Doc update

NAMESPACE

@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.0.1): do not edit by hand
+# Generated by roxygen2 (4.0.2): do not edit by hand
 
 export(aggr6hToDailyMean)
 export(analogs)
@@ -25,7 +25,7 @@ export(isimip)
 export(loadGridData)
 export(loadMultiField)
 export(loadStationData)
-export(login_SMG)
+export(login_TAP)
 export(makeAggregatedDataset)
 export(makeMultiField)
 export(makeSubset)

man/aggr6hToDailyMean.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{aggr6hToDailyMean}
 \alias{aggr6hToDailyMean}
 \title{Performs the aggregation of 6 hourly data to daily mean}

man/analogs.Rd

@@ -1,9 +1,10 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{analogs}
 \alias{analogs}
 \title{Analog downscaling}
 \usage{
-analogs(obs, pred, sim, n.neigh = 1, sel.fun = c("random", "mean"))
+analogs(obs, pred, sim, n.neigh = 1, sel.fun = c("random", "mean"),
+  analog.dates = FALSE)
 }
 \arguments{
 \item{obs}{A field or station data containing the observed climate data for the training period}
@@ -19,6 +20,12 @@ the same variable as \code{obs}, in the case of model calibration (bias correcti
 
 \item{sel.fun}{Criterion for the construction of analogs when several neigbours are chosen. Ignored when \code{n.neig = 1}.
 Current values are \code{"random"} (the default) and \code{"mean"}. See details.}
+
+\item{analog.dates}{Logical flag indicating whether the dates of the analogs should be returned. If set to TRUE,
+ the analog dates will be returned as a global attribute named \code{"analog.dates"}. The analog
+  dates can be only returned for one single neighbour selections (argument \code{n.neigh = 1}),
+   otherwise it will give an error. Note that the analog dates are different for each member in case of
+   multimember downscaling, and are returned as a list, each element of the list corresponding to one member.}
 }
 \description{
 Implementation of the downscaling analogs method

man/array3Dto2Dmat.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{array3Dto2Dmat}
 \alias{array3Dto2Dmat}
 \title{Conversion of a 3D array to a 2D matrix}

man/biasCorrection.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{biasCorrection}
 \alias{biasCorrection}
 \title{Bias correction methods}
@@ -19,11 +19,11 @@ the same variable as \code{obs}, in the case of model calibration (bias correcti
 \item{method}{method applied. Current accepted values are \code{"qqmap"}, \code{"delta"},
 \code{"scaling"}, \code{"unbiasing"} and \code{"piani"}. See details.}
 
-\item{multi.member}{Should members be adjusted sepparately (TRUE, default), or jointly (FALSE)?.
-Ignored if the dataset has no members.}
-
 \item{pr.threshold}{The minimum value that is considered as a non-zero precipitation. Ignored for
  \code{varcode} values different from \code{"pr"}. Default to 1 (assuming mm).}
+
+\item{multi.member}{Should members be adjusted sepparately (TRUE, default), or jointly (FALSE)?.
+Ignored if the dataset has no members.}
 }
 \value{
 A calibrated object of the same spatio-temporal extent of the input field

man/bubbleValidation.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{bubbleValidation}
 \alias{bubbleValidation}
 \title{Bubble plot for visualization of the skill of an ensemble forecast prediction}

man/calibrateProj.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{calibrateProj}
 \alias{calibrateProj}
 \title{Bias correction methods}

man/dataInventory.ASCII.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{dataInventory.ASCII}
 \alias{dataInventory.ASCII}
 \title{Data inventory of standard ASCII station datasets}

man/dataInventory.NetCDF.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{dataInventory.NetCDF}
 \alias{dataInventory.NetCDF}
 \title{Inventory of a gridded dataset}

man/dataInventory.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{dataInventory}
 \alias{dataInventory}
 \title{Dataset inventory}

man/dateReplacement.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{dateReplacement}
 \alias{dateReplacement}
 \title{Compute dates of a downscaled observational dataset}

man/deaccum.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{deaccum}
 \alias{deaccum}
 \title{Performs deaccumulation}

man/dictionaryLookup.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{dictionaryLookup}
 \alias{dictionaryLookup}
 \title{Searches variable string in the dictionary}

man/dictionaryTransform.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{dictionaryTransform}
 \alias{dictionaryTransform}
 \title{Performs variable transformation}

man/dictionaryTransformGrid.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{dictionaryTransformGrid}
 \alias{dictionaryTransformGrid}
 \title{Performs variable transformation}
@@ -8,9 +8,9 @@ dictionaryTransformGrid(dic, timePars, mdArray)
 \arguments{
 \item{dic}{Dictionary line for the variable, as returned by \code{dictionaryLookup} or \code{dictionaryLookup.ECOMS}}
 
