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#' Interface to the LAGOSNE lakes database
#' @name LAGOSNE-package
#' @aliases LAGOSNE
#' @docType package
#' @importFrom magrittr %>%
#' @title R interface to the LAGOSNE lakes database
#' @author \email{stachel2@msu.edu}
NULL
#' Latest LAGOSNE version
#' @name lagosne_version
#' @export
#' @examples
#' lagosne_version()
lagosne_version <- function(){"1.087.3"}
#' LAGOSNE Spatial Classifications Metadata
#'
#' Data frames containing metadata for each spatial classification at which
#' ecological context data are derived in LAGOSNE. The spatial classifications
#' include 100m buffers (buffer100m),
#' 500m buffers (buffer500m), interlake watersheds (iws),
#' hydrologic units (hu12, hu8, hu4), ecological drainage units (edu),
#' counties (county), and states (state). Each abbreviation is the name of the
#' data frame, with all or a subset of the following variables. For more
#' information about derivation of each spatial classification, see Details
#' below or Additional file 7 from \doi{10.1186/s13742-015-0067-4}.
#'
#' The nine LAGOSNE spatial classifications were used to summarize the ecological
#' context of each lake. Ecological context themes include
#' land use/land cover (LULC), connectivity (CONN), and climate, hydrology,
#' atmospheric deposition, and groundwater (CHAG). Not all themes were derived
#' at all classifications due to data availability. Briefly:
#' \itemize{
#' \item iws: a dataframe with 51065 observations of 12 variables. The area
#' of land that drains directly into a lake, and into all
#' upstream-connected, permanent streams to that lake exclusive of any
#' upstream lake watersheds for lakes greater than 10 ha that are
#' connected via permanent streams. For details on how the watersheds were
#' delineated, see additional file 8 in Soranno et al. (2015). Themes
#' derived at the iws classification include LULC and CONN.
#' \item buffer100m: a dataframe with 51065 of 3 variables.
#' Buffers are a 100 m equidistant buffer of the land that is 100 m from
#' the lake shoreline, calculated using the ArcGIS Buffer tool. Themes
#' derived at the 100m buffer classification include LULC.
#' \item buffer500m: a dataframe with 51065 of 3 variables.
#' Buffers are a 500 m equidistant buffer of the land that is 500 m from
#' the lake shoreline, calculated using the ArcGIS Buffer tool. Themes
#' derived at the 500m buffer classification include LULC and CONN.
#' \item hu12: a dataframe with 20257 observations of 11 variables. The
#' Watershed Boundary Dataset defines boundaries based on surface water
#' drainage and creates nested Hydrologic Units (sometimes abbreviated and
#' referred to as HUCs, which are hydrologic unit codes) that are
#' georeferenced to the USGS 1:24,000 topographic base map. HUC12s are the
#' sixth level of classificiation. HUC12s are defined along natural
#' hydrologic breaks based on land surface and surface-water flow and they
#' have a single flow outlet except in frontal, lake, braided-stream, or
#' closed-basin hydrologic units. Themes derived at the HUC12
#' classification include LULC, CONN and CHAG.
#' \item hu8: a data frame with 511 observations of 9 variables. HUC8s are
#' the fourth level of classificiation. Sometimes called 'watersheds', a
#' HUC8 is a geographic area representing part or all of a surface
#' drainage basin, a combination of drainage basins, or a distinct
#' hydrologic feature. Themes derived at the HUC8 classification include
#' LULC, CONN, and CHAG.
#' \item hu4: a data frame with 65 observations of 9 variables. HUC4s are
#' the second level of classification, called a 'subregion'. A subregion
#' includes the area drained by a river system, a reach of a river and its
#' tributaries in that reach, a closed basin(s), or a group of streams
#' forming a coastal drainage area. Themes derived at the HUC4
#' classification include LULC, CONN, and CHAG.
#' \item edu: a data frame with 91 observations of 10 variables.
#' Ecological drainage units (EDUs) follow the WBD boundaries, and are of
#' roughly similar size to HUC6s. EDUs were delineated by grouping the
#' HUC8 watersheds based on common zoogeographic history, and
#' physiographic and climatic characteristics. Themes derived at the EDU
#' classification include LULC, CONN, and CHAG.
#' \item county: a data frame with 955 observations of 8 variables.
#' Counties (political boundary) within the 17-state region of LAGOSNE.
#' Themes derived at the county classification include LULC, CONN, and
#' CHAG.
#' \item state: a dataframe with 17 observations of 7 variables. Themes
#' derived at the state classification include LULC, CONN, and CHAG.
#' }
#'
#' @format Data frames with all or a subset of the following variables. Number
#' of observations is equal to the number of zones in each spatial
#' classification (see Details below).
