Use linters line_length and mutliple_dots

R/EOBS.R

@@ -84,7 +84,8 @@ GetEOBS <- function(filename, variable, area, period, na.rm) {
  result[, year := as.numeric(format(time, "%Y"))]
  result[, month := as.numeric(format(time, "%m"))]
  result[, day := as.numeric(format(time, "%d"))]
- setcolorder(result, c("time", "year", "month", "day", "lat", "lon", variable, "pointID"))
+ setcolorder(result, c("time", "year", "month", "day", "lat", "lon",
+ variable, "pointID"))
  return(result)
 }
 
@@ -109,7 +110,7 @@ SanitizeInputEOBS <- function(variable, period, area, grid) {
  stop()
  },
  error = function(e) {
- stop("Period should be either Numeric, timeBased or ISO-8601 style.")
+ stop("Period should be either Numeric, timeBased or ISO-8601 style.") # nolint
  })
  if (!class(area) %in% c("SpatialPolygons", "SpatialPolygonsDataFrame")) {
  stop("Area should be of class SpatialPolygons or SpatialPolygonsDataFrame.")
@@ -164,7 +165,7 @@ GetEobsBbox <- function(filename, variableName, bbox, period){
  # the bounding box
  validRange <- list()
  validRange$time <- which(findInterval(values$time,
-  periodBoundaries(values$time, period)) == 1)
+ periodBoundaries(values$time, period)) == 1)
  validRange$lat <- which(findInterval(values$lat, bbox[2, ]) == 1)
  validRange$lon <- which(findInterval(values$lon, bbox[1, ]) == 1)
 
@@ -198,11 +199,11 @@ CreateDataTableMelt <- function(variable, validValues) {
  if (length(validValues$time) > 1) {
  meltedValues <- reshape2::melt(validValues[[variable]],
  varnames = c("lon", "lat", "time"))
- result <- as.data.table(meltedValues)
+ result <- as.data.table(meltedValues) # nolint
  } else {
  meltedValues <- reshape2::melt(validValues[[variable]],
  varnames = c("lon", "lat"))
- result <- as.data.table(meltedValues)
+ result <- as.data.table(meltedValues) # nolint
  result[, time := 1]
  }
  setkey(result, lon, lat)
@@ -230,7 +231,7 @@ removeOutsiders <- function(data, area) {
  by = pointID][, list(lon, lat)]
  points <- sp::SpatialPoints(coords, area@proj4string)
  index <- data[, unique(pointID)][which(!is.na(sp::over(points,
-  as(area, "SpatialPolygons"))))]
+ as(area, "SpatialPolygons"))))]
  data <- data[pointID %in% index]
  setkey(data, lon, lat)
  return(data[, pointID := .GRP, by = key(data)])

R/ImportData.R

@@ -28,7 +28,9 @@ HomogenizedPrecipitation <- function(stationId, periodStart=1910) {
 HomogenPrecip <- function(location, period, whichSet = "automatic", path="") {
  cl <- match.call()
  SanitizeInput(type = "HomogenPrecip", location, period, whichSet)
- if (is.null(path)) tmp <- PrecipitationDownload(location, period, whichSet, cl)
+ if (is.null(path)) {
+ tmp <- PrecipitationDownload(location, period, whichSet, cl)
+ }
  else {
  fileName <- SpecifyFileName("HomogenPrecip", path, location, period)
  if (!file.exists(fileName)) {
@@ -46,7 +48,8 @@ PrecipitationDownload <- function(location, period, whichSet, call) {
  DownloadMessage("HomogenPrecip")
  periodStart <- HomogenPrecipPeriodStart(period)
  if (is.numeric(location)) {
- tmpStart <- ifelse(stationMetaData[list(location), longRecord] & whichSet != 1951, 1910, 1951)
+ tmpStart <- ifelse(stationMetaData[list(location), longRecord] &
+ whichSet != 1951, 1910, 1951)
  tmp <- HomogenizedPrecipitation(location, tmpStart)
  } else {
  standardCRSstring <- "+proj=longlat +ellps=WGS84"
@@ -57,11 +60,14 @@ PrecipitationDownload <- function(location, period, whichSet, call) {
  if (periodStart == 1910 | whichSet == 1910) {
  tmpMetaData <- tmpMetaData[longRecord == TRUE, ]
  }
- stationLocations <- sp::SpatialPoints(tmpMetaData[, list(lon, lat)], CRS(standardCRSstring))
- tmpMetaData[, inArea := sp::over(stationLocations, as(location, "SpatialPolygons"))]
+ stationLocations <- sp::SpatialPoints(tmpMetaData[, list(lon, lat)],
+ CRS(standardCRSstring))
+ tmpMetaData[, inArea := sp::over(stationLocations,
+ as(location, "SpatialPolygons"))]
  tmpMetaData <- na.omit(tmpMetaData)
  tmp <- foreach(i = 1 : tmpMetaData[, .N], .combine = "rbind") %do% {
- tmpStart <- ifelse(tmpMetaData[i, longRecord] & whichSet != 1951, 1910, 1951)
+ tmpStart <- ifelse(tmpMetaData[i, longRecord] &
+ whichSet != 1951, 1910, 1951)
  HomogenizedPrecipitation(tmpMetaData[i, stationId], tmpStart)
  }
  }
@@ -76,9 +82,11 @@ DownloadMessage <- function(name) {
 }
 
