data}.
#' @param icunits integer, optional.
#' \cr\code{getICunitBSunit}: Data for specified ICunits will be retrieved from the
#' \code{Omraade_Kommune} table. The default (\code{NULL}) is to retrieve BSunits for all ICunits.
#' @param refYear character, optional.
#' \cr\code{getIndicatorValues2}: Years of the observations to retrieve and
#' whether to retreive reference values. E.g. \code{refYear = c("2010","Referanseverdi")}
#' returns observations from 2010 together with reference values. Default = (\code{NULL}),
#' which means you get all observations as well as reference values.
#'
#' @return All functions except \code{getIndicatorValues2} returns a data frame
#' with content according to the above table, or an error message if extraction of data
#' from the database fails.
#' \cr\cr\code{getIndicatorValues2} returns a list of two elements:
#' \cr 1) a data frame \code{indicatorValues} of indicator observations content
#' according to the above table, and
#' \cr 2) a list \code{customDistributions} of optional distribution objects associated
#' with some of the observations. Distribution objects are identified through
#' the variable \code{indicatorValues$customDistributionUUID}
#'
#' @section Note:
#' Column names of returned objects are generated by the API and differ somewhat from the
#' column headings in the corresponding table in the NI database.
#'
#' @examples
#' \dontrun{
#' getBSunits()
#' getEcosystems()
#' getEcosystemBSunitData()
#' getFunctionalGroupData()
#' getICunits()
#' getICunitBSunit()
#' getIndicators2()
#' getIndicatorEcosystemData()
#' getIndicatorValues2(indicatorIds = 1:2,refYear = c("2010","Referanseverdi"))
#' getRefYearData()
#' getScalingModelData()
#' }
#'
NULL
#' @rdname getNIdata
#' @export
getBSunits <- function(BSunitIds = NULL) {
# Location of resource - API for Kommune_Okosystem table in Norwegian NI database
APIUrl = .url
token = .niToken
methodPath <- "/api/Calculation/municipalities"
if (!is.null(BSunitIds)) {
BSunitData <- NULL
for (bsui in 1:length(BSunitIds)) {
methodPath <- paste0("/api/Calculation/municipalities/",BSunitIds[bsui])
# Extract content from API
rawContent <- extractContentFromNiapi(APIUrl,methodPath,token,as = "text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API for BSunitId = ", BSunitIds[bsui]," at\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
rawResult <- data.frame(RJSONIO::fromJSON(rawContent,simplifyDataFrame = TRUE,nullValue = NA),
stringsAsFactors = FALSE)
BSunitData <- rbind(BSunitData,rawResult)
}
} else {
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
BSunitData <- plyr::ldply(RJSONIO::fromJSON(rawContent,simplifyDataFrame = TRUE,nullValue = NA),
data.frame, stringsAsFactors = F)
}
return(BSunitData)
}
#' @rdname getNIdata
#' @export
getEcosystems <- function() {
# Location of resource - API for ecosystem table in Norwegian NI database
APIUrl = .url
token = .niToken
methodPath <- "/api/Calculation/ecosystems"
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API\n",
APIUrl, methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
ecosystems <- jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE)
return(ecosystems)
}
#' @rdname getNIdata
#' @export
getEcosystemBSunitData <- function() {
# Location of resource - API for Indikator_Okosystem table in Norwegian NI database
APIUrl = .url
token = .niToken
methodPath <- "/api/Calculation/municipalityEcosystems"
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
BSunitEcosystem <- jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE)
return(BSunitEcosystem)
}
#' @rdname getNIdata
#' @export
getFunctionalGroupData <- function() {
# Location of resource - API for T_FunksjonellGruppe table in Norwegian NI database
APIUrl = .url
token = .niToken
methodPath <- "/api/Calculation/functionalGroups"
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
functionalGroups <- jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE)
return(functionalGroups)
}
#' @rdname getNIdata
#' @export
getICunits <- function(indicatorIds = NULL) {
# Location of resource - API for Omraade table in Norwegian NI database
APIUrl = .url
token = .niToken
methodPath <- "/api/Area"
if (!is.null(indicatorIds)) {
icunitData <- NULL
for (ind in 1:length(indicatorIds)) {
methodPath <- paste0("/api/Area/indicator/",indicatorIds[ind])
# Extract content from API
rawContent <- extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API for indicatorId = ", indicatorIds[ind]," at\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
icunitData <- rbind(icunitData,jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE))
}
} else {
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