#' \itemize{
#' \item *_nhdid: permanent lake-specific identifier from the National
#' Hydrography Dataset (* = buffer100m, buffer500m, iws)
#' \item *_name: text name of the zone (* = iws, hu12, hu8, hu4,
#' county, state)
#' \item hu*: unique zone identifier (* = 12, 8, 4)
#' \item *_ha: area of spatial classification in hectares
#' (* = buffer100m, buffer500m, hu12, hu8, hu4, edu,
#' county)
#' \item *_areaha: area of spatial classification in hectares (* = iws, )
#' \item *_perimkm: perimeter of spatial classification in kilometers
#' (* = iws, )
#' \item *_lat: latitude of centroid of polygon in decimal degrees (NAD83)
#' (* = iws, hu12, hu8, hu4, edu, county, state)
#' \item *_long: longitude of centroid of polygon in decimal degrees
#' (NAD83) (* = iws, hu12, hu8, hu4, edu, county, state)
#' \item *_lakeareaha: lake area (ha) of focal lake associated with polygon
#' (* = iws, )
#' \item *_country: whether the polygon lies within the US ("US") or the
#' US and Canada (US_CA) (* = hu12, edu)
#' \item *_pct_in_usa: percent of polygon within the US boundary (* = iws,
#' hu12, edu)
#' \item *_ha_in_usa: area (ha) of polygon within the US boundary (* = iws,
#' hu12, edu)
#' \item *_pct_in_nwi: percent of polygon within the USFWS National Wetland
#' Inventory (NWI) boundary (* = hu12, hu8, hu4, edu, county, state)
#' \item *_ha_in_nwi: area (ha) of polygon within the USFWS National
#' Wetland Inventory (NWI) boundary (* = hu12, hu8, hu4, edu, county,
#' state)
#' \item *_zoneid: a unique identifier for each IWS in LAGOSNE, numbered 1:n
#' with classification prefix (e.g., HU12_1) (* = iws, hu12, hu8, hu4, edu,
#' county, state)
#' \item lagoslakeid: LAGOSNE unique identifier for focal lake
#' \item hu4_states: states that intersect hu4 zone polygon
#' \item state: 2-letter state abbreviation
#' \item county_state: state where county is located
#' }
#'
#' @docType data
#' @keywords datasets
#' @name classifications
#' @references Soranno et al. (2017) \doi{10.1093/gigascience/gix101}
#' @aliases buffer100m buffer500m iws hu12 hu8 hu4 edu county state classification scales lakeareaha
#' @seealso \code{\link[LAGOSNE]{conn}} \code{\link[LAGOSNE]{lakes.geo}} \code{\link{chag}} \code{\link{lulc}}
NULL
#' Land Use Land Cover (LULC) Data Frames
#'
#' Datasets containing information on the land use and land cover (LULC)
#' characteristics calculated at all LAGOSNE spatial classifications
#' (see ?scales) from the National Land Cover Dataset (NLCD).
#'
#' Original data sources and layers from which each metric was derived can be
#' found in additional file 5 of Soranno et al. (2015).
#'
#' @format Data frames with all or a subset of the following variables. Number
#' of observations is equal to the number of zones in each spatial scale
#' (see Details below). Wildcard options include the 9 LAGOSNE spatial scales
#' (* = buffer100m, buffer500m, iws, hu12, hu8, hu4, edu,
#' county, state), year of measurement (** = 1992, 2001, 2006, 2011), and unit
#' of measurement in hectares or percent of zone area (*** = ha, pct unless
#' noted otherwise). Each variable is available at each scale, year, and unit
#' unless otherwise noted.
#' \itemize{
#' \item *_nhdid (* = buffer100m, buffer500m, iws)
#' \item *_canopy2001_***: per pixel tree canopy percent measured 2001.
#' Summary statistics include minimum, maximum, mean and standard deviation
#' (*** = min, max, mean, std).
#' \item *_damdensity_***: dams in zone. Summary statistics include a point
#' count, points per hectare, and points per square kilometer
#' (*** = pointcount, pointsperha, pointspersqkm)
#' \item *_nlcd**_***_0: No data
#' \item *_nlcd**_***_11: Open water
#' \item *_nlcd1992_***_21: Residential, low intensity
#' \item *_nlcd**_***_21: Developed, open space. Note, this variable was
#' not measured in 1992 (** = 2001, 2006, 2011)
#' \item *_nlcd1992_***_22: Residential, high intensity
#' \item *_nlcd**_***_22: Developed, low intensity. Note, this variable was
#' not measured in 1992 (** = 2001, 2006, 2011)
#' \item *_nlcd1992_***_23: Commercial/industrial/transportation
#' \item *_nlcd**_***_23: Developed, medium intensity. Note, this variable was
#' not measured in 1992 (** = 2001, 2006, 2011)
#' \item *_nlcd**_***_24: Developed, high Intensity. Note, this variable was
#' not measured in 1992 (** = 2001, 2006, 2011)
#' \item *_nlcd**_***_31: Bare rock/sand/clay
#' \item *_nlcd1992_***_32: Quarries/strip mines/gravel pits measured in
#' 1992
#' \item *_nlcd1992_***_33: Transitional (barren) measured in 1992
#' \item *_nlcd**_***_41: Deciduous forest
#' \item *_nlcd**_***_42: Evergreen forest
#' \item *_nlcd**_***_43: Mixed forest
#' \item *_nlcd1992_***_51: Shrubland measured in 1992.
#' \item *_nlcd1992_***_52: Scrub/shrub. Note, this variable not measured in
#' 1992
#' (** = 2001, 2006, 2011)
#' \item *_nlcd1992_***_61: Orchards/vineyards/other measured in 1992.
#' \item *_nlcd**_***_71: Grasslands/herbaceous
#' \item *_nlcd**_***_81: Pasture/hay
#' \item *_nlcd**_***_82: Row crops
#' \item *_nlcd1992_***_83: Small grains measured in 1992.
#' \item *_nlcd1992_***_85: Urban/recreational grasses measured in 1992.
#' \item *_nlcd**_***_90: Woody wetlands. Note, this variable not calculated
#' in 1992
#' (** = 2001, 2006, 2011). Equivalent code for 1992 = 91.
#' \item *_nlcd1992_***_91: Woody wetlands measured in 1992. Equivalent code
#' for 2001, 2006 and 2011 = 90.
#' \item *_nlcd1992_***_92: Emergent herbaceous wetlands measured in 1992.
#' Equivalent code for 2001, 2006, and 2011 = 95.
