## Edwards
#' Nutrient utilization traits of phytoplankton.
#'
#' Data from Kyle F. Edwards, Christopher A. Klausmeier, and Elena Litchman (2015).
#' Nutrient utilization traits of phytoplankton. Ecology 96:2311.
#' http://dx.doi.org/10.1890/14-2252.1.
#'
#' Table 1 of Ecological Archives E096-202-D1.
#'
#'
#' @section Corrections:
#'
#' The value for "system" was corrected from "fresh" to "freshwater" for one entry
#'
#' @usage data(Edwards_nutrient_traits)
#'
#' @format A data frame with 384 rows and 42 variables:
#'
#' \bold{Encoding }
#' \encoding{UTF-8}
#' \tabular{llll}{
#' \bold{Column name} \tab \bold{Variable definition} \tab \bold{Units} \tab \bold{Storage type} \cr
#' species \tab Species name \tab text \tab string \cr
#' isolate \tab Isolate ID \tab text \tab string \cr
#' taxon \tab Taxon name \tab text \tab string \cr
#' system \tab Freshwater/marine \tab text \tab string \cr
#' temperature \tab Culture temperature \tab °C \tab floating point\cr
#' irradiance \tab Culture irradiance \tab µmol photons m^-2^ s^-1^ \tab floating point\cr
#' light_hours \tab Culture daylength \tab hr \tab integer \cr
#' synonym \tab Former species name \tab text \tab string \cr
#' volume \tab Cell volume \tab µm^3^ \tab floating point\cr
#' c_per_cell \tab Carbon per cell \tab µmol cell^-1^ \tab floating point\cr
#' c_citation \tab C per cell citation \tab integer \tab integer \cr
#' mu_inf_amm \tab µ~inf~ for ammonium-limited growth \tab day^-1^ \tab floating point\cr
#' mu_amm \tab µ~max~ for ammonium-limited growth \tab day^-1^ \tab floating point\cr
#' k_amm_m \tab K~m~ for ammonium-limited growth \tab µmol L^-1^ \tab floating point\cr
#' k_amm \tab K for ammonium uptake \tab µmol L^-1^ \tab floating point\cr
#' vmax_amm \tab V~max~ for ammonium uptake \tab µmol N cell^-1^ day^-1^ \tab floating point\cr
#' vmax_amm_c \tab V~max~:C for ammonium uptake \tab µmol N µmol C^-1^ day ^-1^ \tab floating point\cr
#' qmin_amm \tab Q~min~ for ammonium-limited growth \tab µmol N cell^-1^ \tab floating point\cr
#' qmin_amm_c \tab Q~min~:C for ammonium-limited growth \tab µmol N µmol C^-1^ \tab floating point\cr
#' qmax_amm \tab Q~max~ for ammonium-limited growth \tab µmol N cell^-1^ \tab floating point\cr
#' qmax_amm_c \tab Q~max~:C for ammonium-limited growth \tab µmol N µmol C^-1^ \tab floating point\cr
#' mu_inf_nit \tab µ~inf~ for nitrate-limited growth \tab day^-1^ \tab floating point\cr
#' mu_nit \tab µ~max~ for nitrate-limited growth \tab day^-1^ \tab floating point\cr
#' k_nit_m \tab K~m~ for nitrate-limited growth \tab µmol L^-1^ \tab floating point\cr
#' k_nit \tab K for nitrate uptake \tab µmol L^-1^ \tab floating point\cr
#' vmax_nit \tab V~max~ for nitrate uptake \tab µmol N cell^-1^ day^-1^ \tab floating point\cr
#' vmax_nit_c \tab V~max~:C for nitrate uptake \tab µmol N µmol C^-1^ day^-1^ \tab floating point\cr
#' qmin_nit \tab Q~min~ for nitrate-limited growth \tab µmol N cell^-1^ \tab floating point\cr
