summarizeData: A function to summarize data from the database

In ProfoundData: Downloading and Exploring Data from the PROFOUND Database

Description

This function allows to summarize datasets for a site from the PROFOUND database.

Usage

summarizeData(
  dataset,
  site,
  location = NULL,
  forcingDataset = NULL,
  forcingCondition = NULL,
  by = "year",
  period = NULL,
  mode = "data"
)

Arguments

dataset	a character string providing the name of a climatic dataset (CLIMATE_LOCAL, CLIMATE_ISIMIP, ...) or the tree dataset.(change this you )
site	a character string providing the name of a site.
location	deprecated argument. Please use site instead.
forcingDataset	a character string providing the name of a forcingDataset. Only relevant for ISIMIP datasets.
forcingCondition	a character string providing the name of a forcingCondition. Only relevant for ISIMIP datasets.
by	a character string indicating how to summarize the data. Currently supports by year and total. The latter refers to the entire available period.
period	a character array with either start or start and end of the subset. It must have the format "YYYY-MM-DD", or c("YYYY-MM-DD", "YYYY-MM-DD").
mode	a character string indicating whether to display the data summary (data) or an overview (overview).

Details

This function is under development and has limited functionality. At the moment, it is possible to summarize daily climate datasets and tree data.

Data are summarized by years. Radiation and precipitation are provided as total yearly values, while the rest of climatic values are year mean values. For ISIMIP datasets a summary for whole period will be returned if the dataset comprises more than one forcing dataset and one forcing condition.

Value

a data frame with the summary values

Summary values

Summary is calculated by year

• Climatic datasets

  • p_mm and rad_Jcm2day are total yearly values

  • tmax_degC, tmean_degC, tmin_degC, relhum_percent, airpress_hPa and wind_ms are mean yearly values

• TREE dataset

  • density_treeha is the number of tree per ha

  • dbhArit_cm is the arithmetic mean diameter

  • dbhBa_cm is the average diameter weighted by basal area calculated as dbhBA = (ba1*dbh1 + ba2*dbh2 + ... + bak*dbhk) / (ba1 + ba2+ ... + bak), where bai and dbhi are the basal area and dbh, respectively, of the tree i, and i = 1, 2, . . , k

  • dbhDQ_cm is the mean squared diameter or quadratic mean diameter calculated as dbhDQ = sqrt( (dbh1^2 + dbh2^2+ ... + dbhk^2) / N), where dbhi is the diameter at breast height of tree i, i = 1, 2, . . , k, N is the total number of trees, and sqrt is the square root

  • heightArith_m is the arithmetic mean height

  • heightArith_m is the average height weighted by basal area or Loreys height calculated as heightBA = (ba1*h1 + ba2*h2 + ... + bak*hk) / (ba1 + ba2+ ... + bak), where bai and hi are the basal area and height, respectively, of the tree i, and i = 1, 2, . . , k

  • heightBA_m

  • ba_m2 is the basal area per hectare

Note

To report errors in the package or the data, please use the issue tracker in the GitHub repository of ProfoundData https://github.com/COST-FP1304-PROFOUND/ProfoundData

Examples

# example requires that a sql DB is registered via setDB(dbfile)
# when run without a registered DB, you will get a file query (depending on OS)

## Not run: 
# Summarize by years
data <-summarizeData(dataset =  "TREE", site = "bily_kriz", by = "year",
                     mode = "data")
data <-summarizeData(dataset =  "CLIMATE_LOCAL", site = "bily_kriz", by = "year",
                     mode = "data")
data <-summarizeData(dataset =  "CLIMATE_ISIMIP2A", site = "bily_kriz", by = "year",
                     mode = "data")

# Specify forcing dataset or condition
data <-summarizeData(dataset ="CLIMATE_ISIMIP2B", site ="soro",
                     forcingDataset="GFDLESM2M", forcingCondition ="rcp2p6")


# Summarize total period
data <-summarizeData(dataset =  "TREE", site = "bily_kriz", by = "total",
                     mode = "data")
data <-summarizeData(dataset =  "CLIMATE_LOCAL", site = "bily_kriz", by = "total",
                     mode = "data")

# Summarize overview
data <-summarizeData(dataset =  "CLIMATE_LOCAL", site = "bily_kriz", mode = "overview")
data <-summarizeData(dataset =  "FLUX", site = "bily_kriz", mode = "overview")
data <-summarizeData(dataset =  "TREE", site = "bily_kriz", mode = "overview")
data <-summarizeData(dataset =  "STAND", site = "bily_kriz", mode = "overview")

## End(Not run)

ProfoundData documentation built on March 31, 2020, 5:24 p.m.