#' \item *_nlcd**_***_95: Emergent herbaceous wetlands. Note, this variable
#' not calculated in 1992 (** = 2001, 2006, 2011). Equivalent code for
#' 1992 = 92.
#' \item *_roaddensity_***: Roads within the zone, calculated as sum of the
#' length in meters, or sum of the length in meters divided by area of zone
#' in hectares (*** = sum_lengthm, density_mperha)
#' \item *_slope_***: The slope at each cell is the slope with respect to
#' its immediate neighbors (10m scale). Cells in zone summarized as either
#' the minimum, maximum, mean, or standard deviation (*** = min, max,
#' mean, std)
#' \item *_tri_***: Terrain ruggedness index (TRI) at each cell is the
#' absolute difference in meters between the elevation of the focal cell and
#' its immediate neighbors (10m scale).
#' Cells in zone summarized as either the minimum, maximum, mean,
#' or standard deviation (*** = min, max, mean, std)
#' \item *_zoneid: unique zone identifier (* = iws, hu12, hu8, hu4, edu,
#' county, state)
#' \item lagoslakeid: unique integer identifier for focal lake
#' \item lakeconnection: connectivity class of focal lake. Only in iws.lulc
#' table.
#' \item borderiws: whether iws zone intersects Canadian border
#' (1 = yes, NA = no). Only in iws.lulc table.
#' }
#'
#' @docType data
#' @keywords datasets
#' @name lulc
#' @aliases buffer100m.lulc buffer500m.lulc iws.lulc hu12.lulc hu8.lulc hu4.lulc edu.lulc county.lulc state.lulc topography nlcd
#' @seealso \code{\link[LAGOSNE]{lakes.geo}}
#' @references Soranno et al. (2017) \doi{10.1093/gigascience/gix101}
NULL
#' Climate, Hydrology, Atmospheric, and Geologic (CHAG) Datasets
#'
#' Datasets containing information on climate, hydrology, atmospheric
#' deposition, and surficial geology characteristics calculated at hu12, hu8,
#' hu4, edu, county and state spatial classifications (see ?scales).
#'
#' Original data sources and layers from which each metric was derived can be
#' found in additional file 5 of Soranno et al. (2015). Briefly, climate data
#' came from the PRISM climate group, hydrology metrics were derived from
#' United States Geologic Survey (USGS) data, atmospheric deposition was from
#' the National Atmospheric Deposition program, and surficial geology were
#' derived from layers USGS data.
#'
#' @format Data frames with all or a subset of the following variables. Number
#' of observations is equal to the number of zones in each spatial scale (see
#' Details below). Wildcard options include a subset of the LAGOSNE spatial
#' scales (* = hu12, hu8, hu4, edu, county, state), years of measurement
#' (** = 1985, 1990, 1995, 2000, 2005, 2010), and summary statistic or
#' units (*** = min, max, mean, std for atmospheric deposition and hydrology;
#' *** = ha, pct for surficial geology)
#' \itemize{
#' \item *_zoneid: unique zone identifier
#' \item *_dep_no3_**_***: nitrate ion wet deposition (kg/ha) in zone during
#' specified year
#' \item *_dep_so4_**_***: sulfate ion wet deposition (kg/ha) in zone during
#' specified year
#' \item *_dep_totaln_**_***: total inorganic nitrogen ion wet deposition
#' (kg/ha) in zone during specified year
#' \item *_baseflowindex_***: % of streamflow that can be attributed to
#' ground-water discharge into streams in the zone (baseflow/totalflow *100)
#' \item *_groundwaterrecharge_***: mean annual natural groundwater recharge
#' (mm/yr) in zone - Baseflow multiplied by mean annual runoff
#' \item *_runoff_***: average annual runoff (in/yr) in the zone, 1951-80
#' \item *_prism_ppt_30yr_normal_800mm2_annual_***: 30-yr long-term (normal)
#' annual mean precipitation (mm/yr) for zone
#' \item *_prism_tmax_30yr_normal_800mm2_annual_***: 30-yr long-term
#' (normal) annual maximum temperature (deg C) for zone
#' \item *_prism_tmean_30yr_normal_800mm2_annual_***: 30-yr long-term
#' (normal) annual mean temperature (deg C) for zone
#' \item *_prism_tmin_30yr_normal_800mm2_annual_***: 30-yr long-term
#' (normal) annual minimum temperature (deg C) for zone
#' \item *_surficialgeology_alluv_***: alluvial of all ages
#' \item *_surficialgeology_beach_***: beach deposits of Holocene age
#' \item *_surficialgeology_colluv_***: colluvium of all ages
#' \item *_surficialgeology_dec_resid_***: decomposition residuum of all
#' ages
#' \item *_surficialgeology_eolian_***: silt (loess), sand of all ages
#' \item *_surficialgeology_gf_out_***: glaciofluvial (outwash) deposits of
#' all ages
#' \item *_surficialgeology_grus_***: glaciated, granitic grus of Quaternary
#' and Tertiary age
#' \item *_surficialgeology_ice_***: ice-contact depositives of lake
#' Wisconsin and Holocene age
#' \item *_surficialgeology_lac_***: combination of: Glacial-lake clay and
#' silt lake deposits of pre-Illinoian and Illinoin age; Glacial and
#' postglacial lake deposits (delta, clay, silt and sand, sand and gravel,
#' density-current underflow-fan) of Holocene and late Wisconsin age; Beach
#' sand and dune sand deposits of Holocene age; and Lake slack-water and
#' alluvium deposits of pre-Illinoian, Illinoian, and late Wisconsin ages
#' \item *_surficialgeology_lac_clay_***: glacial and postglacial lake
#' deposits (clay and silt) of Holocene and late Wisconsin age
#' \item *_surficialgeology_marine_***: coastal-plain marine deposits of
#' Pleistocene and Pliocene ages, and glaciomarine deposits of late
#' Wisconsin age
#' \item *_surficialgeology_open_water_***: open water