icunitData <- jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE)
}
icunitData$definitinonArea[is.na(icunitData$definitinonArea)] <- 0
icunitData$common[is.na(icunitData$common)] <- 0
icunitData <- icunitData[icunitData$definitinonArea != 1 & icunitData$common != 1,c("id","name","indicatorId")]
return(icunitData)
}
#' @rdname getNIdata
#' @export
getICunitBSunit <- function(icunits = NULL) {
# Location of resource - API for Kommune_Okosystem table in Norwegian NI database
serverUrl <- "https://ninweb17.nina.no"
apiPath <- "/NaturindeksAPI/api/Area/municipalities"
APIUrl = .url
token = .niToken
methodPath <- "/api/Area/municipalities"
if (!is.null(icunits)) {
icunitData <- NULL
for (icu in 1:length(icunits)) {
methodPath <- paste0("/api/Area/",icunits[icu],"/municipalities")
# Extract content from API
rawContent <- extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API for ICunit = ",icunits[icu]," at\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
icunitData <- rbind(icunitData,jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE))
}
} else {
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
icunitData <- jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE)
}
# icunitData <- icunitData[icunitData$indId %in% indicators$id,]
return(icunitData)
}
#' @rdname getNIdata
#' @export
getIndicators2 <- function(indicatorIds = NULL) {
# Location of resource - API for Indikator table in Norwegian NI database
APIUrl = .url
token = .niToken
methodPath <- "/api/Calculation/indicators"
if (!is.null(indicatorIds)) {
indicatorData <- NULL
for (ind in 1:length(indicatorIds)) {
methodPath <- paste0("/api/Calculation/indicators/",indicatorIds[ind])
# Extract content from API
rawContent <- extractContentFromNiapi(APIUrl,methodPath,token,as = "text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API for indicatorId = ", indicatorIds[ind]," at\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
rawResult <- data.frame(RJSONIO::fromJSON(rawContent,simplifyDataFrame = TRUE,nullValue = NA),
stringsAsFactors = FALSE)
indicatorData <- rbind(indicatorData,rawResult)
}
} else {
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as = "text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
indicatorData <- plyr::ldply(RJSONIO::fromJSON(rawContent,simplifyDataFrame = TRUE,nullValue = NA),
data.frame, stringsAsFactors = F)
}
return(indicatorData)
}
#' @rdname getNIdata
#' @export
getIndicatorEcosystemData <- function(ecosystemIds = NULL, indicatorIds = NULL) {
# Location of resource - API for Indikator_Okosystem table in Norwegian NI database
APIUrl = .url
token = .niToken
methodPath <- "/api/Calculation/indicatorEcosystems"
methodPath2 <- "/api/Calculation/indicatorEcosystems"
if (!is.null(ecosystemIds)) {
indicatorEcosystem <- NULL
for (eco in 1:length(ecosystemIds)) {
methodPath <- paste0("/api/Calculation/indicatorEcosystems/ecosystem/",ecosystemIds[eco])
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API for ecosystemId = ", ecosystemIds[eco]," at\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
indicatorEcosystem <- rbind(indicatorEcosystem,jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE))
}
# Remove items with zero fidelities
indicatorEcosystem <- indicatorEcosystem[indicatorEcosystem$percent > 0,]
if (!is.null(indicatorIds)) {
indicatorEcosystem <- indicatorEcosystem[indicatorEcosystem$indicatorId %in% indicatorIds,]
if (length(indicatorEcosystem$indicatorId) == 0) {
warning(paste0("No nonzero fidelities received from API for indicators ",
paste0(indicatorIds,collapse=" , ")," in ecosystems ",
paste0(ecosystemIds,collapse=" , "), " at\n",APIUrl,methodPath2, sep=""),
call. = FALSE)
}
}
} else if (!is.null(indicatorIds)) {
indicatorEcosystem <- NULL
for (ind in 1:length(indicatorIds)) {
methodPath <- paste0("/api/Calculation/indicatorEcosystems/indicator/",indicatorIds[ind])
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API for indicatorId = ", indicatorIds[ind]," at\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
indicatorEcosystem <- rbind(indicatorEcosystem,jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE))
}
# Remove items with zero fidelities
indicatorEcosystem <- indicatorEcosystem[indicatorEcosystem$percent > 0,]
} else {
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
indicatorEcosystem <- jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE)
# Remove items with zero fidelities
indicatorEcosystem <- indicatorEcosystem[indicatorEcosystem$percent > 0,]
}
return(indicatorEcosystem)
}
#' @rdname getNIdata
#' @export
getIndicatorValues2 <- function(indicatorIds = NULL, refYear = NULL) {
APIUrl = .url