#' qmin_nit_c \tab Q~min~:C for nitrate-limited growth \tab µmol N µmol C^-1^ \tab floating point\cr
#' qmax_nit \tab Q~max~ for nitrate-limited growth \tab µmol N cell^-1^ \tab floating point\cr
#' qmax_nit_c \tab Q~max~:C for nitrate-limited growth \tab µmol N µmol C^-1^ \tab floating point\cr
#' mu_inf_p \tab µ~inf~ for phosphate-limited growth \tab day^-1^ \tab floating point\cr
#' mu_p \tab µmax for phosphate-limited growth \tab day^-1^ \tab floating point\cr
#' k_p_m \tab Km for phosphate-limited growth \tab µmol L^-1^ \tab floating point\cr
#' k_p \tab K for phosphate uptake \tab µmol L^-1^ \tab floating point\cr
#' vmax_p \tab V~max~ for phosphate uptake \tab µmol P cell^-1^ day^-1^ \tab floating point\cr
#' vmax_p_c \tab V~max~:C for phosphate uptake \tab µmol P µmol C^-1^ day^-1^ \tab floating point\cr
#' qmin_p \tab Q~min~ for phosphate-limited growth \tab µmol P cell^-1^ \tab floating point\cr
#' qmin_p_c \tab Q~min~:C for phosphate-limited growth \tab µmol P µmol C^-1^ \tab floating point\cr
#' qmax_p \tab Q~max~ for phosphate-limited growth \tab µmol P cell^-1^ \tab floating point\cr
#' qmax_p_c \tab Q~max~:C for phosphate-limited growth \tab µmol P µmol C^-1^ \tab floating point\cr
#' citation \tab Publication code \tab integer \tab integer
#'}
#'
#'
#' @source \url{http://www.esapubs.org/archive/ecol/E096/202/}
"Edwards_nutrient_traits"
#' Citation information for nutrient utilization traits.
#'
#' Data from Kyle F. Edwards, Christopher A. Klausmeier, and Elena Litchman (2015).
#' Nutrient utilization traits of phytoplankton. Ecology 96:2311.
#' http://dx.doi.org/10.1890/14-2252.1.
#'
#' Table 2 of Ecological Archives E096-202-D1.
#'
#' @usage data(Edwards_citations)
#'
#' @source \url{http://www.esapubs.org/archive/ecol/E096/202/}
"Edwards_citations"
#' Cell volumes of phytoplankton.
#'
#' Data from Kyle F. Edwards, Christopher A. Klausmeier, and Elena Litchman (2015).
#' Nutrient utilization traits of phytoplankton. Ecology 96:2311.
#' http://dx.doi.org/10.1890/14-2252.1.
#'
#' Table 3 of Ecological Archives E096-202-D1.
#'
#' @usage data(Edwards_cell_volumes)
#'
#' @format A data frame with 134 rows and 4 variables:
#'
#' \bold{Encoding }
#' \encoding{UTF-8}
#' \tabular{llll}{
#' \bold{Column name} \tab \bold{Variable definition} \tab \bold{Units} \tab \bold{Storage type} \cr
#' species \tab Species name \tab text \tab string \cr
#' isolate \tab Isolate ID \tab text \tab string \cr
#' volume \tab Cell volume \tab µm^3^ \tab floating point\cr
#' volume_citation \tab Citation for volume measurement \tab text \tab string
#'}
#' @source \url{http://www.esapubs.org/archive/ecol/E096/202/}
"Edwards_cell_volumes"
################################################################################
################################################################################
## Chen
#' Chen (2015) Thermal Traits.
#'
#' Data from Chen B. (2015) Patterns of thermal limits of phytoplankton.
#' Journal of Plankton Research 37, 285–292.