#' \item *_surficialgeology_other_***: surficial deposits, surficial
#' materials, and bedrock masses that were deformed and (or) transported
#' intact by glacial ice
#' \item *_surficialgeology_peat_mrsh_***: coastal or inland deposits of
#' freshwater, brackish-water, peat and muck or freshwater swamps of
#' Holocene and late Wisconsin age
#' \item *_surficialgeology_saprol_***: saprolite of quaternary and tertiary
#' age on crystalline igneous and metamorphic rocks mostly
#' \item *_surficialgeology_solif_***: solifluction deposits of Holocene and
#' late to middle Pleistocene age, and lake Wisconsin age
#' \item *_surficialgeology_solut_***: solution residuum of Quaternary and
#' tertiary age
#' \item *_surficialgeology_till_clay_***: till, clay of pre-Illinoian age,
#' late Wisconsin and Holocene(?) age
#' \item *_surficialgeology_till_loam_***: till, loam of pre-Illinoian,
#' Illinoian, and late Wisconsin and Holocene(?) age
#' \item *_surficialgeology_till_oth_***: till, complex depositions of lake
#' Wisconsin and Illinoian age
#' \item *_surficialgeology_till_sand_***: till, sand of pre-Illinoian age,
#' late Wisconsin and Holocene(?) age
#'}
#'
#' @docType data
#' @keywords datasets
#' @name chag
#' @aliases hu12.chag hu8.chag hu4.chag edu.chag county.chag state.chag deposition climate hydrology geology baseflow runoff
#' @references Soranno et al. (2017) \doi{10.1093/gigascience/gix101}
NULL
#' Epilimnion Water Quality Data
#'
#' A dataset containing physical and chemical observations in the epilimnion
#' (surface waters).
#' Each row is a sampling event, and lakes can have multiple sampling events.
#'
#' @format A data frame with observations of 93 variables:
#' \itemize{
#' \item eventida1087: unique combination of programid, lakeid, and
#' date for each sampling event in LAGOSNE
#' \item lagoslakeid: unique integer identifier for each lake in
#' LAGOSNE
#' \item programname: name of the sampling/monitoring program that
#' collected the data
#' \item programtype: categorical description of the type of
#' sampling/monitoring effort (Federal Agency, LTER = Long Term
#' Ecological Research program, National Survey Program, Non-Profit
#' Agency, State Agency, State Agency/Citizen Monitoring Program,
#' State Agency/University/Citizen Monitoring Program,
#' State Agency/Citizen Monitoring Program, Tribal Agency,
#' University)
#' \item lagosversion: current version of LAGOSNE that the data
#' record belongs to
#' \item sampledate: date at which the sample was collected, stored
#' in date format (YYYY-MM-DD)
#' \item chla: chlorophyll a (µg/l)
#' \item colora: color, apparent (PCU)
#' \item colort: color, true (PCU)
#' \item dkn: nitrogen, dissolved Kjeldahl (µg/l as N)
#' \item doc: carbon, dissolved organic (µg/l as C)
#' \item nh4: nitrogen, ammonium NH4 (µg/l as N)
#' \item no2: nitrogen, nitrite NO2 (µg/l as N)
#' \item no2no3: nitrogen, nitrite NO2 + nitrate NO3 nitrogen
#' (µg/l as N)
#' \item srp: phosphorus, soluble reactive (µg/l as P)
#' \item tdn: nitrogen, total dissolved (µg/l as N)
#' \item tdp: phosphorus, total dissolved (µg/l as P)
#' \item tkn: nitrogen, total Kjeldahl (µg/l as N)
#' \item tn: nitrogen, total (µg/l as N)
#' \item toc: carbon, total organic (µg/l as C)
#' \item ton: nitrogen, total organic (µg/l as N)
#' \item tp: phosphorus, total (µg/l as P)
#' \item secchi: Secchi disk transparency (m).
#' \item *_qual: data flags (qualifiers) from the source program
#' for each water quality parameter (* = all water quality
#' parameters listed above). For example, "chla_qual" is the
#' variable name for the data flag for chlorophyll a observations.
#' \item *_censorcode: identifies whether a data value is censored
#' and the censor type for each water quality parameter (* = all
#' water quality parameters listed above). For example,
#' "chla_censorcode" is the variable name for censor information
#' regarding chlorophyll a observations.
#' \itemize{
#' \item NC1: has detection limit and data value is above
#' detection limit and has no qualifier or comments
#' \item NC2: has detection limit and data value is above
#' detection limit, and has qualifier or comments
#' \item NC3: has no detection limit and has qualifier or
#' comments
#' \item NC4: has no detection limit and has no qualifiers or
#' comments
#' \item LE1: has detection limit, data value is less than or
#' equal to detection limit, has qualifier or comments
#' \item LE2: has detection limit, data value is less than or
#' equal to detection limit, has no qualifier or comments
#' \item LE3: has no detection limit, < than comes from source
#' program, has qualifier or comments
#' \item LE4: has no detection limit, < than comes from source
#' program, has no qualifier or comments
#' }
#' \item *_detectionlimit: the detection limit used by the source
#' program for each water quality parameter (* = all water quality
#' parameters listed above). For example, "chla_detectionlimit" is
#' the name of the variable that reports detection limits for
#' chlorophyll a observations.
#' \item *_labmethodname: analytical procedure, from a standards
#' body if available for each water quality parameter (* = all
#' water quality parameters listed above). For example,
#' "chla_labmethodname" is the variable name for lab methods
#' associated with each chlorophyll a observation.