token = .niToken
methodPath2 <- "/api/Calculation/indicator/values"
if (is.null(indicatorIds)) {
indicatorValues <- NULL
} else if (is.null(refYear)) {
rawResult <- NULL
for (ind in 1:length(indicatorIds)) {
message(paste("\nReading values for indicator",indicatorIds[ind]))
methodPath <- paste0("/api/Calculation/indicator/",indicatorIds[ind],"/values")
# Extract content from API
rawContent <- extractContentFromNiapi(APIUrl,methodPath,token,as ="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
# Issue a warning if content received from API is empty
warning(paste0("No data received from API for indicator = ",indicatorIds[ind]," at\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
} else {
# Parse the content into a suitable R object - a data.frame using column names set by the API
xxx <- jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE)
rm(rawContent)
# Add parsed content to the rawResult data.frame
rawResult <- rbind(rawResult,xxx)
}
}
# Restructure the parsed object into an object of type indicatorData
indicatorValues <- list("indicatorValues" = rawResult[!(names(rawResult) %in% c("customDistributionObject"))])
customDistributions <- as.list(rawResult$customDistributionObject[!is.na(rawResult$customDistributionObject)])
names(customDistributions) <- rawResult$customDistributionUUID[!is.na(rawResult$customDistributionUUID)]
backToDist <- function(x){
unserialize(charToRaw(x[[1]]))
}
indicatorValues$customDistributions <- lapply(customDistributions, backToDist)
class(indicatorValues) <- c("indicatorData", "list")
} else {
rawResult <- NULL
for (ind in 1:length(indicatorIds)) {
message(paste("\nReading values for indicator",indicatorIds[ind]))
for (reff in 1:length(refYear)) {
methodPath <- paste0("/api/Calculation/indicator/",indicatorIds[ind],"/values/years/",refYear[reff])
# Extract content from API
rawContent <- extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
# Issue a warning if content received from API is empty
warning(paste0("No data received from API for indicator = ",indicatorIds[ind]," at\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
} else {
# Parse the content into a suitable R object - a data.frame using column names set by the API
xxx <- jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE)
rm(rawContent)
# Add parsed content to the rawResult data.frame
rawResult <- rbind(rawResult,xxx)
}
}
}
# Restructure the parsed object into an object of type indicatorData
indicatorValues <- list("indicatorValues" = rawResult[!(names(rawResult) %in% c("customDistributionObject"))])
customDistributions <- as.list(rawResult$customDistributionObject[!is.na(rawResult$customDistributionObject)])
names(customDistributions) <- rawResult$customDistributionUUID[!is.na(rawResult$customDistributionUUID)]
backToDist <- function(x){
unserialize(charToRaw(x[[1]]))
}
indicatorValues$customDistributions <- lapply(customDistributions, backToDist)
class(indicatorValues) <- c("indicatorData", "list")
}
if (length(indicatorValues$indicatorValues) == 0) {
# Issue a warning if content received from API is empty
warning(paste0("No data received from API for indicators ",indicatorIds," at\n",
APIUrl,methodPath2, sep=""),
call. = FALSE)
} else if (length(which(!(indicatorIds %in% indicatorValues$indicatorValues$indicatorId))) > 0) {
# Issue a warning if data for some indicators are missing from content received from API
xxx <- which(!(indicatorIds %in% indicatorValues$indicatorValues$indicatorId))
warning(paste0("No data received from API for indicators ",indicatorIds[xxx]," at\n",
APIUrl,methodPath2, sep=""),
call. = FALSE)
}
return(indicatorValues)
}
#' @rdname getNIdata
#' @export
getRefYearData <- function() {
# Location of resource - API for T_RefAar table in Norwegian NI database
APIUrl = .url
token = .niToken
methodPath <- "/api/Calculation/refYears"
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl, methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API\n",
APIUrl, methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
refYearTable <- jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE)
return(refYearTable)
}
#' @rdname getNIdata
#' @export
getScalingModelData <- function() {
# Location of resource - API for T_Skaleringsmodell table in Norwegian NI database
serverUrl <- "https://ninweb17.nina.no"
apiPath <- "/NaturindeksAPI/api/Calculation/scalingModels"
APIUrl = .url
token = .niToken
methodPath <- "/api/Calculation/scalingModels"
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
scalingModels <- jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE)
return(scalingModels)
}
NINAnor/NIcalc documentation built on Oct. 26, 2023, 9:37 a.m.
