Package 'rerddapUtils' reference manual

Title:	Miscellaneous Utilities for 'rerddap'
Description:	The 'rerddapUtils' package is an 'R' package that is a set of four main functions designed to work with and extend the 'rerddap' package. These functions includes one for restricting by season, one for splitting large requests, and two for working with projected datasets. There are also two utility functions that provide estimates of the size of a proposed 'rerddap::griddap()' request.
Authors:	Roy Mendelssohn [aut, cre]
Maintainer:	Roy Mendelssohn <[email protected]>
License:	CC0
Version:	1.0.0
Built:	2026-05-20 00:07:25 UTC
Source:	https://github.com/cran/rerddapUtils

Estimate the size of a rerddap::griddap() request

Description

Uses coordinate metadata from an ERDDAP info() object to estimate how many grid cells will be returned and the total uncompressed byte count for each requested data variable. No network request is made.

Usage

estimate_griddap_size(
  info,
  ...,
  fields = "all",
  stride = 1L,
  spacing = list(),
  verbose = TRUE
)
estimate_griddap_size(
  info,
  ...,
  fields = "all",
  stride = 1L,
  spacing = list(),
  verbose = TRUE
)

Arguments

info

An object returned by rerddap::info().

...

Named dimension constraints, one per coordinate variable to constrain. Names must exactly match the coordinate variable names in the dataset (as returned by dimvars(info)). Each value is c(min, max); for time use ISO 8601 strings.

fields

Character vector of data variable names, or "all" (default).

stride

Integer scalar or named list of per-dimension stride values, using the same convention as griddap(). Default 1.

spacing

Optional named list to override auto-detected spacing for one or more dimensions. For time, supply seconds as time_sec (e.g. spacing = list(time_sec = 86400)). For other dimensions use the coordinate variable name (e.g. spacing = list(latitude = 0.01, xi_rho = 1)).

verbose

Logical; print a formatted summary (default TRUE).

Details

Coordinate dimension names are taken directly from the info object using the same logic as rerddap:::dimvars() — the set-difference between all keys in info$alldata and the data variable names plus "NC_GLOBAL". This means any coordinate system works: geographic lat/lon, projected x/y, sigma-layer depth, ROMS xi_rho/eta_rho, etc.

Dimension constraints are passed via ... using the exact coordinate variable names reported by the dataset, the same way griddap() accepts them. Each constraint is a numeric (or character for time) vector of length 2: c(min, max).

Spacing is resolved in this order for each dimension:

User-supplied override in the spacing argument.
For time: (t_max - t_min) / (nValues - 1) derived from the dimension's nValues row and actual_range attribute. This correctly handles running composites where time steps are daily even though the composite window is e.g. 8 days.
NC_GLOBAL attributes: geospatial_lat_resolution, geospatial_lon_resolution, time_coverage_resolution (ISO 8601).
Coordinate variable attributes: point_spacing, resolution, spacing.
For time: averageSpacing string from the nValues row as a last resort.
If the constraint min == max the dimension contributes 1 point.
Otherwise: NA — a warning is issued and 1 point is assumed.

Value

Invisibly, a named list containing per-dimension point counts, spacing values, per-variable byte estimates, and total bytes.

Examples

## Not run: 
  library(rerddap)

  myURL <- "https://coastwatch.pfeg.noaa.gov/erddap/"
  response <- try(httr::HEAD(myURL, httr::timeout(10)), silent = TRUE)
  if (inherits(response, "try-error")) {
     stop("The ERDDAP\u2122 server is not responding")
  }
  info <- rerddap::info("erdMH1chla8day", url = myURL)
  estimate_griddap_size(info,
    latitude  = c(30, 50),
    longitude = c(-140, -110),
    time      = c("2020-01-01", "2020-12-31"))

## End(Not run)
## Not run: 
  library(rerddap)

  myURL <- "https://coastwatch.pfeg.noaa.gov/erddap/"
  response <- try(httr::HEAD(myURL, httr::timeout(10)), silent = TRUE)
  if (inherits(response, "try-error")) {
     stop("The ERDDAP\u2122 server is not responding")
  }
  info <- rerddap::info("erdMH1chla8day", url = myURL)
  estimate_griddap_size(info,
    latitude  = c(30, 50),
    longitude = c(-140, -110),
    time      = c("2020-01-01", "2020-12-31"))

