downloadSoilData: Download NEON Soil Data Associated with Marker Gene...

In claraqin/neonMicrobe: Downloading, Pre-processing, and Assembling NEON Soil Microbe Marker Gene Sequence Data

Download NEON Soil Data Associated with Marker Gene Sequencing Data

Description

Downloads the following NEON data product:

• DP1.10086.001: "Soil physical and chemical properties, periodic", tables sls_soilCoreCollection, sls_soilMoisture, sls_soilpH, and sls_soilChemistry. This function uses loadByProduct to conduct the downloads.

Usage

downloadSoilData(
  sites = "all",
  startYrMo = NA,
  endYrMo = NA,
  dpID = c("DP1.10086.001"),
  outDir = NULL,
  rmSamplingImpractical = TRUE,
  rmNTransBouts = TRUE,
  rmFailedCNDataQF = TRUE
)

Arguments

sites	Either the string 'all' (default), meaning all available sites, or a character vector of 4-letter NEON site codes, e.g. c('ONAQ','RMNP'). Defaults to PRESET_SITES parameter in params.R.
startYrMo, endYrMo	Either NA (default), meaning all available dates, or a character vector in the form YYYY-MM, e.g. 2017-01. Defaults to PRESET_START_YR_MO in params.R.
dpID	NEON data product(s) of interest. Default is DP1.10086.001 ("Soil physical and chemical properties, periodic").
outDir	Directory where a copy of the downloaded soil data will be saved. By default (NULL), this is NEONMICROBE_DIR_SOIL(). If no copy should be saved, set outDir=FALSE.
rmSamplingImpractical	Default TRUE. Whether to remove soil data records when sampling did not actually occur.
rmNTransBouts	Default TRUE. Whether to remove soil data records from bouts to collect N-transformation incubation tubes. These are only useful for calculating N-transformation rates and aren't associated with microbial data.
rmFailedCNDataQF	Default TRUE. Whether to remove soil data records where cnPercentQF indicates failure. While other QF fields exist and are simply passed to output, this particular check may be desirable because this function later aggregates nitrogenPercent and organicCPercent values for cnSampleIDs with analytical replicates.

Value

A dataframe consisting of joined soil data records from DP1.10086 ("Soil physical and chemical properties, periodic"). Otherwise, no value is returned.

claraqin/neonMicrobe documentation built on April 11, 2024, 11:47 a.m.