R/data.R
In EDUCE-UBC/educer: A Collection of Tutorials on Using R in Data Science
#' Full geochemical data set from Saanich Inlet 2006 to 2014
#'
#' Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island
#' British Columbia, is a model ecosystem for monitoring microbial community
#' structure, function and dynamics in relation to changing levels of water
#' column oxygen-deficiency extensible to coastal and open ocean OMZs. This data
#' set contains nine years of monthly time series observations in Saanich Inlet
#' encompassing water column chemistry. Chemical bottle data collected from
#' Station S3 (-123.505, 48.59166667) in Saanich Inlet, BC, Canada. Subset of a
#' combination of "Saanich_TimeSeries_Chemical_DATA.csv" (all variables) and
#' "Saanich_TimeSeries_CTD_DATA.csv" (Temperature, Salinity, Density) data sets.
#'
#' @format A data frame with 1605 rows and 29 variables:
#' \describe{
#' \item{Longitude}{Unique geographical coordinates for sampling station.
#' Units: Decimal degrees}
#' \item{Latitude}{Unique geographical coordinates for sampling station.
#' Units: Decimal degrees}
#' \item{Cruise}{Numerical identifier of individual cruises. Units: Numeric
#' string}
#' \item{Date}{Date of cruise. Units: YYYY-MM-DD}
#' \item{Depth}{Sampling depth. Units: Meters}
#' \item{CTD_O2}{Oxygen concentration calculated from CTD SBE. Units:
#' Micromolar}
#' \item{PO4}{Phosphate (Bran Luebbe AutoAnalyser - colorimetric). Units:
#' Micromolar}
#' \item{SI}{Silicate (Bran Luebbe AutoAnalyser - colorimetric). Units:
#' Micromolar}
#' \item{NO3}{Nitrate (Bran Luebbe AutoAnalyser - colorimetric). Units:
#' Micromolar}
#' \item{Mean_NH4}{Average concentration of Ammonium for each depth
#' (fluorometric assay). Units: Micromolar}
#' \item{Std_NH4}{Standard deviation for Ammonium average concentration.
#' Units: NA}
#' \item{Mean_NO2}{Average concentration of Nitrite for each depth
#' (colorimetric assay). Units: Micromolar}
#' \item{Std_NO2}{Standard deviation for Nitrite average concentration. Units:
#' NA}
#' \item{Mean_H2S}{Average concentration of Hydrogen sulfide for each depth
#' (colorimetric assay). Units: Micromolar}
#' \item{Std_H2S}{Standard deviation for Hydrogen sulfide average
#' concentration. Units: NA}
#' \item{Cells/ml}{Cell counts value quantified by flow cytometry. Units:
#' Number of cells per millilitre (cells/mL)}
#' \item{Mean_N2}{Average concentration of Nitrogen gas (headspace). Units:
#' Micromolar}
#' \item{Std_N2}{Standard deviation for Nitrogen gas. Units: NA}
#' \item{Mean_O2}{Average concentration of Oxygen (headspace). Units:
#' Micromolar}
#' \item{Std_O2}{Standard deviation for Oxygen. Units: NA}
#' \item{Mean_CO2}{Average concentration of Carbon dioxide (headspace). Units:
#' Micromolar}
#' \item{Std_CO2}{Standard deviation for Carbon dioxide. Units: NA}
#' \item{Mean_N2O}{Average concentration of Nitrous oxide (headspace or
#' automated purge-and-trap). Units: Nanomolar}
#' \item{Std_N2O}{Standard deviation for Nitrous oxide. Units: NA}
#' \item{Mean_CH4}{Average concentration of Methane (headspace or automated
#' purge-and-trap). Units: Nanomolar}
#' \item{Std_CH4}{Standard deviation for Methane. Units: NA}
#' \item{Temperature}{CTD temperature. Units: Celsius degrees}
#' \item{Salinity}{CTD salinity measurement at each pressure point. Units:
#' Practical salinity unit}
#' \item{Density}{CTD density measurement at each pressure point. Units:
#' Sigma-theta}
#' }
#' @source For a brief introduction to the data, see Hallam SJ \emph{et al.}
#' 2017. Monitoring microbial responses to ocean deoxygenation in a model
#' oxygen minimum zone. Sci Data 4: 170158. doi:
#' \href{https://www.nature.com/articles/sdata2017158}{10.1038/sdata.2017.158}.