#'
#' @usage data(Chen_thermal_traits)
#'
#' @format A data frame with 339 rows and 21 variables:
#'
#' \bold{Encoding }
#' \encoding{UTF-8}
#' \tabular{lll}{
#' \bold{Variable} \tab \bold{Description} \tab \bold{Units} \cr
#' References \tab References \tab NA \cr
#' ID \tab ID \tab NA \cr
#' Phylum \tab Phylum \tab NA \cr
#' Class \tab Class \tab NA \cr
#' Order \tab Order \tab NA \cr
#' Family \tab Family \tab NA \cr
#' Genus \tab Genus \tab NA \cr
#' Species \tab Species \tab NA \cr
#' Habitat \tab Habitat \tab NA \cr
#' T_g_min \tab Lowest growth temperature °C \tab °C \cr
#' T_g_max \tab Highest growth temperature °C \tab °C \cr
#' T_g_opt \tab Optimal growth temperature °C \tab °C \cr
#' mu_max \tab Maximal growth rate d^-1 ^ \tab d^-1 \cr
#' Longitude \tab Longitude °E \tab °E \cr
#' Latitude \tab Latitude °N \tab °N \cr
#' Cell_volume \tab Cell Volume µm^3^ \tab µm^3^\cr
#' Thermal_breadth \tab Thermal breadth °C \tab °C \cr
#' T_env_mean \tab Environmental annual mean temperature °C \tab °C \cr
#' T_env_min \tab Environmental lowest temperature °C \tab °C \cr
#' T_env_max \tab Environmental highest temperature °C \tab °C \cr
#' T_env_range \tab Environmental temperature range °C \tab °C
#'}
#' @source \url{http://plankt.oxfordjournals.org/content/37/2/285/suppl/DC1}
"Chen_thermal_traits"
#' Chen (2015) Thermal Traits references.
#'
#' References for data from Chen B. (2015) Patterns of thermal limits of phytoplankton.
#' Journal of Plankton Research 37, 285–292.
#'
#' @usage data(Chen_thermal_traits_references)
#' @source \url{http://plankt.oxfordjournals.org/content/37/2/285/suppl/DC1}
"Chen_thermal_traits_references"
#' Chen (2015) Thermal Traits key
#'
#' Key for data from Chen B. (2015) Patterns of thermal limits of phytoplankton.
#' Journal of Plankton Research 37, 285–292.
#'
#' @usage data(Chen_thermal_traits_key)
#' @source \url{http://plankt.oxfordjournals.org/content/37/2/285/suppl/DC1}
"Chen_thermal_traits_key"
################################################################################
################################################################################
#' Phytoplankton cell and natural unit biovolumes.
#' Raw biovolume data - pre quality control.
#'
#' Kremer C.T., Gillette J.P., Rudstam L.G., Brettum P. & Ptacnik R. (2014)
#' A compendium of cell and natural unit biovolumes for >1200 freshwater phytoplankton species.
#' Ecology 95, 2984.
#'
#' Ecological Archives E095-257-D1
#'
#'
#' @usage data(Kremer_raw)
#'
#' @format A data frame with 312238 rows and 18 variables:
#'
#' \bold{Encoding }
#' \encoding{UTF-8}
#' \tabular{lll}{
#' \bold{Variable} \tab \bold{Definition} \tab \bold{Units} \cr
#' nu.measurement.ID \tab Index for individual estimate of a natural unit's biovolume \tab - \cr
#' data.source \tab Source of biovolume data \tab - \cr
#' location \tab Sampling location as reported in original data source \tab - \cr
#' sample.date \tab Date of biovolume sample, from original data source (when reported) \tab Days \cr
#' source.ID \tab Sample ID from original data source \tab - \cr
#' source.taxa.name \tab Taxa name reported in source data. \tab - \cr
#' source.taxa.ID \tab Taxonomic ID code from original data source \tab - \cr
#' original.taxa.name \tab Taxa name, combining genus or genus + species names from original data source. \tab - \cr
#' genus \tab Genus name \tab - \cr
#' species \tab Species name \tab - \cr
#' subspecies \tab Subspecies name \tab - \cr
#' variety \tab Variety name \tab - \cr
#' form \tab Form name \tab - \cr
#' nu \tab Descriptor of natural unit type \tab - \cr
#' cells.per.nu \tab Cells per natural unit \tab Cells per natural unit\cr
#' nu.biovol \tab Biovolume corresponding to a natural unit of the specified taxa \tab log10(μm^3^) \cr
#' cell.biovol \tab Biovolume of an individual cell of the specified taxa (which may be the same as a natural unit) \tab log10(μm^3^) \cr
#' comments \tab Notes from original data source \tab -
#'}
#'
#' @source \url{http://www.esapubs.org/archive/ecol/E095/257/}
"Kremer_raw"
#' Phytoplankton cell and natural unit biovolumes.