 DownloadMessageContent <- function(name) {
+ urlQuake <- "www.knmi.nl/kennis-en-datacentrum/dataset/aardbevingscatalogus"
+ urlClimExp <- "www.climexp.knmi.nl"
  switch(name,
- "Earthquakes" = return("www.knmi.nl/kennis-en-datacentrum/dataset/aardbevingscatalogus"),
- "HomogenPrecip" = return("www.climexp.knmi.nl")
+ "Earthquakes" = return(urlQuake),
+ "HomogenPrecip" = return(urlClimExp)
  )
 }
 
@@ -92,8 +100,10 @@ HomogenPrecipDates <- function(period) {
 #' Loads the KNMI earthquake catalogue
 #' @param type Type of catalogue c('induced', 'tectonic')
 #' @param area Inheriting from spatial polygon
-#' @param period Either numeric, timeBased or ISO-8601 style (see \code{\link[xts]{.subset.xts}})
-#' @param path for saving data (if set to NULL data are always downloaded but not saved)
+#' @param period Either numeric, timeBased or ISO-8601 style
+#' (see \code{\link[xts]{.subset.xts}})
+#' @param path for saving data (if set to NULL data are always downloaded
+#' but not saved)
 #' @return data.table with rows being the single events
 #' @export
 #' @examples
@@ -155,7 +165,7 @@ IsInArea <- function(points, area) {
  tmp <- sp::over(points, area)
  index <- as.vector(!is.na(tmp[, 1, drop = FALSE]))
  } else {
- stop("Area should be of class `SpatialPolygons' or `SpatialPolygonsDataFrame'")
+ stop("Area should be of class `SpatialPolygons' or `SpatialPolygonsDataFrame'") # nolint
  }
  if (class(index) != "logical" & length(points) != length(index)) {
  stop("index should be a logical of the same length as points")

R/KIS.R

@@ -99,7 +99,7 @@ ExecuteKISRecipe <- function(recipeName, period) {
 
  flog.info("Start data download.")
  download.file(url, destFile, method = "wget", quiet = T,
- extra = c('--header="Content-Type:application/x-www-form-urlencoded"',
+ extra = c('--header="Content-Type:application/x-www-form-urlencoded"', # nolint
  paste0('--post-file="', recipeName, '"')))
  flog.info("Download finished.")
 