#' More detailed information on the geochemical data can be found in
#' Torres-Beltrán M \emph{et al.} 2017. A compendium of geochemical
#' information from the Saanich Inlet water column. Sci Data 4: 170159. doi:
#' \href{https://www.nature.com/articles/sdata2017159}{10.1038/sdata.2017.159}
#' (\href{https://datadryad.org/stash/dataset/doi:10.5061/dryad.nh035}{dataset}).
"geochemicals"
#' Abundance of OTUs for Saanich Inlet Cruise 72
#'
#' Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island
#' British Columbia, is a model ecosystem for monitoring microbial community
#' structure, function and dynamics in relation to changing levels of water
#' column oxygen-deficiency extensible to coastal and open ocean OMZs. This data
#' set contains cruise 72 of monthly time series observations in Saanich Inlet
#' encompassing environmental sequence information. Sequencing data was
#' processed using the mothur_pipeline R Markdown file to bin the data into
#' operational taxonomic units and determine their abundance (alternatively, use
#' the \link[=normalized_OTUs]{normalized data set}).
#' % Find way to link Rmd file
#'
#' @format A data frame with 30,576 rows and 4 variables:
#' \describe{
#' \item{Cruise}{Numerical identifier of individual cruises. Units: Numeric
#' string}
#' \item{Depth}{Sampling depth. Units: Meters}
#' \item{OTU}{Numerical identifier of OTU. Units: Numeric string}
#' \item{Count}{Count of OTU sequences. Units: Numeric string}
#' }
#' @source For a brief introduction to the data, see Hallam SJ \emph{et al.}
#' 2017. Monitoring microbial responses to ocean deoxygenation in a model
#' oxygen minimum zone. Sci Data 4: 170158. doi:
#' \href{https://www.nature.com/articles/sdata2017158}{10.1038/sdata.2017.158}.
#' More detailed information on the mutli-omic microbial data can be found in
#' Hawley AK *et al*. 2017. A compendium of multi-omic sequence information
#' from the Saanich Inlet water column. Sci Data 4: 170160. doi:
#' \href{https://www.nature.com/articles/sdata2017160}{10.1038/sdata.2017.160}.
"OTUs"
#' Normalized abundance of OTUs for Saanich Inlet Cruise 72
#'
#' Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island
#' British Columbia, is a model ecosystem for monitoring microbial community
#' structure, function and dynamics in relation to changing levels of water
#' column oxygen-deficiency extensible to coastal and open ocean OMZs. This data
#' set contains cruise 72 of monthly time series observations in Saanich Inlet
#' encompassing environmental sequence information. Sequencing data was
#' processed using the mothur_pipeline R Markdown file to bin the data into
#' operational taxonomic units and determine their abundance
#' (\link[=OTUs]{non-normalized data set}) and then normalized to 100,000
#' sequences for each sample (seed = 4832).
#' % Find way to Rmd link file
#'
#' @format A data frame with 30,576 rows and 4 variables:
#' \describe{
#' \item{Cruise}{Numerical identifier of individual cruises. Units: Numeric
#' string}
#' \item{Depth}{Sampling depth. Units: Meters}
#' \item{OTU}{Numerical identifier of OTU. Units: Numeric string}
#' \item{Count}{Count of OTU sequences. Units: Numeric string}
#' }
#' @source For a brief introduction to the data, see Hallam SJ \emph{et al.}
#' 2017. Monitoring microbial responses to ocean deoxygenation in a model
#' oxygen minimum zone. Sci Data 4: 170158. doi:
#' \href{https://www.nature.com/articles/sdata2017158}{10.1038/sdata.2017.158}.
#' More detailed information on the mutli-omic microbial data can be found in
#' Hawley AK \emph{et al.} 2017. A compendium of multi-omic sequence
#' information from the Saanich Inlet water column. Sci Data 4: 170160. doi:
#' \href{https://www.nature.com/articles/sdata2017160}{10.1038/sdata.2017.160}.
"normalized_OTUs"
#' Combined data set of geochemicals and OTU abundance
#'
#' A subset of the \link[=geochemicals]{geochemical} and
#' \link[=normalized_OTUs]{normalized OTU abundance} data sets at 7 depths for
#' Saanich Inlet Cruise 72.