#' \item chla_methodinfo: flag to indicate variable was sampled
#' using different methods. "CHLA_UNFILTERED" means that a sample
#' was
#' \item secchi_methodinfo: flag to indicate variable was sampled
#' using different methods. "SECCHI_VIEW" means that Secchi depth
#' was measured using a viewer box, whereas "SECCHI_VIEW_UNKNOWN"
#' reports observations where it is unclear if a Secchi viewer box
#' was used. A secchi observation without a methodinfo code means
#' the Secchi depth was made without the viewer box.
#' \item sampleyear: year (4-digit) in which sample was collected
#' \item samplemonth: month in which sample was collected
#' }
#'
#' @docType data
#' @keywords datasets
#' @name epi_nutr
#' @aliases nutrients chla colora doc phosphorus nitrogen chlorophyll waterquality censorcode qualifiers detectionlimit secchi
#' @references Soranno et al. (2017) \doi{10.1093/gigascience/gix101}
NULL
#' Metadata for Lakes with Water Quality
#'
#' A dataset containing depth and names for lakes included in the limno
#' module.
#'
#' @format A data frame with observations of 8 variables:
#' \itemize{
#' \item lagoslakeid: unique lake identifier developed for
#' LAGOS-NE
#' \item nhdid: the 'Permanent_identifier' from the NHD,
#' but is called the NHDID in LAGOS-NE
#' \item lagosname1: name of lake from source dataset used as
#' the authoritative lake name for LAGOSNE
#' \item meandepth: mean lake depth (meters)
#' \item meandepthsource: source of mean depth data, see
#' "lagos_source_program" for definitions
#' \item maxdepth: maximum lake depth (meters)
#' \item maxdepthsource: source of maximum depth data, see
#' "lagos_source_program" for definitions
#' \item legacyid: unique lake identifier from the original
#' water quality source dataset, this is not standardized and each
#' source dataset has its own system
#' }
#'
#' @docType data
#' @keywords datasets
#' @name lakes_limno
#' @aliases meandepth maxdepth legacyid depth
#' @seealso \code{\link[LAGOSNE]{lakes.geo}}
#' @references Soranno et al. (2017) \doi{10.1093/gigascience/gix101}{Gigascience 6:12}
NULL
#' Metadata for all lakes > 1ha
#'
#' A dataset containing identifying information for all lakes > 1ha. This includes
#' lake name, lake size (area and perimeter), location (lat/long), elevation,
#' and codes identifying zones in which the lake is located.
#'
#' @format A data frame with 141265 observations of 17 variables:
#' \itemize{
#' \item lagoslakeid: unique identifier for each lake in LAGOS-NE.
#' For each row of data in this table, the lagoslakeid identifies the focal lake
#' for which other measures are calculated
#' \item nhdid: the 'Permanent_identifier' from the NHD,
#' but is called the NHDID in LAGOS-NE
#' \item gnis_name: lake name from the GNIS database
#' \item nhd_lat: latitude of centroid of the NHD lake polygon in decimal
#' degrees (NAD83)
#' \item nhd_long: longitude of centroid of the NHD lake polygon in decimal
#' degrees (NAD83)
#' \item lake_area_ha: surface area (in hectares) of lake waterbody polygon from NHD
#' \item lake_perim_meters: perimeter (in meters) of lake waterbody polygon from the NHD
#' \item nhd_fcode: NHD five-digit integer code with feature code plus additional
#' characteristics/values
#' \item nhd_ftype: NHD three-digit integer code providing a unique identifier of feature
#' type for the waterbody
#' \item iws_zoneid: the unique ID of the IWS that is estimated for the focal lake
#' in the row of data that is identified by the lagoslakeid.
#' \item hu4_zoneid: the unique ID of the HU4 zone that the focal lake is located within
#' \item hu6_zoneid: the unique ID of the HU6 zone that the focal lake is located within
#' \item hu8_zoneid: the unique ID of the HU8 zone that the focal lake is located within
#' \item hu12_zoneid: the unique ID of the HU12 zone that the focal lake is located within
#' \item edu_zoneid: the unique ID of the EDU zone that the focal lake is located within
#' \item county_zoneid: the unique ID of the county that the focal lake is located within
#' \item state_zoneid: the unique ID of the state that the focal lake is located within
#' \item elevation_m: the elevation of the lake centroid, in meters (referenced to the
#' North American Vertical Datum of 1988 (NAVD88)) and obtained from the National Elevation Dataset
#' }
#'
#' @docType data
#' @keywords datasets
#' @name locus
#' @aliases location
#' @seealso \code{\link[LAGOSNE]{lakes.geo}}
#' @references Soranno et al. (2017) \doi{10.1093/gigascience/gix101}
NULL
#' Connectivity Datasets
#'
#' Datasets containing lake, stream, and wetland abundance and connectivity
#' metrics calculated at the 500m buffer (buffer500m.conn), HUC12
#' (hu12.conn), HUC8 (hu8.conn), HUC4 (hu4.conn), EDU (edu.conn), county
#' (county.conn) and state (state.conn) classifications.
#'
#' @format Data frames with all or a subset of the following variables. Number
#' of observations is equal to the number of zones in each spatial
#' classification (see ?classifications). Wildcard options include a subset of
#' the LAGOSNE spatial classifications (* = buffer500m, iws,
#' hu12, hu8, hu4, edu, county, state) and additional wildcards described
#' below.