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Defines functions getScalingModelData getRefYearData getIndicatorValues2 getIndicatorEcosystemData getIndicators2 getICunitBSunit getICunits getFunctionalGroupData getEcosystemBSunitData getEcosystems getBSunits
Documented in getBSunits getEcosystemBSunitData getEcosystems getFunctionalGroupData getICunitBSunit getICunits getIndicatorEcosystemData getIndicators2 getIndicatorValues2 getRefYearData getScalingModelData
#' Read a Table in the NI Database
#'
#' Functions that reads data from tables in the NI database via
#' [The Nature Index Application Programming Interface](https://www8.nina.no/NaturindeksNiCalc/index.html)
#' and imports the content as a data.frame.
#'
#' Each function reads one table in the database:
#' \tabular{llll}{
#' Function \tab Table in NI database \tab Content
#' \tab Column names in returned dataframe\cr
#' \code{getBSunits} \tab \code{Kommune}
#' \tab Characteristics for all BSunits.
#' \tab \code{[,1]} \code{"id"},\cr
#' \tab \tab \tab \code{[,2]} \code{"name"},\cr
#' \tab \tab \tab \code{[,3]} \code{"area"},\cr
#' \tab \tab \tab \code{[,4]} \code{"terrestrial"},\cr
#' \tab \tab \tab \code{[,5]} \code{"marine"},\cr
#' \tab \tab \tab \code{[,6]} \code{"county"},\cr
#' \tab \tab \tab \code{[,7]} \code{"part"},\cr
#' \tab \tab \tab \code{[,8]} \code{"centerLat"},\cr
#' \tab \tab \tab \code{[,9]} \code{"centerLong"}\cr\cr
#' \code{getEcosystems} \tab \code{T_Okosystem}
#' \tab Ecosystem names and ids.\tab \code{[,1]} \code{"id"},\cr
#' \tab \tab \tab \code{[,2]} \code{"name"},\cr
#' \tab \tab \tab \code{[,3]} \code{"nameEnglish"}.\cr\cr
#' \code{getEcosystemBSunitData} \tab \code{Kommune_Okosystem}
#' \tab Area of major ecosystems
#' \tab \code{[,1]} \code{"ecosystemId"},\cr
#' \tab \tab per BSunit \tab \code{[,2]} \code{"municipalityId"},\cr
#' \tab \tab \tab \code{[,3]} \code{"area"}.\cr\cr
#' \code{getFunctionalGroupData} \tab \code{T_FunksjonellGruppe}
#' \tab names of functional groups
#' \tab \code{[,1]} \code{"id"},\cr
#' \tab \tab \tab \code{[,2]} \code{"name"},\cr
#' \tab \tab \tab \code{[,3]} \code{"nameEnglish"}.\cr\cr
#' \code{getICunits} \tab \code{Omraade} \tab ICunit for each indicator
#' \tab \code{[,1]} \code{"id"},\cr
#' \tab \tab \tab \code{[,2]} \code{"name"},\cr
#' \tab \tab \tab \code{[,3]} \code{"indicatorId"}.\cr\cr
#' \code{getICunitBSunit} \tab \code{Omraade_Kommune} \tab BSunits within each ICunit.
#' \tab \code{[,1]} \code{"areaId"},\cr
#' \tab \tab \tab \code{[,2]} \code{"municipalityId"}.\cr\cr
#' \code{getIndicators2} \tab \code{Indikator} \tab Characteristics for all indicators
#' \tab \code{[, 1]} \code{"id"},\cr
#' \tab \tab \tab \code{[, 2]} \code{"active"},\cr
#' \tab \tab \tab \code{[, 3]} \code{"name"},\cr
#' \tab \tab \tab \code{[, 4]} \code{"nameEnglish"},\cr
#' \tab \tab \tab \code{[, 5]} \code{"nameLatin"},\cr
#' \tab \tab \tab \code{[, 6]} \code{"indicatorTypeId"},\cr
#' \tab \tab \tab \code{[, 7]} \code{"taxaDetailId"},\cr
#' \tab \tab \tab \code{[, 8]} \code{"functionalGroupId"},\cr
#' \tab \tab \tab \code{[, 9]} \code{"scalingModel"},\cr
#' \tab \tab \tab \code{[,10]} \code{"taxaKingdomId"},\cr
#' \tab \tab \tab \code{[,11]} \code{"keyElement"},\cr
#' \tab \tab \tab \code{[,12]} \code{"referenceStateId"}.\cr\cr
#' \code{getIndicatorEcosystemData} \tab \code{Indikator_Okosystem}
#' \tab Fidelity of indicators
#' \tab \code{[,1]} \code{"indicatorId"},\cr
#' \tab \tab per major ecosystem \tab \code{[,2]} \code{"ecosystemId"},\cr
#' \tab \tab \tab \code{[,3]} \code{"percent"}.\cr\cr