#'
#' @format A data frame with 7 rows and 10 variables:
#' \describe{
#' \item{Cruise}{Numerical identifier of individual cruises. Units: Numeric
#' string}
#' \item{Depth}{Sampling depth. Units: Meters}
#' \item{OTU0001}{Operational taxonomic unit 1}
#' \item{OTU0002}{Operational taxonomic unit 2}
#' \item{OTU0003}{Operational taxonomic unit 3}
#' \item{OTU0004}{Operational taxonomic unit 4}
#' \item{NO3}{Nitrate (Bran Luebbe AutoAnalyser - colorimetric). Units:
#' Micromolar}
#' \item{Mean_NO2}{Average concentration of Nitrite for each depth
#' (colorimetric assay). Units: Micromolar}
#' \item{Mean_N2O}{Average concentration of Nitrous oxide (headspace or
#' automated purge-and-trap). Units: Nanomolar}
#' \item{Mean_NH4}{Average concentration of Ammonium for each depth
#' (fluorometric assay). Units: Micromolar}
#' }
#' @source For a brief introduction to the data, see Hallam SJ \emph{et al.}
#' 2017. Monitoring microbial responses to ocean deoxygenation in a model
#' oxygen minimum zone. Sci Data 4: 170158. doi:
#' \href{https://www.nature.com/articles/sdata2017158}{10.1038/sdata.2017.158}.
#' More detailed information on the geochemical data can be found in
#' Torres-Beltrán M \emph{et al.} 2017. A compendium of geochemical
#' information from the Saanich Inlet water column. Sci Data 4: 170159. doi:
#' \href{https://www.nature.com/articles/sdata2017159}{10.1038/sdata.2017.159}
#' (\href{https://datadryad.org/stash/dataset/doi:10.5061/dryad.nh035}{dataset}).
#' More detailed information on the mutli-omic microbial data can be found in
#' Hawley AK \emph{et al.} 2017. A compendium of multi-omic sequence
#' information from the Saanich Inlet water column. Sci Data 4: 170160. doi:
#' \href{https://www.nature.com/articles/sdata2017160}{10.1038/sdata.2017.160}.
"combined"
EDUCE-UBC/educer documentation built on Sept. 1, 2021, 3:46 p.m.
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#' Full geochemical data set from Saanich Inlet 2006 to 2014
#'
#' Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island
#' British Columbia, is a model ecosystem for monitoring microbial community
#' structure, function and dynamics in relation to changing levels of water
#' column oxygen-deficiency extensible to coastal and open ocean OMZs. This data
#' set contains nine years of monthly time series observations in Saanich Inlet
#' encompassing water column chemistry. Chemical bottle data collected from
#' Station S3 (-123.505, 48.59166667) in Saanich Inlet, BC, Canada. Subset of a
#' combination of "Saanich_TimeSeries_Chemical_DATA.csv" (all variables) and
#' "Saanich_TimeSeries_CTD_DATA.csv" (Temperature, Salinity, Density) data sets.
#'
#' @format A data frame with 1605 rows and 29 variables:
#' \describe{
#' \item{Longitude}{Unique geographical coordinates for sampling station.
#' Units: Decimal degrees}
#' \item{Latitude}{Unique geographical coordinates for sampling station.
#' Units: Decimal degrees}
#' \item{Cruise}{Numerical identifier of individual cruises. Units: Numeric
#' string}
#' \item{Date}{Date of cruise. Units: YYYY-MM-DD}
#' \item{Depth}{Sampling depth. Units: Meters}
#' \item{CTD_O2}{Oxygen concentration calculated from CTD SBE. Units:
#' Micromolar}
#' \item{PO4}{Phosphate (Bran Luebbe AutoAnalyser - colorimetric). Units:
#' Micromolar}
#' \item{SI}{Silicate (Bran Luebbe AutoAnalyser - colorimetric). Units:
#' Micromolar}
#' \item{NO3}{Nitrate (Bran Luebbe AutoAnalyser - colorimetric). Units:
#' Micromolar}
#' \item{Mean_NH4}{Average concentration of Ammonium for each depth
#' (fluorometric assay). Units: Micromolar}
#' \item{Std_NH4}{Standard deviation for Ammonium average concentration.