#' \itemize{
#' \item Identifiers and Zone Metadata
#' \itemize{
#' \item *_zoneid: unique zone identifier
#' \item *_nwiexclusions: zones that are not completely covered by
#' the National Wetlands Inventory
#' }
#' \item Lake Connectivity Metrics. Lake abundance metrics are derived for
#' all lakes, isolated lakes ("isolated" - no inflow or outflow streams),
#' headwater lakes ("headwater" - no inflowing streams), stream
#' drainage lakes ("drstream" - lakes with inflowing stream(s), with or
#' without outflows, and no upstream lakes greater than 10 ha), and lake
#' drainage lakes ("drlakeStream" lakes with inflowing stream(s) and at
#' least one upstream lake greater than 10 ha).
#' \itemize{
#' \item *_lakes_**_***: all lakes that are within or intersect the
#' zone boundary and are in a particular size class (** = lakes4ha,
#' lakes4to10ha, lakes10ha), expressed as average lake area
#' (*** = agsize_ha) or count (** = count)
#' \item *_lakes_**_overlapping_***: all lakes that are clipped to the
#' zone boundary and are in a particular size class (** = lakes4ha,
#' lakes4to10ha, lakes10ha), expressed as sum of lake area
#' (*** = area_ha) or percent of zone area (*** = area_pct)
#' \item *_lakes_**_contributing_area_ha: all lakes that are within or
#' intersect the zone boundary, and are in a particular size class
#' (** = lakes4ha, lakes4to10ha, lakes10ha), expressed as sum of lake
#' area
#' \item *_lakes_**_isolated_***: all isolated lakes that are within
#' or intersect the zone boundary, and are in a particular size class
#' (** = lakes4ha, lakes4to10ha, lakes10ha), expressed as average size
#' in hectares (*** = avgsize_ha) or count (*** = count
#' \item *_lakes_**_isolated_overlapping_***: all isolated lakes that
#' are clipped to the zone boundary and are in a particular size class
#' (** = lakes4ha, lakes4to10ha, lakes10ha), expressed as sum of lake
#' area (*** = area_ha) or percent of zone area (*** = area_pct)
#' \item *_lakes_**_isolated_contributing_area_ha: all isolated lakes
#' that are within or intersect the zone boundary, and are in a
#' particular size class (** = lakes4ha, lakes4to10ha, lakes10ha),
#' expressed as sum of lake area
#' \item *_lakes_**_headwater_***: all headwater lakes that are within
#' or intersect the zone boundary, and are in a particular size class
#' (** = lakes4ha, lakes4to10ha, lakes10ha), expressed as average
#' size in hectares (*** = avgsize_ha) or count (*** = count
#' \item *_lakes_**_headwater_overlapping_***: all headwater lakes
#' that are clipped to the zone boundary and are in a particular size
#' class (** = lakes4ha, lakes4to10ha, lakes10ha), expressed
#' as sum of lake area (*** = area_ha) or percent of zone area
#' (*** = area_pct)
#' \item *_lakes_**_headwater_contributing_area_ha: all headwater
#' lakes that are within or intersect the zone boundary, and are in a
#' particular size class (** = lakes4ha, lakes4to10ha, lakes10ha),
#' expressed as sum of lake area
#' \item *_lakes_**_drstream_***: all drstream lakes that are within
#' or intersect the zone boundary, and are in a particular size class
#' (** = lakes4ha, lakes4to10ha, lakes10ha), expressed as average
#' size in hectares (*** = avgsize_ha) or count (*** = count
#' \item *_lakes_**_drstream_overlapping_***: all drstream lakes that
#' are clipped to the zone boundary and are in a particular size class
#' (** = lakes4ha, lakes4to10ha, lakes10ha), expressed as sum of lake
#' area (*** = area_ha) or percent of zone area (*** = area_pct)
#' \item *_lakes_**_drstream_contributing_area_ha: all drstream lakes
#' that are within or intersect the zone boundary,
#' and are in a particular size class (** = lakes4ha, lakes4to10ha,
#' lakes10ha), expressed as sum of lake area
#' \item *_lakes_**_drlakestream_***: all drlakestream lakes that are
#' within or intersect the zone boundary, and are in a particular size
#' class (** = lakes4ha, lakes4to10ha, lakes10ha), expressed
#' as average size in hectares (*** = avgsize_ha) or
#' count (*** = count
#' \item *_lakes_**_drlakestream_overlapping_***: all drlakestream
#' lakes that are clipped to the zone boundary and are in a particular
#' size class (** = lakes4ha, lakes4to10ha,
#' lakes10ha), expressed as sum of lake area (*** = area_ha) or
#' percent of zone area (*** = area_pct)
#' \item *_lakes_**_drlakestream_contributing_area_ha: all
#' drlakestream lakes that are within or intersect the zone boundary,
#' and are in a particular size class (** = lakes4ha, lakes4to10ha,
#' lakes10ha), expressed as sum of lake area
#' \item *_latewisconsinglaciation_glaciation: zone glaciation status
#' during the late Wisconsin glaciation (Glaciated, Not_Glaciated,
#' Partially)
#' }
#' \item Stream Connectivity Metrics
#' \itemize{
#' \item *_streamdensity_streams_**: all streams (NHDFlowline minus
#' artificial lines through lakes)
#' within the zone expressed as sum of length in meters
#' (** = sum_lengthm) or density in meters per hectare (** = mperha)
#' \item *_streamdensity_headwaters_*: headwater streams
#' (1st-3rd Strahler order) within the zone
#' expressed as sum of length in meters (** = sum_lengthm) or density
#' in meters per hectare (** = mperha)
#' \item *_streamdensity_midreaches_*: Midreach streams
#' (4th-6th Strahler order) within the zone
#' expressed as sum of length in meters (** = sum_lengthm) or density
#' in meters per hectare (** = mperha)
#' \item *_streamdensity_rivers_*: large river-streams (>6th Strahler
#' order) within the zone
#' expressed as sum of length in meters (** = sum_lengthm) or density
#' in meters per hectare (** = mperha)
#' \item *_canalditchdensity_**: canals within the zone,
#' expressed as sum of length in meters (** = sum_lengthm) or density
#' in meters per hectare (** = mperha)
#' }
#' \item Wetland Connectivity Metrics
#' \itemize{
#' \item *_wl_allwetlandsdissolved_**: all wetlands (regardless of
#' vegetation,
#' connection, or regime), expressed as average size in hectares
#' (** = avgsize_ha), total area of wetlands that is contained within
#' or partially intersect the border of this zone
#' (** = overlapping_area_ha),
#' total land area of this zone that is covered by all wetlands
#' (** = contributing_area_ha),
#' or percent of land area of this zone that is covered by all
#' wetlands (** = overlapping_area_pct).