#' Species-level biovolume data.
#'
#' Kremer C.T., Gillette J.P., Rudstam L.G., Brettum P. & Ptacnik R. (2014)
#' A compendium of cell and natural unit biovolumes for >1200 freshwater phytoplankton species.
#' Ecology 95, 2984.
#'
#' Ecological Archives E095-257-D1
#'
#'
#' @usage data(Kremer_volumes_species)
#'
#' @format A data frame with 162176 rows and 12 variables:
#'
#' \bold{Encoding }
#' \encoding{UTF-8}
#' \tabular{lll}{
#' \bold{Variable} \tab \bold{Definition} \tab \bold{Units} \cr
#' nu.measurement.ID \tab Index for individual estimate of a natural unit's biovolume \tab - \cr
#' data.source \tab Source of biovolume data \tab - \cr
#' location \tab Sampling location as reported in original data source \tab - \cr
#' original.taxa.name \tab Genus + species name generated from original data source's taxa identification \tab - \cr
#' accepted.taxa.name \tab Accepted genus + species name based on the ITIS categorization of original.taxa.name \tab - \cr
#' level \tab Level to which taxa was identified \tab - \cr
#' genus \tab Genus name \tab - \cr
#' species \tab Species name \tab - \cr
#' nu \tab Descriptor of natural unit type \tab - \cr
#' cells.per.nu \tab Cells per natural unit \tab Cells per natural unit\cr
#' nu.biovol \tab Biovolume corresponding to a natural unit of the specified taxa \tab log10(µm^3^) \cr
#' cell.biovol \tab Biovolume of an individual cell of the specified taxa (which may be the same as a natural unit) \tab log10(µm^3^)
#'}
#'
#' @source \url{http://www.esapubs.org/archive/ecol/E095/257/}
"Kremer_volumes_species"
#' Phytoplankton cell and natural unit biovolumes.
#' Genus-level biovolume data.
#'
#' Kremer C.T., Gillette J.P., Rudstam L.G., Brettum P. & Ptacnik R. (2014)
#' A compendium of cell and natural unit biovolumes for >1200 freshwater phytoplankton species.
#' Ecology 95, 2984.
#'
#' Ecological Archives E095-257-D1
#'
#'
#' @usage data(Kremer_volumes_genus)
#'
#' @format A data frame with 273666 rows and 12 variables:
#'
#' \bold{Encoding }
#' \encoding{UTF-8}
#' \tabular{lll}{
#' \bold{Variable} \tab \bold{Definition} \tab \bold{Units} \cr
#' nu.measurement.ID \tab Index for individual estimate of a natural unit's biovolume \tab - \cr
#' data.source \tab Source of biovolume data \tab - \cr
#' location \tab Sampling location as reported in original data source \tab - \cr
#' original.taxa.name \tab Genus or genus + species name generated from original data source's taxa identification \tab - \cr
#' accepted.taxa.name \tab Accepted genus or genus + species name based on the ITIS categorization of original.taxa.name \tab - \cr
#' level \tab Level to which taxa was identified \tab - \cr
#' genus \tab Genus name \tab - \cr
#' species \tab Species name \tab - \cr
#' nu \tab Descriptor of natural unit type \tab - \cr
#' cells.per.nu \tab Cells per natural unit \tab Cells per natural unit\cr
#' nu.biovol \tab Biovolume corresponding to a natural unit of the specified taxa \tab log10(µm^3^) \cr
#' cell.biovol \tab Biovolume of an individual cell of the specified taxa (which may be the same as a natural unit) \tab log10(µm^3^)
#'}
#'
#' @source \url{http://www.esapubs.org/archive/ecol/E095/257/}
"Kremer_volumes_genus"
#' Phytoplankton cell and natural unit biovolumes.