## End(Not run)

Estimate the size of a single split in a rerddap::griddap() request

Description

Takes the result of estimate_griddap_size() together with a named list of split counts per dimension and reports the estimated uncompressed size of one split. The total number of splits is the product of all split counts (e.g. splits = list(time = 5, latitude = 2, longitude = 2) means 20 total splits). Per-split point counts use ceiling(n_pts / split_count) so uneven divisions are handled correctly and estimates are conservative.

Usage

estimate_griddap_split_size(size_est, splits, verbose = TRUE)
estimate_griddap_split_size(size_est, splits, verbose = TRUE)

Arguments

size_est

The list returned invisibly by estimate_griddap_size().

splits

Named list of split counts per dimension. Dimensions not listed are assumed to have a split count of 1 (no split).

verbose

Logical; print a summary (default TRUE).

Value

Invisibly, a named list with the total split count, per-split cell count, per-variable byte estimates, total per-split bytes, and a formatted size string.

Examples

## Not run: 
  library(rerddap)

  myURL = 'https://coastwatch.pfeg.noaa.gov/erddap/'
  response <- try(httr::HEAD(myURL, httr::timeout(10)), silent = TRUE)
  if (inherits(response, "try-error")) {
     stop("The ERDDAP\u2122 server is not responding")
  }
  wind_info <- info("erdQMekm14day", url = myURL)
  sz <- estimate_griddap_size(wind_info,
    latitude  = c(20, 40),
    longitude = c(-140, -110),
    time      = c("2015-01-01", "2016-01-01"),
    fields    = "mod_current")

  estimate_griddap_split_size(sz,
    splits = list(time = 5, altitude = 1, latitude = 2, longitude = 2))

## End(Not run)
## Not run: 
  library(rerddap)

  myURL = 'https://coastwatch.pfeg.noaa.gov/erddap/'
  response <- try(httr::HEAD(myURL, httr::timeout(10)), silent = TRUE)
  if (inherits(response, "try-error")) {
     stop("The ERDDAP\u2122 server is not responding")
  }
  wind_info <- info("erdQMekm14day", url = myURL)
  sz <- estimate_griddap_size(wind_info,
    latitude  = c(20, 40),
    longitude = c(-140, -110),
    time      = c("2015-01-01", "2016-01-01"),
    fields    = "mod_current")

  estimate_griddap_split_size(sz,
    splits = list(time = 5, altitude = 1, latitude = 2, longitude = 2))

## End(Not run)

Title Get ERDDAP gridded data restricted to a given season of the year

Description

griddap_season uses the R program 'rerddap::griddap()' to extract environmental data from an 'ERDDAP' server in an (time, z, y ,x) bounding box where time is restricted to a given season of the year (see below). Arguments are the same in 'rerddap::griddap()' except for the added 'season' parameter. 'read' and 'fmt' options are ignored.

Usage

griddap_season(
  datasetx,
  ...,
  fields = "all",
  stride = 1,
  season = NULL,
  fmt = "nc",
  url = rerddap::eurl(),
  store = rerddap::disk(),
  read = TRUE,
  callopts = list()
)
griddap_season(
  datasetx,
  ...,
  fields = "all",
  stride = 1,
  season = NULL,
  fmt = "nc",
  url = rerddap::eurl(),
  store = rerddap::disk(),
  read = TRUE,
  callopts = list()
)

Arguments

datasetx

Anything coercable to an object of class info. So the output of a call to info, or a datasetid, which will internally be passed through info

...