#' \code{getIndicatorValues2} \tab \code{Verdier}
#' \tab Reference values and
#' \tab \code{[, 1]} \code{"indicatorId"},\cr
#' \tab \tab indicator observations \tab \code{[, 2]} \code{"indicatorName"},\cr
#' \tab \tab \tab \code{[, 3]} \code{"areaId"},\cr
#' \tab \tab \tab \code{[, 4]} \code{"areaName"},\cr
#' \tab \tab \tab \code{[, 5]} \code{"yearId"},\cr
#' \tab \tab \tab \code{[, 6]} \code{"yearName"},\cr
#' \tab \tab \tab \code{[, 7]} \code{"verdi"},\cr
#' \tab \tab \tab \code{[, 8]} \code{"nedre_Kvartil"},\cr
#' \tab \tab \tab \code{[, 9]} \code{"ovre_Kvartil"},\cr
#' \tab \tab \tab \code{[,10]} \code{"datatypeId"},\cr
#' \tab \tab \tab \code{[,11]} \code{"datatypeName"},\cr
#' \tab \tab \tab \code{[,12]} \code{"unitOfMeasurement"},\cr
#' \tab \tab \tab \code{[,13]} \code{"customDistributionUUID"},\cr
#' \tab \tab \tab \code{[,14]} \code{"distributionName"},\cr
#' \tab \tab \tab \code{[,15]} \code{"distributionId"},\cr
#' \tab \tab \tab \code{[,16]} \code{"distParam1"},\cr
#' \tab \tab \tab \code{[,17]} \code{"distParam2"}.\cr\cr
#' \code{getRefYearData} \tab \code{T_RefAar}
#' \tab Ids for observation years and
#' \tab \code{[,1]} \code{"id"},\cr
#' \tab \tab the reference value category\tab \code{[,2]} \code{"name"},\cr
#' \tab \tab \tab \code{[,3]} \code{"nameEnglish"}.\cr\cr
#' \code{getScalingModelData} \tab \code{T_Skaleringsmodell}
#' \tab names of scaling models
#' \tab \code{[,1]} \code{"id"},\cr
#' \tab \tab \tab \code{[,2]} \code{"name"}.
#' }
#'
#' @seealso \code{\link{getToken}} for retrieving tokens from the Nature Index API,
#' \code{\link{extractContentFromNiapi}}, a general purpose utility function called
#' by the functions described here that retrieves data from the specified tables
#' in the Nature Index database, and \code{\link{importDatasetApi}} for importing
#' from the database all required data for calculating the Nature Index for an
#' ecosystem.
#'
#' @encoding UTF-8
#' @author Bård Pedersen
#' @name getNIdata
#'
#' @importFrom plyr ldply
#'
#' @param BSunitIds integer, optional.
#' \cr\code{getBSunits}: Data for specified BSunits will be retrieved from the
#' \code{Kommune} table. The default (\code{NULL}) is to retrieve data for all BSunits.
#' @param ecosystemIds integer, optional.
#' \cr\code{getIndicatorEcosystemData}: Fidelity of all indicators (or of
#' those specified in \code{indicatorIds}) to the specified ecosystems, will
#' be retrieved from the \code{Indikator_Okosystem} table. The default
#' (\code{ecosystemIds = NULL}) is to retrieve fidelity of all indicators
#' to all ecosystems.
#' @param indicatorIds integer, optional. \cr\code{getIndicators2}: Data for specified indicators
#' will be retrieved from the \code{Indikator} table. The default (\code{NULL}) is to
#' retrieve data for all indicators.
#' \cr\code{getIndicatorEcosystemData}: Fidelity of specified indicators to all
#' ecosystems or those given in \code{ecosystemIds}, will be retrieved from the
#' \code{Indikator_Okosystem} table.
#' \cr\code{getICunits}: ICunits for specified indicators will be retrieved from
#' \code{Omraade}. The default (\code{NULL}) is to retrieve all ICunits.
#' \cr\code{getIndicatorValues2}: Observations for specified indicators will be
#' retrieved from \code{Verdier}. The default (\code{NULL}) \emph{is to retrieve no data}.
#' @param icunits integer, optional.
#' \cr\code{getICunitBSunit}: Data for specified ICunits will be retrieved from the
#' \code{Omraade_Kommune} table. The default (\code{NULL}) is to retrieve BSunits for all ICunits.