R/Sanitation.R

@@ -24,7 +24,7 @@ SanitizeHomogenPrecip <- function(location, period, whichSet) {
  stop()
  },
  error = function(e) {
- stop("Period should be either Numeric, timeBased or ISO-8601 style.")
+ stop("Period should be either Numeric, timeBased or ISO-8601 style.") # nolint
  })
  periodStart <- HomogenPrecipPeriodStart(period)
  isStationId <- FALSE
@@ -38,15 +38,17 @@ SanitizeHomogenPrecip <- function(location, period, whichSet) {
  }
  }
  if (!(isStationId | isArea)) {
- stop("Location should be either valid station id or spatial polygon, with non-empty intersection.")
+ stop("Location should be either valid station id or spatial polygon, with non-empty intersection.") # nolint
  }
  if (isStationId) CheckStationId(location, periodStart)
  if (whichSet != "automatic") {
  if (periodStart < whichSet) {
  lastDate <- as.Date(xts::.parseISO8601(period)$last.time)
  warning(paste0("Period is restricted to 1951-01-01/", lastDate))
  }
- else if (periodStart > whichSet & isArea) message("You could consider more stations for the given period by choosing whichSelect='automatic'")
+ else if (periodStart > whichSet & isArea) {
+ message("You could consider more stations for the given period by choosing whichSelect='automatic'") # nolint
+ }
  }
 }
 

R/SpecifyFileName.R

@@ -51,7 +51,8 @@ GetFullySpecifiedArea <- function(name, area = NULL) {
 GetMaxDomain <- function(name) {
  lon <- lat <- NULL
  switch (name,
- "HomogenPrecip" = return(sp::bbox(sp::SpatialPoints(stationMetaData[, cbind(lon, lat)]))),
+ "HomogenPrecip" = return(sp::bbox(sp::SpatialPoints(stationMetaData[,
+ cbind(lon, lat)]))),
  "InducedQuakes" = return(EarthquakesBoundaryBox),
  "TectonicQuakes" = return(EarthquakesBoundaryBox))
 }

R/TechnicalImport.R

@@ -9,7 +9,7 @@ ReadZippedFile <- function(url, colNames) {
 
 UpdateJsonTable <- function(jsonTable) {
  depth <- lat <- lon <- mag <- NULL
- tmp <- as.data.table(jsonTable)
+ tmp <- as.data.table(jsonTable) # nolint
  tmp[, date := as.Date(date, tz = "CET")]
  tmp[, depth := as.numeric(depth)]
  tmp[, lat := as.numeric(lat)]

inst/.lintr

@@ -1,7 +1,5 @@
 linters: with_defaults(
  camel_case_linter = NULL, # 283
- line_length_linter = NULL, # 64
  commented_code_linter = NULL, # 27
- multiple_dots_linter = NULL, # 3
  NULL
  )

inst/MetaDataDefinition/MetaDataDefinition.R

@@ -1,3 +1,4 @@
+# nolint start
 dataDescription <- list()
 dataDescription$Earthquakes <- "Induced Earthquakes"
 dataDescription$HomogenPrecip <- "Obtained from <a href='http:https://climexp.knmi.nl'>KNMI</a>
@@ -17,6 +18,7 @@ availableDataSets <- c("Earthquakes", "HomogenPrecip")
 stationMetaData <- data.table::fread("./inst/MetaDataDefinition/stationMetaData.csv",
  stringsAsFactors = FALSE)
 data.table::setkey(stationMetaData, stationId)
+# nolint end
 
 devtools::use_data(dataDescription, dataCitation, dataLicense,
  availableDataSets, stationMetaData,

tests/testthat/test-DataSources.R

@@ -8,8 +8,10 @@ today <- as.Date(Sys.time())
 test_that("Actuality", {
  skip_on_travis()
  skip_on_appveyor()
- expect_gt(HomogenPrecip(11, paste0(today - 45, "/", today), path = NULL)[, .N], 0)
- recentQuakes <- Earthquakes("induced", NULL, paste0(today - 14, "/", today), path = NULL)
+ expect_gt(HomogenPrecip(11, paste0(today - 45, "/", today),
+ path = NULL)[, .N], 0)
+ recentQuakes <- Earthquakes("induced", NULL, paste0(today - 14, "/", today),
+ path = NULL)
  expect_gt(recentQuakes[, .N], 0)
  expect_match(License(recentQuakes), "Open data")
 })

tests/testthat/test-EOBS.R

@@ -5,18 +5,24 @@ adm0 <- raster::getData("GADM", country = "NL", level = 0)
 