#' Species-level aggregated biovolume data and full taxonomy.
#'
#' Kremer C.T., Gillette J.P., Rudstam L.G., Brettum P. & Ptacnik R. (2014)
#' A compendium of cell and natural unit biovolumes for >1200 freshwater phytoplankton species.
#' Ecology 95, 2984.
#'
#' Ecological Archives E095-257-D1
#'
#'
#' @usage data(Kremer_volumes_species_agg)
#'
#' @format A data frame with 1261 rows and 23 variables:
#'
#' \bold{Encoding }
#' \encoding{UTF-8}
#' \tabular{lll}{
#' \bold{Variable} \tab \bold{Definition} \tab \bold{Units} \cr
#' accepted.taxa.name \tab Accepted genus + species name based on the ITIS categorization of original.taxa.name Used for aggregating biovolume data \tab - \cr
#' min_nu.biovol \tab Taxon specific minimum biovolume \tab log10(µm^3^) \cr
#' mn_nu.biovol \tab Taxon specific mean biovolume \tab log10(µm^3^) \cr
#' mdn_nu.biovol \tab Taxon specific median biovolume \tab log10(µm^3^) \cr
#' max_nu.biovol \tab Taxon specific maximum biovolume \tab log10(µm^3^) \cr
#' sd_nu.biovol \tab Taxon specific standard deviation of biovolume \tab log10(µm^3^) \cr
#' n \tab Number of biovolume estimates for given taxa \tab - \cr
#' mn_cells.per.nu \tab Mean number of cells per natural unit \tab Cells per natural unit\cr
#' n_sources \tab Number of distinct data sources containing biovolume estimates for given taxa \tab - \cr
#' w.tsn \tab Working TSN from ITIS classification for given taxa \tab - \cr
#' level \tab Lowest level of identification \tab - \cr
#' kingdom \tab Name of the taxa at this level \tab - \cr
#' subkingdom \tab Name of the taxa at this level \tab - \cr
#' infrakingdom \tab Name of the taxa at this level \tab - \cr
#' division \tab Name of the taxa at this level \tab - \cr
#' subdivision \tab Name of the taxa at this level \tab - \cr
#' phylum \tab Name of the taxa at this level \tab - \cr
#' class \tab Name of the taxa at this level \tab - \cr
#' subclass \tab Name of the taxa at this level \tab - \cr
#' order \tab Name of the taxa at this level \tab - \cr
#' family \tab Name of the taxa at this level \tab - \cr
#' genus \tab Name of the taxa at this level \tab - \cr
#' species \tab Name of the taxa at this level \tab -
#'}
#' @source \url{http://www.esapubs.org/archive/ecol/E095/257/}
"Kremer_volumes_species_agg"
#' Phytoplankton cell and natural unit biovolumes.
#' Genus-level aggregated biovolume data and full taxonomy.
#'
#' Kremer C.T., Gillette J.P., Rudstam L.G., Brettum P. & Ptacnik R. (2014)
#' A compendium of cell and natural unit biovolumes for >1200 freshwater phytoplankton species.
#' Ecology 95, 2984.