Dimension arguments. See examples. Can be any 1 or more of the dimensions for the particular dataset - and the dimensions vary by dataset. For each dimension, pass in a vector of length two, with min and max value desired. at least 1 required.

fields

(character) Fields to return, in a character vector.

stride

(integer) How many values to get. 1 = get every value, 2 = get every other value, etc. Default: 1 (i.e., get every value)

season

(character) a character array with the times of the trajectory in the form c("MM-DD", "MM-DD")

fmt

(character) ignored

url

A URL for an ERDDAP server. Default: https://upwell.pfeg.noaa.gov/erddap/ - See rerddap::eurl() for more information

store

ignored

read

ignored

callopts

Curl options passed on to verb-GET

Value

An object of class griddap_csv if csv chosen or griddap_nc if nc file format chosen.

Examples

myURL <- "https://coastwatch.pfeg.noaa.gov/erddap/"
response <- try(httr::HEAD(myURL, httr::timeout(20)), silent = TRUE)
if (inherits(response, "try-error")) {
   message("The ERDDAP\u2122 server is not responding")
} else
{
season <- c('03-01', '03-04')
season_extract <- try(griddap_season(wind_info,
                                 time = c('2015-01-01','2016-01-01'),
                                 latitude = c(20, 21),
                                 longitude = c(220, 221),
                                 fields = 'mod_current',
                                 season = season
                                 ), silent = TRUE)
if (inherits(season_extract, "try-error")) {
   message("Unable to retrieve data from the ERDDAP\u2122 server")
   }
 }
myURL <- "https://coastwatch.pfeg.noaa.gov/erddap/"
response <- try(httr::HEAD(myURL, httr::timeout(20)), silent = TRUE)
if (inherits(response, "try-error")) {
   message("The ERDDAP\u2122 server is not responding")
} else
{
season <- c('03-01', '03-04')
season_extract <- try(griddap_season(wind_info,
                                 time = c('2015-01-01','2016-01-01'),
                                 latitude = c(20, 21),
                                 longitude = c(220, 221),
                                 fields = 'mod_current',
                                 season = season
                                 ), silent = TRUE)
if (inherits(season_extract, "try-error")) {
   message("Unable to retrieve data from the ERDDAP\u2122 server")
   }
 }

Title Get ERDDAP gridded data restricted to a given season of the year

Description

griddap_season uses the R program 'rerddap::griddap()' to extract environmental data from an 'ERDDAP' server in an (time, z, y ,x) bounding box where time is restricted to a given season of the year (see below). Arguments are the same as in 'rerddap::griddap()' except for the added 'season' parameter. 'read' and 'fmt' options are ignored.

Usage

griddap_split(
  datasetx,
  ...,
  fields = "all",
  stride = 1,
  request_split = NULL,
  fmt = "nc",
  url = rerddap::eurl(),
  store = rerddap::disk(),
  read = TRUE,
  callopts = list(),
  aggregate_file = NULL
)
griddap_split(
  datasetx,
  ...,
  fields = "all",
  stride = 1,
  request_split = NULL,
  fmt = "nc",
  url = rerddap::eurl(),
  store = rerddap::disk(),
  read = TRUE,
  callopts = list(),
  aggregate_file = NULL
)

Arguments

datasetx

Anything coercable to an object of class info. So the output of a call to info, or a datasetid, which will internally be passed through info

...

fields

(character) Fields to return, in a character vector.

stride

(integer) How many values to get. 1 = get every value, 2 = get every other value, etc. Default: 1 (i.e., get every value)

request_split

A numeric vector indicating the number of splits for each dimension, used to segment the request into manageable chunks. This is particularly useful for large datasets.

fmt

(character) One of:

nc: save output to a netcdf file
memory: save output in a dataframe in memory
duckdb: save data in a duckdb database

url

A URL for an ERDDAP server. Default: https://upwell.pfeg.noaa.gov/erddap/ - See rerddap::eurl() for more information

store

ignored

read

ignored

callopts

Curl options passed on to verb-GET

aggregate_file

A string specifying:

if is.null(aggregate_file) then a temporary file is created that does not overwrite user space
if "fmt = nc" the path to the NetCDF file to store the results
if "fmt = duckdb" the path to the duckdb file to store the results
if "fmt = memory" the value is ignored

Value

Varies by format requested:

if "fmt = nc" the path to the NetCDF file where the results are stored
if "fmt = duckdb" the path to the duckdb file where the results are stored
if "fmt = memory" the usual rerddap::griddap dataframe