#' Units: NA}
#' \item{Mean_NO2}{Average concentration of Nitrite for each depth
#' (colorimetric assay). Units: Micromolar}
#' \item{Std_NO2}{Standard deviation for Nitrite average concentration. Units:
#' NA}
#' \item{Mean_H2S}{Average concentration of Hydrogen sulfide for each depth
#' (colorimetric assay). Units: Micromolar}
#' \item{Std_H2S}{Standard deviation for Hydrogen sulfide average
#' concentration. Units: NA}
#' \item{Cells/ml}{Cell counts value quantified by flow cytometry. Units:
#' Number of cells per millilitre (cells/mL)}
#' \item{Mean_N2}{Average concentration of Nitrogen gas (headspace). Units:
#' Micromolar}
#' \item{Std_N2}{Standard deviation for Nitrogen gas. Units: NA}
#' \item{Mean_O2}{Average concentration of Oxygen (headspace). Units:
#' Micromolar}
#' \item{Std_O2}{Standard deviation for Oxygen. Units: NA}
#' \item{Mean_CO2}{Average concentration of Carbon dioxide (headspace). Units:
#' Micromolar}
#' \item{Std_CO2}{Standard deviation for Carbon dioxide. Units: NA}
#' \item{Mean_N2O}{Average concentration of Nitrous oxide (headspace or
#' automated purge-and-trap). Units: Nanomolar}
#' \item{Std_N2O}{Standard deviation for Nitrous oxide. Units: NA}
#' \item{Mean_CH4}{Average concentration of Methane (headspace or automated
#' purge-and-trap). Units: Nanomolar}
#' \item{Std_CH4}{Standard deviation for Methane. Units: NA}
#' \item{Temperature}{CTD temperature. Units: Celsius degrees}
#' \item{Salinity}{CTD salinity measurement at each pressure point. Units:
#' Practical salinity unit}
#' \item{Density}{CTD density measurement at each pressure point. Units:
#' Sigma-theta}
#' }
#' @source For a brief introduction to the data, see Hallam SJ \emph{et al.}
#' 2017. Monitoring microbial responses to ocean deoxygenation in a model
#' oxygen minimum zone. Sci Data 4: 170158. doi:
#' \href{https://www.nature.com/articles/sdata2017158}{10.1038/sdata.2017.158}.
#' More detailed information on the geochemical data can be found in
#' Torres-Beltrán M \emph{et al.} 2017. A compendium of geochemical
#' information from the Saanich Inlet water column. Sci Data 4: 170159. doi:
#' \href{https://www.nature.com/articles/sdata2017159}{10.1038/sdata.2017.159}
#' (\href{https://datadryad.org/stash/dataset/doi:10.5061/dryad.nh035}{dataset}).
"geochemicals"
#' Abundance of OTUs for Saanich Inlet Cruise 72
#'
#' Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island
#' British Columbia, is a model ecosystem for monitoring microbial community
#' structure, function and dynamics in relation to changing levels of water
#' column oxygen-deficiency extensible to coastal and open ocean OMZs. This data
#' set contains cruise 72 of monthly time series observations in Saanich Inlet
#' encompassing environmental sequence information. Sequencing data was
#' processed using the mothur_pipeline R Markdown file to bin the data into
#' operational taxonomic units and determine their abundance (alternatively, use
#' the \link[=normalized_OTUs]{normalized data set}).
#' % Find way to link Rmd file
#'
#' @format A data frame with 30,576 rows and 4 variables:
#' \describe{
#' \item{Cruise}{Numerical identifier of individual cruises. Units: Numeric
#' string}
#' \item{Depth}{Sampling depth. Units: Meters}
#' \item{OTU}{Numerical identifier of OTU. Units: Numeric string}
#' \item{Count}{Count of OTU sequences. Units: Numeric string}
#' }
#' @source For a brief introduction to the data, see Hallam SJ \emph{et al.}
#' 2017. Monitoring microbial responses to ocean deoxygenation in a model
#' oxygen minimum zone. Sci Data 4: 170158. doi:
#' \href{https://www.nature.com/articles/sdata2017158}{10.1038/sdata.2017.158}.
#' More detailed information on the mutli-omic microbial data can be found in
#' Hawley AK *et al*. 2017. A compendium of multi-omic sequence information
#' from the Saanich Inlet water column. Sci Data 4: 170160. doi:
#' \href{https://www.nature.com/articles/sdata2017160}{10.1038/sdata.2017.160}.