-\item{foreTimePars}{A list of time selection parameters, as returned by \code{getTimeDomain}}
-
 \item{mdArray}{A n-dimensional array, as returned by \code{makeSubset}}
+
+\item{foreTimePars}{A list of time selection parameters, as returned by \code{getTimeDomain}}
 }
 \value{
 The transformed n dimensional array of data. See details.

man/fieldFromPCs.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{fieldFromPCs}
 \alias{fieldFromPCs}
 \title{Reconstruct a Field from EOFs and principal components}

man/findPointXYindex.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{findPointXYindex}
 \alias{findPointXYindex}
 \title{Define user-defined geolocation parameters}

man/findVerticalLevel.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{findVerticalLevel}
 \alias{findVerticalLevel}
 \title{Finds vertical level from variable definition}

man/getCoordinates.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{getCoordinates}
 \alias{getCoordinates}
 \title{Get geographical coordinates of a climate data object}

man/getGrid.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{getGrid}
 \alias{getGrid}
 \title{Get regular grid definition}

man/getLatLonDomain.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{getLatLonDomain}
 \alias{getLatLonDomain}
 \title{Determine the geo-location parameters of an arbitrary user selection}

man/getLatLonDomainStations.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{getLatLonDomainStations}
 \alias{getLatLonDomainStations}
 \title{Define geolocation of station datasets}

man/getSeason.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{getSeason}
 \alias{getSeason}
 \title{Get season from a station or field object}

man/getTimeDomain.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{getTimeDomain}
 \alias{getTimeDomain}
 \title{Selection of time slices of gridded datasets}

man/getTimeDomainStations.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{getTimeDomainStations}
 \alias{getTimeDomainStations}
 \title{Time  index positions for station dataset selections}

man/getVerticalLevelPars.Rd

@@ -1,14 +1,14 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{getVerticalLevelPars}
 \alias{getVerticalLevelPars}
 \title{Definition of vertical dimension slices}
 \usage{
 getVerticalLevelPars(grid, level)
 }
 \arguments{
-\item{gcs}{An object of the java class \sQuote{GeoGrid})}
-
 \item{level}{Vertical level. Passed by \code{loadGridDataset}, obtained via \code{findVerticalLevel}}
+
+\item{gcs}{An object of the java class \sQuote{GeoGrid})}
 }
 \value{
 A list with the level value and either a java Range or a java null reference

man/getYearsAsINDEX.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{getYearsAsINDEX}
 \alias{getYearsAsINDEX}
 \title{Get years as a factor}

man/glimpr.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{glimpr}
 \alias{glimpr}
 \title{GLM downscaling}

man/hurs2huss.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{hurs2huss}
 \alias{hurs2huss}
 \title{Specific humidity from relative humidity}

man/iberia_ncep_hus850.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{iberia_ncep_hus850}
 \alias{iberia_ncep_hus850}
 \title{Field containing NCEP reanalysis data of specific humidity at 850mb for the Iberian Peninsula.}

man/iberia_ncep_psl.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{iberia_ncep_psl}
 \alias{iberia_ncep_psl}
 \title{Field containing NCEP reanalysis data of sea-level pressure for the Iberian Peninsula.}

man/iberia_ncep_ta850.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{iberia_ncep_ta850}
 \alias{iberia_ncep_ta850}
 \title{Field containing NCEP reanalysis data of air temperature at 850mb for the Iberian Peninsula.}

man/interpGridData.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{interpGridData}
 \alias{interpGridData}
 \title{Interpolate a dataset to a grid}

man/isimip.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{isimip}
 \alias{isimip}
 \title{Bias correction ISI-MIP method}

man/loadGridData.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{loadGridData}
 \alias{loadGridData}
 \title{Load a field from a dataset}
@@ -16,6 +16,12 @@ this is the path to the directory the dataset lives in.}
  by the \dQuote{@} symbol (e.g. \code{var = "z@700"} for geopotential heigth at 700 mb isobaric surface pressure level).
  It is also possible to enter the variable name as originally coded in the dataset to skip data homogenization.}
 
+\item{dictionary}{Default to TRUE, indicating that a dictionary is used and the .dic file is stored in the same path than the
+dataset. If the .dic file is stored elsewhere, then the argument is the full path to the .dic file (including the extension,
+e.g.: \code{"/path/to/the/dictionary_file.dic"}). This is the case for instance when the dataset is stored in a remote URL,
+and we have a locally stored dictionary for that particular dataset. If FALSE no variable homogenization takes place,
+and the raw variable, as originally stored in the dataset, will be returned. See details for dictionary specification.}
+
 \item{lonLim}{Vector of length = 2, with minimum and maximum longitude coordinates, in decimal degrees, of the bounding box selected.
 For single-point queries, a numeric value with the longitude coordinate. If \code{NULL} (default), the whole longitudinal range
  is selected (Note that this may lead to a large output object size).}
@@ -28,12 +34,6 @@ Options include one to several (contiguous) months. Default to \code{NULL}, indi
 \item{years}{Optional vector of years to select. Default (\code{NULL}) to all available years. If the requested variable is static (e.g. orography)
 it will be ignored.}
 