Examples

myURL <- "https://coastwatch.pfeg.noaa.gov/erddap/"
response <- try(httr::HEAD(myURL, httr::timeout(20)), silent = TRUE)
if (inherits(response, "try-error")) {
  message("The ERDDAP\u2122 server is not responding")
} else
{
request_split <- list(time = 2, altitude = 1, latitude = 1, longitude = 1)
res <- try(griddap_split(wind_info,
                     time = c('2015-12-31','2016-01-01'),
                     latitude = c(20, 21),
                     longitude = c(220, 221),
                     fields = 'mod_current',
                     request_split = request_split
                     ), silent = TRUE)
if (inherits(res, "try-error")) {
   message("Unable to retrieve data from the ERDDAP\u2122 server")
   }
}
myURL <- "https://coastwatch.pfeg.noaa.gov/erddap/"
response <- try(httr::HEAD(myURL, httr::timeout(20)), silent = TRUE)
if (inherits(response, "try-error")) {
  message("The ERDDAP\u2122 server is not responding")
} else
{
request_split <- list(time = 2, altitude = 1, latitude = 1, longitude = 1)
res <- try(griddap_split(wind_info,
                     time = c('2015-12-31','2016-01-01'),
                     latitude = c(20, 21),
                     longitude = c(220, 221),
                     fields = 'mod_current',
                     request_split = request_split
                     ), silent = TRUE)
if (inherits(res, "try-error")) {
   message("Unable to retrieve data from the ERDDAP\u2122 server")
   }
}

Projected ice dataset info

Description

rerddap::info() call to Projected ice dataset

Usage

iceInfo
iceInfo

Format

A list of class info with elements:

variables: a data frame with a list of the variables in the extraction
alldata: metadata summary
base_url: a character string givng the base URL of the extract

Source

https://coastwatch.noaa.gov/erddap/

Convert Latitude-Longitude to Projected Coordinates

Description

This function converts geographic coordinates (latitude and longitude) into projected coordinates based on a specified Coordinate Reference System (CRS). The function can automatically detect the CRS from provided metadata (dataInfo) or use a specified CRS code. It is designed to work with datasets obtained from rerddap::griddap() but can be used with any geographic data that requires coordinate transformation.

Usage

latlon_to_xy(
  dataInfo,
  longitude,
  latitude,
  xName = "rows",
  yName = "cols",
  crs = NULL
)
latlon_to_xy(
  dataInfo,
  longitude,
  latitude,
  xName = "rows",
  yName = "cols",
  crs = NULL
)

Arguments

dataInfo

Metadata object containing CRS information, typically obtained from a rerddap::info() call on a dataset. It should include global attributes that contain CRS information.

longitude

Numeric vector of longitudes to be converted.

latitude

Numeric vector of latitudes to be converted.

xName

Name of the longitude coordinate in the output projection. Defaults to 'longitude'.

yName

Name of the latitude coordinate in the output projection. Defaults to 'latitude'.

crs

Optional. A character string specifying the CRS to use for the projection. This can be an EPSG code (e.g., 'EPSG:4326' for WGS84) or a PROJ string. If NULL, the function attempts to detect the CRS from dataInfo.

Value

A matrix with columns corresponding to the projected x and y coordinates (in the order specified by xName and yName). Each row in the matrix corresponds to a pair of input latitude and longitude values.

Examples

# myURL <- 'https://coastwatch.noaa.gov/erddap/'
# iceInfo <- rerddap::info('noaacwVIIRSn20icethickNP06Daily', url = myURL)
latitude <- c( 80., 85.)
longitude <- c(-170., -165)
coords <- latlon_to_xy(iceInfo,  longitude, latitude)

# myURL <- 'https://coastwatch.noaa.gov/erddap/'
# iceInfo <- rerddap::info('noaacwVIIRSn20icethickNP06Daily', url = myURL)
latitude <- c( 80., 85.)
longitude <- c(-170., -165)
coords <- latlon_to_xy(iceInfo,  longitude, latitude)