#' @param refYear character, optional.
#' \cr\code{getIndicatorValues2}: Years of the observations to retrieve and
#' whether to retreive reference values. E.g. \code{refYear = c("2010","Referanseverdi")}
#' returns observations from 2010 together with reference values. Default = (\code{NULL}),
#' which means you get all observations as well as reference values.
#'
#' @return All functions except \code{getIndicatorValues2} returns a data frame
#' with content according to the above table, or an error message if extraction of data
#' from the database fails.
#' \cr\cr\code{getIndicatorValues2} returns a list of two elements:
#' \cr 1) a data frame \code{indicatorValues} of indicator observations content
#' according to the above table, and
#' \cr 2) a list \code{customDistributions} of optional distribution objects associated
#' with some of the observations. Distribution objects are identified through
#' the variable \code{indicatorValues$customDistributionUUID}
#'
#' @section Note:
#' Column names of returned objects are generated by the API and differ somewhat from the
#' column headings in the corresponding table in the NI database.
#'
#' @examples
#' \dontrun{
#' getBSunits()
#' getEcosystems()
#' getEcosystemBSunitData()
#' getFunctionalGroupData()
#' getICunits()
#' getICunitBSunit()
#' getIndicators2()
#' getIndicatorEcosystemData()
#' getIndicatorValues2(indicatorIds = 1:2,refYear = c("2010","Referanseverdi"))
#' getRefYearData()
#' getScalingModelData()
#' }
#'
NULL
#' @rdname getNIdata
#' @export
getBSunits <- function(BSunitIds = NULL) {
# Location of resource - API for Kommune_Okosystem table in Norwegian NI database
APIUrl = .url
token = .niToken
methodPath <- "/api/Calculation/municipalities"
if (!is.null(BSunitIds)) {
BSunitData <- NULL
for (bsui in 1:length(BSunitIds)) {
methodPath <- paste0("/api/Calculation/municipalities/",BSunitIds[bsui])
# Extract content from API
rawContent <- extractContentFromNiapi(APIUrl,methodPath,token,as = "text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API for BSunitId = ", BSunitIds[bsui]," at\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
rawResult <- data.frame(RJSONIO::fromJSON(rawContent,simplifyDataFrame = TRUE,nullValue = NA),
stringsAsFactors = FALSE)
BSunitData <- rbind(BSunitData,rawResult)
}
} else {
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
BSunitData <- plyr::ldply(RJSONIO::fromJSON(rawContent,simplifyDataFrame = TRUE,nullValue = NA),
data.frame, stringsAsFactors = F)
}
return(BSunitData)
}
#' @rdname getNIdata
#' @export
getEcosystems <- function() {
# Location of resource - API for ecosystem table in Norwegian NI database
APIUrl = .url
token = .niToken
methodPath <- "/api/Calculation/ecosystems"
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API\n",
APIUrl, methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
ecosystems <- jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE)
return(ecosystems)
}
#' @rdname getNIdata
#' @export
getEcosystemBSunitData <- function() {
# Location of resource - API for Indikator_Okosystem table in Norwegian NI database
APIUrl = .url
token = .niToken
methodPath <- "/api/Calculation/municipalityEcosystems"
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
BSunitEcosystem <- jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE)
return(BSunitEcosystem)
}
#' @rdname getNIdata
#' @export
getFunctionalGroupData <- function() {
# Location of resource - API for T_FunksjonellGruppe table in Norwegian NI database
APIUrl = .url
token = .niToken
methodPath <- "/api/Calculation/functionalGroups"
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
functionalGroups <- jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE)
return(functionalGroups)
}
#' @rdname getNIdata
#' @export
getICunits <- function(indicatorIds = NULL) {
# Location of resource - API for Omraade table in Norwegian NI database
APIUrl = .url
token = .niToken
methodPath <- "/api/Area"
if (!is.null(indicatorIds)) {
icunitData <- NULL
for (ind in 1:length(indicatorIds)) {
methodPath <- paste0("/api/Area/indicator/",indicatorIds[ind])
# Extract content from API
rawContent <- extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API for indicatorId = ", indicatorIds[ind]," at\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
icunitData <- rbind(icunitData,jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE))
}
} else {
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
icunitData <- jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE)
}
icunitData$definitinonArea[is.na(icunitData$definitinonArea)] <- 0
icunitData$common[is.na(icunitData$common)] <- 0