-\item{dictionary}{Default to TRUE, indicating that a dictionary is used and the .dic file is stored in the same path than the
-dataset. If the .dic file is stored elsewhere, then the argument is the full path to the .dic file (including the extension,
-e.g.: \code{"/path/to/the/dictionary_file.dic"}). This is the case for instance when the dataset is stored in a remote URL,
-and we have a locally stored dictionary for that particular dataset. If FALSE no variable homogenization takes place,
-and the raw variable, as originally stored in the dataset, will be returned. See details for dictionary specification.}
-
 \item{time}{A character vector indicating the temporal filtering/aggregation
 of the output data. Default to \code{"none"}, which returns the original time
 series as stored in the dataset. For sub-daily variables, instantantaneous data at

man/loadGridDataset.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{loadGridDataset}
 \alias{loadGridDataset}
 \title{Loads a user-defined subset of a gridded CDM dataset}

man/loadMultiField.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{loadMultiField}
 \alias{loadMultiField}
 \title{Load several gridded variables}

man/loadStationData.ASCII.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{loadStationData.ASCII}
 \alias{loadStationData.ASCII}
 \title{Load station data in standard ASCII format}

man/loadStationData.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{loadStationData}
 \alias{loadStationData}
 \title{Load station data}
@@ -11,11 +11,16 @@ loadStationData(dataset, file.format = "ascii", var, stationID = NULL,
 pointing to a netCDF or NcML file in the case of netCDF and/or gridded datasets. For station data in standard ASCII format,
 this is the path to the directory the dataset lives in.}
 
+\item{file.format}{Wether the stations data are stored in a netCDF or ASCII (default) file.
+Currently only the standard \dQuote{ASCII} format supported. See references for details.}
+
 \item{var}{Variable code (character string). This is the name of the variable according to the R standard naming
 (see the next argument). For variables with vertical levels, the vertical level is specified next to the variable name followed
  by the \dQuote{@} symbol (e.g. \code{var = "z@700"} for geopotential heigth at 700 mb isobaric surface pressure level).
  It is also possible to enter the variable name as originally coded in the dataset to skip data homogenization.}
 
+\item{stationID}{Optional. A character vector indicating the code names of the stations to be loaded.}
+
 \item{lonLim}{Vector of length = 2, with minimum and maximum longitude coordinates, in decimal degrees, of the bounding box selected.
 For single-point queries, a numeric value with the longitude coordinate. If \code{NULL} (default), the whole longitudinal range
  is selected (Note that this may lead to a large output object size).}
@@ -28,11 +33,6 @@ Options include one to several (contiguous) months. Default to \code{NULL}, indi
 \item{years}{Optional vector of years to select. Default (\code{NULL}) to all available years. If the requested variable is static (e.g. orography)
 it will be ignored.}
 
-\item{file.format}{Wether the stations data are stored in a netCDF or ASCII (default) file.
-Currently only the standard \dQuote{ASCII} format supported. See references for details.}
-
-\item{stationID}{Optional. A character vector indicating the code names of the stations to be loaded.}
-
 \item{tz}{A time zone specification to be used for the conversion of dates, if one is required
 (i.e., if the time zone of the dataset does not correspond to the system-specific one; see
 \code{\link[base]{timezones}} for details). Default to unspecified (i.e. \code{tz = ""}).}

man/login_SMG.Rd → man/login_TAP.Rd

@@ -1,9 +1,9 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
-\name{login_SMG}
-\alias{login_SMG}
-\title{Login to the Santander Met Group Data Server}
+% Generated by roxygen2 (4.0.2): do not edit by hand
+\name{login_TAP}
+\alias{login_TAP}
+\title{Login to the Santander Met Group Thredds Data Server}
 \usage{
-login_SMG(username, password, proxy.host = NULL, proxy.port = NULL)
+login_TAP(username, password, proxy.host = NULL, proxy.port = NULL)
 }
 \arguments{
 \item{username}{A character string with a valid user ID. See details.}

man/makeAggregatedDataset.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{makeAggregatedDataset}
 \alias{makeAggregatedDataset}
 \title{Create a dataset from a collection of (netCDF) files}

man/makeMultiField.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{makeMultiField}
 \alias{makeMultiField}
 \title{Constructor of a multifield from various fields, supporting multimember fields.}