#' Before calculating this value, contiguous patches of different
#' types of wetlands were first dissolved to represent a single patch.
#' \item *_wl_allwetlandsundissolved_**: all wetlands (regardless of
#' vegetation, connection, or regime), expressed as count
#' (** = count), average size in hectares (** = avgsize_ha), total
#' area of wetlands that is contained within or partially intersect
#' the border of this zone (** = overlapping_area_ha), total land area
#' of this zone that is covered by all wetlands
#' (** = contributing_area_ha), or percent of land area of this zone
#' that is covered by all wetlands (** = overlapping_area_pct).
#' Before calculating this value, contiguous patches of different
#' types of wetlands were first dissolved to represent a single patch.
#' \item *_wl_isolatedwetlandsundissolved_**: isolated wetland patches
#' (no intersecting streams within a 30 m buffer of the wetland patch)
#' in this zone.all wetlands (regardless of vegetation, connection,
#' or regime), expressed as count (** = count), average size in
#' hectares (** = avgsize_ha), total area of wetlands that
#' is contained within or partially intersect the border of this zone
#' (** = overlapping_area_ha), total land area of this zone that is
#' covered by this wetland type (** = contributing_area_ha), or
#' percent of land area of this zone that is covered by this wetland
#' type (** = overlapping_area_pct).
#' The patches were left as delineated by the National Wetlands
#' Inventory ("undissolved") for calculating this variable.
#' \item *_wl_singlewetlandsundissolved_**: single wetland patches
#' (intersected within a 30 m buffer
#' by a single first order stream) in this zone, expressed as count
#' (** = count), average size in hectares (** = avgsize_ha), total
#' area of wetlands that
#' is contained within or partially intersect the border of this zone
#' (** = overlapping_area_ha),
#' total land area of this zone that is covered by this wetland type
#' (** = contributing_area_ha),
#' or percent of land area of this zone that is covered by this
#' wetland type (** = overlapping_area_pct).
#' The patches were left as delineated by the National Wetlands
#' Inventory ("undissolved") for calculating this variable.
#' \item *_wl_connectedwetlandsundissolved_**: connected wetland
#' patches (intersected within a 30 m buffer by a higher
#' order stream or by multiple streams) in this zone, expressed as
#' count (** = count), average size in hectares (** = avgsize_ha),
#' total area of wetlands that
#' is contained within or partially intersect the border of this zone
#' (** = overlapping_area_ha),
#' total land area of this zone that is covered by this wetland type
#' (** = contributing_area_ha),
#' or percent of land area of this zone that is covered by this
#' wetland type (** = overlapping_area_pct).
#' The patches were left as delineated by the National Wetlands
#' Inventory ("undissolved") for calculating this variable.
#' \item *_wl_forestedwetlandsundissolved_**: forested wetland
#' patches (dominated by woody vegetation 6m or taller) in this zone,
#' expressed as count (** = count), average size in hectares
#' (** = avgsize_ha), total area of wetlands that
#' is contained within or partially intersect the border of this zone
#' (** = overlapping_area_ha),
#' total land area of this zone that is covered by this wetland type
#' (** = contributing_area_ha),
#' or percent of land area of this zone that is covered by this
#' wetland type (** = overlapping_area_pct).
#' The patches were left as delineated by the National Wetlands
#' Inventory ("undissolved") for calculating this variable.
#' \item *_wl_scrubshrubwetlandsundissolved_**: scrub-shrub wetland
#' patches (dominated by woody vegetation < 6m tall) in this zone,
#' expressed as count (** = count), average size in hectares
#' (** = avgsize_ha), total area of wetlands that
#' is contained within or partially intersect the border of this zone
#' (** = overlapping_area_ha),
#' total land area of this zone that is covered by this wetland type
#' (** = contributing_area_ha),
#' or percent of land area of this zone that is covered by this
#' wetland type (** = overlapping_area_pct).
#' The patches were left as delineated by the National Wetlands
#' Inventory ("undissolved") for calculating this variable.
#' \item *_wl_openwaterwetlandsundissolved_**: open water wetland
#' patches (dominated by woody vegetation < 6m tall) in this zone,
#' expressed as count (** = count), average size in hectares
#' (** = avgsize_ha), total area of wetlands that
#' is contained within or partially intersect the border of this zone
#' (** = overlapping_area_ha),
#' total land area of this zone that is covered by this wetland type
#' (** = contributing_area_ha),
#' or percent of land area of this zone that is covered by this
#' wetland type (** = overlapping_area_pct).
#' The patches were left as delineated by the National Wetlands
#' Inventory ("undissolved") for calculating this variable.