 test_that("EOBS error messages", {
  expect_error(EOBS("foo"), "Variable foo not known.")
- expect_error(EOBS("tg", "A", "foo"), "Period should be either Numeric, timeBased or ISO-8601 style.")
- expect_error(EOBS("tg", "2014", "foo"), "Area should be of class SpatialPolygons or SpatialPolygonsDataFrame.")
- expect_error(EOBS("tg", "2014", adm0, "foo"), "Grid should be specified correctly.")
+ expect_error(EOBS("tg", "A", "foo"),
+ "Period should be either Numeric, timeBased or ISO-8601 style.")
+ expect_error(EOBS("tg", "2014", "foo"),
+ "Area should be of class SpatialPolygons or SpatialPolygonsDataFrame.")
+ expect_error(EOBS("tg", "2014", adm0, "foo"),
+ "Grid should be specified correctly.")
 })
 
 test_that("EOBS regression tests", {
  skip_on_appveyor()
- expect_equal_to_reference(EOBS("tg", "2014", adm0, "0.50reg"), file = "EOBSreference/output.rds")
- expect_equal_to_reference(EOBS("rr", "2014", adm0, "0.50reg"), file = "EOBSreference/output_rr.rds")
+ expect_equal_to_reference(EOBS("tg", "2014", adm0, "0.50reg"),
+ file = "EOBSreference/output.rds")
+ expect_equal_to_reference(EOBS("rr", "2014", adm0, "0.50reg"),
+ file = "EOBSreference/output_rr.rds")
  expect_equal_to_reference(EOBS("tg", "2015-06-01", adm0, grid = "0.50reg"),
  file = "EOBSreference/output_one_timestep.rds")
- expect_equal_to_reference(EOBSLocal("tg", "tg_0.50deg_reg_v12.0_plus_2015_ANN_avg.nc",
- "2000/2015", adm0),
+ expect_equal_to_reference(EOBSLocal("tg",
+ "tg_0.50deg_reg_v12.0_plus_2015_ANN_avg.nc",
+ "2000/2015", adm0),
  file = "EOBSreference/output_local.rds")
 })

tests/testthat/test-KISdata.R

@@ -10,11 +10,13 @@ test_that("Obtain temperature", {
  skip_on_travis()
  skip_if_not(grepl("knmi.nl", node))
  expect_match(WriteKISRecipe("TG", "260_H", "2016"), "KIStable.txt")
- expect_error(KIS("rr", "260_H", "2016"), "Must be element of set {'TG', 'MOR_10'}.", fixed = TRUE)
+ expect_error(KIS("rr", "260_H", "2016"),
+ "Must be element of set {'TG', 'MOR_10'}.", fixed = TRUE)
  result <- KIS("TG", "260_H", "2016-08/2016-09")
  expect_equal_to_reference(result, file = "testOutput/temperatureDeBilt.rds")
  result <- KIS("TG", "310_H", "2016-08/2016-09")
- expect_equal_to_reference(result, file = "testOutput/temperatureVlissingen.rds")
+ expect_equal_to_reference(result,
+ file = "testOutput/temperatureVlissingen.rds")
 })
 
 test_that("Obtain MOR_10", {
@@ -26,5 +28,6 @@ test_that("Obtain MOR_10", {
 
 test_that("Get error outside", {
  skip_if_not(!grepl("knmi.nl", node))
- expect_error(KIS("TG", "260_H", "2016"), "function works only inside KNMI", fixed = TRUE)
+ expect_error(KIS("TG", "260_H", "2016"),
+ "function works only inside KNMI", fixed = TRUE)
 })

tests/testthat/testEarthquakes.R

@@ -16,7 +16,7 @@ test_that("Earthquakes catalogue gives the same results", {
  check.attributes = FALSE)
  expect_equal_to_reference(Earthquakes("induced", Groningen, "1980/2015-11-15",
  path = NULL),
- file = "./referenceOutput/outputQuakesGroningen.rds",
+ file = "./referenceOutput/outputQuakesGroningen.rds", # nolint
  check.attributes = FALSE)
 })