#'
#' Ecological Archives E095-257-D1
#'
#'
#' @usage data(Kremer_volumes_genus_agg)
#'
#' @format A data frame with 393 rows and 22 variables:
#'
#' \bold{Encoding }
#' \encoding{UTF-8}
#' \tabular{lll}{
#' \bold{Variable} \tab \bold{Definition} \tab \bold{Units} \cr
#' accepted.taxa.name \tab Accepted genus name based on the ITIS categorization of original.taxa.name Used for aggregating biovolume data \tab - \cr
#' min_nu.biovol \tab Taxon specific minimum biovolume \tab log10(µm^3^) \cr
#' mn_nu.biovol \tab Taxon specific mean biovolume \tab log10(µm^3^) \cr
#' mdn_nu.biovol \tab Taxon specific median biovolume \tab log10(µm^3^) \cr
#' max_nu.biovol \tab Taxon specific maximum biovolume \tab log10(µm^3^) \cr
#' sd_nu.biovol \tab Taxon specific standard deviation of biovolume \tab log10(µm^3^) \cr
#' n \tab Number of biovolume estimates for given taxa \tab - \cr
#' mn_cells.per.nu \tab Mean number of cells per natural unit \tab Cells per natural unit\cr
#' n_sources \tab Number of distinct data sources containing biovolume estimates for given taxa \tab - \cr
#' w.tsn \tab Working TSN from ITIS classification for given taxa \tab - \cr
#' level \tab Lowest level of identification \tab - \cr
#' kingdom \tab Name of the taxa at this level \tab - \cr
#' subkingdom \tab Name of the taxa at this level \tab - \cr
#' infrakingdom \tab Name of the taxa at this level \tab - \cr
#' division \tab Name of the taxa at this level \tab - \cr
#' subdivision \tab Name of the taxa at this level \tab - \cr
#' phylum \tab Name of the taxa at this level \tab - \cr
#' class \tab Name of the taxa at this level \tab - \cr
#' subclass \tab Name of the taxa at this level \tab - \cr
#' order \tab Name of the taxa at this level \tab - \cr
#' family \tab Name of the taxa at this level \tab - \cr
#' genus \tab Name of the taxa at this level \tab -
#'}
#' @source \url{http://www.esapubs.org/archive/ecol/E095/257/}
"Kremer_volumes_genus_agg"
#' Phytoplankton cell and natural unit biovolumes.
#' Taxonomic look-up table based on ITIS classifications
#'
#' Kremer C.T., Gillette J.P., Rudstam L.G., Brettum P. & Ptacnik R. (2014)
#' A compendium of cell and natural unit biovolumes for >1200 freshwater phytoplankton species.
#' Ecology 95, 2984.
#'
#' Ecological Archives E095-257-D1
#'
#'
#' @usage data(Kremer_taxa)
#'
#' @format A data frame with 2572 rows and 23 variables:
#'
#' \bold{Encoding }
#' \encoding{UTF-8}
#' \tabular{lll}{
#' \bold{Variable} \tab \bold{Definition} \tab \bold{Storage type} \cr
#' original.taxa.name \tab Genus or genus + species name generated from original data source's taxa identification \tab Character\cr
#' accepted.taxa.name \tab Accepted genus or genus + species name based on the ITIS categorization of original.taxa.name \tab Character\cr
#' original.genus \tab Genus name from original data source's taxa identification \tab Character\cr
#' w.tsn \tab Working TSN from ITIS classification for given taxa \tab Integer \cr
#' tsn \tab TSN matching original.taxa.name, if any \tab Integer \cr
#' genus.tsn \tab TSN matching original.genus, if any \tab Integer \cr
#' a.tsn \tab Accepted TSN reflecting taxonomic changes in ITIS to original tsn match \tab Integer \cr
#' a.genus.tsn \tab Accepted genus TSN reflecting taxonomic changes in ITIS to original genus.tsn match \tab Integer \cr
#' level \tab Lowest level of taxonomic identificantion \tab Character\cr
#' kingdom \tab Name of the taxa at this level \tab Character\cr
#' subkingdom \tab Name of the taxa at this level \tab Character\cr
#' infrakingdom \tab Name of the taxa at this level \tab Character\cr
#' division \tab Name of the taxa at this level \tab Character\cr
#' subdivision \tab Name of the taxa at this level \tab Character\cr
#' phylum \tab Name of the taxa at this level \tab Character\cr
#' class \tab Name of the taxa at this level \tab Character\cr
#' subclass \tab Name of the taxa at this level \tab Character\cr
#' order \tab Name of the taxa at this level \tab Character\cr
#' family \tab Name of the taxa at this level \tab Character\cr
#' genus \tab Name of the taxa at this level \tab Character\cr
#' species \tab Name of the taxa at this level \tab Character\cr
#' variety \tab Name of the taxa at this level \tab Character\cr
#' form \tab Name of the taxa at this level \tab Character
#'}
#' @source \url{http://www.esapubs.org/archive/ecol/E095/257/}
"Kremer_taxa"
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