icunitData <- icunitData[icunitData$definitinonArea != 1 & icunitData$common != 1,c("id","name","indicatorId")]
return(icunitData)
}
#' @rdname getNIdata
#' @export
getICunitBSunit <- function(icunits = NULL) {
# Location of resource - API for Kommune_Okosystem table in Norwegian NI database
serverUrl <- "https://ninweb17.nina.no"
apiPath <- "/NaturindeksAPI/api/Area/municipalities"
APIUrl = .url
token = .niToken
methodPath <- "/api/Area/municipalities"
if (!is.null(icunits)) {
icunitData <- NULL
for (icu in 1:length(icunits)) {
methodPath <- paste0("/api/Area/",icunits[icu],"/municipalities")
# Extract content from API
rawContent <- extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API for ICunit = ",icunits[icu]," at\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
icunitData <- rbind(icunitData,jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE))
}
} else {
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
icunitData <- jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE)
}
# icunitData <- icunitData[icunitData$indId %in% indicators$id,]
return(icunitData)
}
#' @rdname getNIdata
#' @export
getIndicators2 <- function(indicatorIds = NULL) {
# Location of resource - API for Indikator table in Norwegian NI database
APIUrl = .url
token = .niToken
methodPath <- "/api/Calculation/indicators"
if (!is.null(indicatorIds)) {
indicatorData <- NULL
for (ind in 1:length(indicatorIds)) {
methodPath <- paste0("/api/Calculation/indicators/",indicatorIds[ind])
# Extract content from API
rawContent <- extractContentFromNiapi(APIUrl,methodPath,token,as = "text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API for indicatorId = ", indicatorIds[ind]," at\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
rawResult <- data.frame(RJSONIO::fromJSON(rawContent,simplifyDataFrame = TRUE,nullValue = NA),
stringsAsFactors = FALSE)
indicatorData <- rbind(indicatorData,rawResult)
}
} else {
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as = "text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
indicatorData <- plyr::ldply(RJSONIO::fromJSON(rawContent,simplifyDataFrame = TRUE,nullValue = NA),
data.frame, stringsAsFactors = F)
}
return(indicatorData)
}
#' @rdname getNIdata
#' @export
getIndicatorEcosystemData <- function(ecosystemIds = NULL, indicatorIds = NULL) {
# Location of resource - API for Indikator_Okosystem table in Norwegian NI database
APIUrl = .url
token = .niToken
methodPath <- "/api/Calculation/indicatorEcosystems"
methodPath2 <- "/api/Calculation/indicatorEcosystems"
if (!is.null(ecosystemIds)) {
indicatorEcosystem <- NULL
for (eco in 1:length(ecosystemIds)) {
methodPath <- paste0("/api/Calculation/indicatorEcosystems/ecosystem/",ecosystemIds[eco])
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API for ecosystemId = ", ecosystemIds[eco]," at\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
indicatorEcosystem <- rbind(indicatorEcosystem,jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE))
}
# Remove items with zero fidelities
indicatorEcosystem <- indicatorEcosystem[indicatorEcosystem$percent > 0,]
if (!is.null(indicatorIds)) {
indicatorEcosystem <- indicatorEcosystem[indicatorEcosystem$indicatorId %in% indicatorIds,]
if (length(indicatorEcosystem$indicatorId) == 0) {
warning(paste0("No nonzero fidelities received from API for indicators ",
paste0(indicatorIds,collapse=" , ")," in ecosystems ",
paste0(ecosystemIds,collapse=" , "), " at\n",APIUrl,methodPath2, sep=""),
call. = FALSE)
}
}
} else if (!is.null(indicatorIds)) {
indicatorEcosystem <- NULL
for (ind in 1:length(indicatorIds)) {
methodPath <- paste0("/api/Calculation/indicatorEcosystems/indicator/",indicatorIds[ind])
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API for indicatorId = ", indicatorIds[ind]," at\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
indicatorEcosystem <- rbind(indicatorEcosystem,jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE))
}
# Remove items with zero fidelities
indicatorEcosystem <- indicatorEcosystem[indicatorEcosystem$percent > 0,]
} else {
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
indicatorEcosystem <- jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE)
# Remove items with zero fidelities
indicatorEcosystem <- indicatorEcosystem[indicatorEcosystem$percent > 0,]
}
return(indicatorEcosystem)
}
#' @rdname getNIdata
#' @export
getIndicatorValues2 <- function(indicatorIds = NULL, refYear = NULL) {
APIUrl = .url
token = .niToken
methodPath2 <- "/api/Calculation/indicator/values"
if (is.null(indicatorIds)) {
indicatorValues <- NULL
} else if (is.null(refYear)) {
rawResult <- NULL
for (ind in 1:length(indicatorIds)) {
message(paste("\nReading values for indicator",indicatorIds[ind]))