"OTUs"
#' Normalized abundance of OTUs for Saanich Inlet Cruise 72
#'
#' Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island
#' British Columbia, is a model ecosystem for monitoring microbial community
#' structure, function and dynamics in relation to changing levels of water
#' column oxygen-deficiency extensible to coastal and open ocean OMZs. This data
#' set contains cruise 72 of monthly time series observations in Saanich Inlet
#' encompassing environmental sequence information. Sequencing data was
#' processed using the mothur_pipeline R Markdown file to bin the data into
#' operational taxonomic units and determine their abundance
#' (\link[=OTUs]{non-normalized data set}) and then normalized to 100,000
#' sequences for each sample (seed = 4832).
#' % Find way to Rmd link file
#'
#' @format A data frame with 30,576 rows and 4 variables:
#' \describe{
#' \item{Cruise}{Numerical identifier of individual cruises. Units: Numeric
#' string}
#' \item{Depth}{Sampling depth. Units: Meters}
#' \item{OTU}{Numerical identifier of OTU. Units: Numeric string}
#' \item{Count}{Count of OTU sequences. Units: Numeric string}
#' }
#' @source For a brief introduction to the data, see Hallam SJ \emph{et al.}
#' 2017. Monitoring microbial responses to ocean deoxygenation in a model
#' oxygen minimum zone. Sci Data 4: 170158. doi:
#' \href{https://www.nature.com/articles/sdata2017158}{10.1038/sdata.2017.158}.
#' More detailed information on the mutli-omic microbial data can be found in
#' Hawley AK \emph{et al.} 2017. A compendium of multi-omic sequence
#' information from the Saanich Inlet water column. Sci Data 4: 170160. doi:
#' \href{https://www.nature.com/articles/sdata2017160}{10.1038/sdata.2017.160}.
"normalized_OTUs"
#' Combined data set of geochemicals and OTU abundance
#'
#' A subset of the \link[=geochemicals]{geochemical} and
#' \link[=normalized_OTUs]{normalized OTU abundance} data sets at 7 depths for
#' Saanich Inlet Cruise 72.
#'
#' @format A data frame with 7 rows and 10 variables:
#' \describe{
#' \item{Cruise}{Numerical identifier of individual cruises. Units: Numeric
#' string}
#' \item{Depth}{Sampling depth. Units: Meters}
#' \item{OTU0001}{Operational taxonomic unit 1}
#' \item{OTU0002}{Operational taxonomic unit 2}
#' \item{OTU0003}{Operational taxonomic unit 3}
#' \item{OTU0004}{Operational taxonomic unit 4}
#' \item{NO3}{Nitrate (Bran Luebbe AutoAnalyser - colorimetric). Units:
#' Micromolar}
#' \item{Mean_NO2}{Average concentration of Nitrite for each depth
#' (colorimetric assay). Units: Micromolar}
#' \item{Mean_N2O}{Average concentration of Nitrous oxide (headspace or
#' automated purge-and-trap). Units: Nanomolar}
#' \item{Mean_NH4}{Average concentration of Ammonium for each depth
#' (fluorometric assay). Units: Micromolar}
#' }
#' @source For a brief introduction to the data, see Hallam SJ \emph{et al.}
#' 2017. Monitoring microbial responses to ocean deoxygenation in a model
#' oxygen minimum zone. Sci Data 4: 170158. doi:
#' \href{https://www.nature.com/articles/sdata2017158}{10.1038/sdata.2017.158}.
#' More detailed information on the geochemical data can be found in
#' Torres-Beltrán M \emph{et al.} 2017. A compendium of geochemical
#' information from the Saanich Inlet water column. Sci Data 4: 170159. doi:
#' \href{https://www.nature.com/articles/sdata2017159}{10.1038/sdata.2017.159}
#' (\href{https://datadryad.org/stash/dataset/doi:10.5061/dryad.nh035}{dataset}).
#' More detailed information on the mutli-omic microbial data can be found in
#' Hawley AK \emph{et al.} 2017. A compendium of multi-omic sequence
#' information from the Saanich Inlet water column. Sci Data 4: 170160. doi:
#' \href{https://www.nature.com/articles/sdata2017160}{10.1038/sdata.2017.160}.
"combined"
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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