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A function that communicates with the the AIMS Data Platform via the AIMS Data Platform API

Usage

aims_data(target, filters = NULL, summary = NA, ...)

Arguments

target

A character vector of length 1 specifying the dataset. Only weather or temp_loggers are currently allowed.

filters

A list containing a set of filters for the data query (see Details).

summary

Should summary tables ("summary-by-series" or "summary-by-deployment") or daily aggregated data ("daily") be returned instead of full data (see Details)?

...

Currently unused. Additional arguments to be passed to non-exported internal functions.

Value

aims_data returns a data.frame of class aimsdf. If summary %in% c("summary-by-series", "summary-by-deployment"), the output shows the summary information for the target dataset (i.e. weather or temperature loggers) (NB: currently, summary only works for the temperature logger database). If summary is not passed as an additional argument, then the output contains raw monitoring data. If summary = "daily", then the output contains mean daily aggregated monitoring data. The output also contains five attributes (empty strings if summary is passed as an additional argument):

  • metadataa DOI link containing the metadata record for the data series.

  • citationthe citation information for the particular dataset.

  • parametersThe measured parameters comprised in the output.

  • typeThe type of dataset. Either "monitoring" if summary is not specified, "monitoring (daily aggregation)" if summary = "daily", or a "summary-by-" otherwise.

  • targetThe input target.

Details

The AIMS Data Platform R Client provides easy access to data sets for R applications to the AIMS Data Platform API. The AIMS Data Platform requires an API Key for requests, which can be obtained at this link. It is preferred that API Keys are not stored in code. We recommend storing the environment variable AIMS_DATAPLATFORM_API_KEY permanently under the user's .Renviron file in order to load the API Key automatically.

There are two types of data currently available through the AIMS Data Platform API: Weather and Sea Water Temperature Loggers. They are searched internally via unique DOI identifiers. Only one data type at a time can be passed to the argument target.

A list of arguments for filters can be exposed for both Weather and Sea Water Temperature Loggers using function aims_expose_attributes.

Note that at present the user can inspect the range of dates for the temperature loggers data only (see usage of argument summary in the examples below). For that, the argument summary must be either the string "summary-by-series" or "summary-by-deployment". In those cases, time filters will be ignored.

Details about available dates for each dataset and time series can be accessed via Metadata on AIMS Data Platform API. We raise this caveat here because these time boundaries are very important; data are collected at very small time intervals, a window of just a few days can yield very large datasets. The query will return and error if it reaches the system's memory capacity.

For that same reason, from version 1.1.0 onwards, we are offering the possibility of downloading a mean daily aggregated version. For that, the user must set summary = "daily". In this particular case, query filter will be taken into account.

Author

AIMS Datacentre [email protected]

Examples

if (FALSE) {
library(dataaimsr)
# assumes that user already has API key saved to
# .Renviron

# start downloads:
# 1. downloads weather data from
# site Yongala
# within a defined date range
wdf_a <- aims_data("weather", api_key = NULL,
                   filters = list(site = "Yongala",
                                  from_date = "2018-01-01",
                                  thru_date = "2018-01-02"))

# 2. downloads weather data from all sites
# under series_id 64 from Davies Reef
# within a defined date range
wdf_b <- aims_data("weather", api_key = NULL,
                   filters = list(series_id = 64,
                                  from_date = "1991-10-18",
                                  thru_date = "1991-10-19"))
head(wdf_b)
range(wdf_b$time)

# 3. downloads weather data from all sites
# under series_id 64 from Davies Reef
# within defined date AND time range
wdf_c <- aims_data("weather", api_key = NULL,
                   filters = list(series_id = 64,
                                  from_date = "1991-10-18T06:00:00",
                                  thru_date = "1991-10-18T12:00:00"))
head(wdf_c)
range(wdf_c$time)

# 4. downloads all parameters from all sites
# within a defined date range
wdf_d <- aims_data("weather", api_key = NULL,
                   filters = list(from_date = "2003-01-01",
                                  thru_date = "2003-01-02"))
# note that there are multiple sites and series
# so in this case, because we did not specify a specific
# parameter, series within sites could differ by both
# parameter and depth
head(wdf_d)
unique(wdf_d[, c("site", "series_id", "series")])
unique(wdf_d$parameter)
range(wdf_d$time)

# 5. downloads chlorophyll from all sites
# within a defined date range
wdf_e <- aims_data("weather", api_key = NULL,
                   filters = list(parameter = "Chlorophyll",
                                  from_date = "2018-01-01",
                                  thru_date = "2018-01-02"))
# note again that there are multiple sites and series
# however in this case because we did specify a specific
# parameter, series within sites differ by depth only
head(wdf_e)
unique(wdf_e[, c("site", "series_id", "series", "depth")])
unique(wdf_e$parameter)
range(wdf_e$time)

# 6. downloads temperature data
# summarised by series
sdf_a <- aims_data("temp_loggers", api_key = NULL,
                   summary = "summary-by-series")
head(sdf_a)
dim(sdf_a)

# 7. downloads temperature data
# summarised by series
# for all sites that contain data
# within a defined date range
sdf_b <- aims_data("temp_loggers", api_key = NULL,
                   summary = "summary-by-series",
                   filters = list("from_date" = "2018-01-01",
                                  "thru_date" = "2018-12-31"))
head(sdf_b)
dim(sdf_b) # a subset of sdf_a

# 8. downloads temperature data
# summarised by deployment
sdf_c <- aims_data("temp_loggers", api_key = NULL,
                   summary = "summary-by-deployment")
head(sdf_c)
dim(sdf_c)

# 9. downloads temperature data
# within a defined date range, averaged by day
sdf_d <- aims_data("temp_loggers", api_key = NULL, summary = "daily",
                   filters = list(series = "DAVFL1",
                                  from_date = "2018-01-01",
                                  thru_date = "2018-01-10"))
# note again that there are multiple sites and series
# however in this case because we did specify a specific
# parameter, series within sites differ by depth only
head(sdf_d)
unique(sdf_d[, c("site", "series_id", "series", "depth")])
unique(sdf_d$parameter)
range(sdf_d$time)
}