Projected ice dataset response

Description

rerddap::griddap() call to Projected ice dataset

Usage

proj_extract
proj_extract

Format

A list of class griddap_nc with elements:

data: a data frame of the extracted ice values
summary: metadata summary

Source

https://coastwatch.noaa.gov/erddap/

Projected 14 day wind info

Description

rerddap::info() call to 14 day wind dataset

Usage

wind_info
wind_info

Format

A list of class info with elements:

variables: a data frame with a list of the variables in the extraction
alldata: metadata summary
base_url: a character string givng the base URL of the extract

Source

https://coastwatch.noaa.gov/erddap/

Convert Projected 'rerddap::griddap()' Coordinates to Latitude-Longitude

Description

This function converts the projected coordinates from a 'rerddap::griddap()' response into geographical coordinates (latitude and longitude). It supports responses from griddap, rxtracto, and rxtracto3D by detecting the response type and applying the appropriate Coordinate Reference System (CRS) transformation.

Usage

xy_to_latlon(resp, yName = "cols", xName = "rows", crs = NULL)
xy_to_latlon(resp, yName = "cols", xName = "rows", crs = NULL)

Arguments

resp

A response object from a call to rerddap::griddap(). It is expected to be of type griddap_nc, rxtracto3D, or rxtractoTrack, which contains the projected coordinate data along with metadata including the dataset's CRS.

yName

The name of the variable in resp that represents the Y coordinate (typically latitude or northing). Defaults to 'cols'.

xName

The name of the variable in resp that represents the X coordinate (typically longitude or easting). Defaults to 'rows'.

crs

An optional CRS code to be used for the transformation. If a CRS is found in the resp metadata this is ignored. CRS code should be a valid EPSG code (e.g., 4326 for WGS84) or a PROJ string.

Value

A matrix with two columns (longitude, latitude) containing the geographic coordinates corresponding to the projected coordinates in the input resp. Each row in the matrix corresponds to a point in resp.

Examples

rows <- c( -889533.8, -469356.9)
cols <- c(622858.3, 270983.4)
# myURL <- 'https://coastwatch.noaa.gov/erddap/'
# icceInfo <- rerddap::info('noaacwVIIRSn20icethickNP06Daily', url = myURL)
# proj_extract <- rerddap::griddap(iceInfo,
#                           time = c('2023-01-01T00:00:00Z', '2023-01-01T00:00:00Z'),
#                            rows = rows,
#                             cols = cols,
#                             altitude = c(0., 0.),
#                             fields = 'IceThickness',
#                            url = myURL
#                             )
test <- xy_to_latlon(proj_extract)

rows <- c( -889533.8, -469356.9)
cols <- c(622858.3, 270983.4)
# myURL <- 'https://coastwatch.noaa.gov/erddap/'
# icceInfo <- rerddap::info('noaacwVIIRSn20icethickNP06Daily', url = myURL)
# proj_extract <- rerddap::griddap(iceInfo,
#                           time = c('2023-01-01T00:00:00Z', '2023-01-01T00:00:00Z'),
#                            rows = rows,
#                             cols = cols,
#                             altitude = c(0., 0.),
#                             fields = 'IceThickness',
#                            url = myURL
#                             )
test <- xy_to_latlon(proj_extract)

Package 'rerddapUtils'

Help Index

Estimate the size of a rerddap::griddap() request

Description

Usage

Arguments

Details

Value

Examples

Estimate the size of a single split in a rerddap::griddap() request

Description

Usage

Arguments

Value

Examples

Title Get ERDDAP gridded data restricted to a given season of the year

Description

Usage

Arguments

Value

Examples

Title Get ERDDAP gridded data restricted to a given season of the year

Description

Usage

Arguments

Value

Examples

Projected ice dataset info

Description

Usage

Format

Source

Convert Latitude-Longitude to Projected Coordinates

Description

Usage

Arguments

Value

Examples

Projected ice dataset response

Description

Usage

Format

Source

Projected 14 day wind info

Description

Usage

Format

Source

Convert Projected 'rerddap::griddap()' Coordinates to Latitude-Longitude

Description

Usage

Arguments

Value

Examples