methodPath <- paste0("/api/Calculation/indicator/",indicatorIds[ind],"/values")
# Extract content from API
rawContent <- extractContentFromNiapi(APIUrl,methodPath,token,as ="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
# Issue a warning if content received from API is empty
warning(paste0("No data received from API for indicator = ",indicatorIds[ind]," at\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
} else {
# Parse the content into a suitable R object - a data.frame using column names set by the API
xxx <- jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE)
rm(rawContent)
# Add parsed content to the rawResult data.frame
rawResult <- rbind(rawResult,xxx)
}
}
# Restructure the parsed object into an object of type indicatorData
indicatorValues <- list("indicatorValues" = rawResult[!(names(rawResult) %in% c("customDistributionObject"))])
customDistributions <- as.list(rawResult$customDistributionObject[!is.na(rawResult$customDistributionObject)])
names(customDistributions) <- rawResult$customDistributionUUID[!is.na(rawResult$customDistributionUUID)]
backToDist <- function(x){
unserialize(charToRaw(x[[1]]))
}
indicatorValues$customDistributions <- lapply(customDistributions, backToDist)
class(indicatorValues) <- c("indicatorData", "list")
} else {
rawResult <- NULL
for (ind in 1:length(indicatorIds)) {
message(paste("\nReading values for indicator",indicatorIds[ind]))
for (reff in 1:length(refYear)) {
methodPath <- paste0("/api/Calculation/indicator/",indicatorIds[ind],"/values/years/",refYear[reff])
# Extract content from API
rawContent <- extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
# Issue a warning if content received from API is empty
warning(paste0("No data received from API for indicator = ",indicatorIds[ind]," at\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
} else {
# Parse the content into a suitable R object - a data.frame using column names set by the API
xxx <- jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE)
rm(rawContent)
# Add parsed content to the rawResult data.frame
rawResult <- rbind(rawResult,xxx)
}
}
}
# Restructure the parsed object into an object of type indicatorData
indicatorValues <- list("indicatorValues" = rawResult[!(names(rawResult) %in% c("customDistributionObject"))])
customDistributions <- as.list(rawResult$customDistributionObject[!is.na(rawResult$customDistributionObject)])
names(customDistributions) <- rawResult$customDistributionUUID[!is.na(rawResult$customDistributionUUID)]
backToDist <- function(x){
unserialize(charToRaw(x[[1]]))
}
indicatorValues$customDistributions <- lapply(customDistributions, backToDist)
class(indicatorValues) <- c("indicatorData", "list")
}
if (length(indicatorValues$indicatorValues) == 0) {
# Issue a warning if content received from API is empty
warning(paste0("No data received from API for indicators ",indicatorIds," at\n",
APIUrl,methodPath2, sep=""),
call. = FALSE)
} else if (length(which(!(indicatorIds %in% indicatorValues$indicatorValues$indicatorId))) > 0) {
# Issue a warning if data for some indicators are missing from content received from API
xxx <- which(!(indicatorIds %in% indicatorValues$indicatorValues$indicatorId))
warning(paste0("No data received from API for indicators ",indicatorIds[xxx]," at\n",
APIUrl,methodPath2, sep=""),
call. = FALSE)
}
return(indicatorValues)
}
#' @rdname getNIdata
#' @export
getRefYearData <- function() {
# Location of resource - API for T_RefAar table in Norwegian NI database
APIUrl = .url
token = .niToken
methodPath <- "/api/Calculation/refYears"
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl, methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API\n",
APIUrl, methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
refYearTable <- jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE)
return(refYearTable)
}
#' @rdname getNIdata
#' @export
getScalingModelData <- function() {
# Location of resource - API for T_Skaleringsmodell table in Norwegian NI database
serverUrl <- "https://ninweb17.nina.no"
apiPath <- "/NaturindeksAPI/api/Calculation/scalingModels"
APIUrl = .url
token = .niToken
methodPath <- "/api/Calculation/scalingModels"
# Extract content from API
rawContent = extractContentFromNiapi(APIUrl,methodPath,token,as="text")
# Issue a warning if content received from API is empty
if (length(rawContent) == 0) {
warning(paste0("No data received from API\n",
APIUrl,methodPath, sep=""),
call. = FALSE)
}
# Parse the content into a suitable R object - a data.frame using column names set by the API
scalingModels <- jsonlite::fromJSON(rawContent, simplifyDataFrame = TRUE)
return(scalingModels)
}
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