#' \item *_wl_regimefwetlandsundissolved_**: regime f
#' (semipermanently flooded) wetland patches where surface water
#' persists throughout the growing season in most years, expressed as
#' count (** = count), average size in hectares (** = avgsize_ha),
#' total area of wetlands that
#' is contained within or partially intersect the border of this zone
#' (** = overlapping_area_ha),
#' total land area of this zone that is covered by this wetland type
#' (** = contributing_area_ha),
#' or percent of land area of this zone that is covered by this
#' wetland type (** = overlapping_area_pct).
#' The patches were left as delineated by the National Wetlands
#' Inventory ("undissolved") for calculating this variable.
#' \item *_wl_regimegwetlandsundissolved_**: regime g (intermittently
#' exposed) wetland patches where surface water persists
#' throughout the growing season in most years, expressed as count
#' (** = count), average size in hectares (** = avgsize_ha), total
#' area of wetlands that
#' is contained within or partially intersect the border of this zone
#' (** = overlapping_area_ha),
#' total land area of this zone that is covered by this wetland type
#' (** = contributing_area_ha),
#' percent of land area of this zone that is covered by this wetland
#' type (** = overlapping_area_pct).
#' The patches were left as delineated by the National Wetlands
#' Inventory ("undissolved") for calculating this variable.
#' \item *_wl_regimeawetlandsundissolved_**: regime a (temporarily
#' flooded) wetland patches where surface water persists
#' throughout the growing season in most years, expressed as count
#' (** = count), average size in hectares (** = avgsize_ha), total
#' area of wetlands that is contained within or partially intersect
#' the border of this zone (** = overlapping_area_ha),
#' total land area of this zone that is covered by this wetland type
#' (** = contributing_area_ha),
#' or percent of land area of this zone that is covered by this
#' wetland type (** = overlapping_area_pct).
#' The patches were left as delineated by the National Wetlands
#' Inventory ("undissolved") for calculating this variable.
#' \item *_wl_regimecwetlandsundissolved_**: regime c (seasonally
#' flooded) wetland patches where surface water persists
#' throughout the growing season in most years, expressed as count
#' (** = count), average size in hectares (** = avgsize_ha), total
#' area of wetlands that
#' is contained within or partially intersect the border of this zone
#' (** = overlapping_area_ha),
#' total land area of this zone that is covered by this wetland type
#' (** = contributing_area_ha),
#' or percent of land area of this zone that is covered by this
#' wetland type (** = overlapping_area_pct).
#' The patches were left as delineated by the National Wetlands
#' Inventory ("undissolved") for calculating this variable.
#' \item *_wl_regimehwetlandsundissolved_**: regime h (permanently
#' flooded) wetland patches where surface water persists
#' throughout the growing season in most years, expressed as count
#' (** = count), average size in hectares (** = avgsize_ha), total
#' area of wetlands that
#' is contained within or partially intersect the border of this zone
#' (** = overlapping_area_ha),
#' total land area of this zone that is covered by this wetland type
#' (** = contributing_area_ha),
#' or percent of land area of this zone that is covered by this
#' wetland type (** = overlapping_area_pct).
#' The patches were left as delineated by the National Wetlands
#' Inventory ("undissolved") for calculating this variable.
#'
#' }
#'}
#' @docType data
#' @keywords datasets
#' @name conn
#' @aliases connectivity buffer500m.conn iws.conn hu12.conn hu8.conn hu4.conn edu.conn county.conn state.conn
#' @seealso \code{\link[LAGOSNE]{lakes.geo}}
#' @references Soranno et al. (2017) \doi{10.1093/gigascience/gix101}{Gigascience 6:12}
NULL
#' Lake Geospatial Metadata
#'
#' A dataset containing geospatial identifiers, upstream lake connectivity, and
#' wetland connectivity of all lakes in LAGOSNE >1 hectare.
#'
#' @format A data frame with 141271 observations and 31 variables:
#' \itemize{
#' \item lagoslakeid: unique lake identifier in LAGOSNE
#' \item lakes_nhdid: unique lake identifier from the National
#' Hydrography Dataset (NHD)
#' \item iws_zoneid: zone ID of interlake watershed (IWS) in which
#' focal lake is located
#' \item hu4_zoneid: zone ID of HUC4 in which focal lake is
#' located
#' \item hu6_zoneid: zone ID of HUC6 in which focal lake is
#' located
#' \item hu8_zoneid: zone ID of HUC8 in which focal lake is
#' located
#' \item hu12_zoneid: zone ID of HU12 in which focal lake is
#' located
#' \item edu_zoneid: zone ID of ecological drainage unit (EDU) in
#' which focal lake is located
#' \item county_zoneid: zone ID of county in which focal lake is
#' located
#' \item state_zoneid: two-letter abbreviation of state in which
#' focal lake is located
#' \item upstream_lakes_4ha_count: count of lakes >= 4 ha upstream of the focal lake,
#' connected via the NHD network of all surface flow connections
#' (defined as ephemeral, intermittent, or permanent streams, or any other connections)
#' \item upstream_lakes_4ha_area_ha: total area of lakes >= 4 ha upstream of the focal lake,
#' connected via the NHD network of all surface flow connections
#' (defined as ephemeral, intermittent, or permanent streams, or any other connections)
#' \item upstream_lakes_10ha_count: count of lakes >= 10 ha upstream of the focal lake,
#' connected via the NHD network of all surface flow connections
#' (defined as ephemeral, intermittent, or permanent streams, or any other connections)
#' \item upstream_lakes_10ha_area_ha: total area of lakes >= 10ha upstream of the focal lake,
#' connected via the NHD network of all surface flow connections
#' (defined as ephemeral, intermittent, or permanent streams, or any other connections)
#' \item latewisconsinglaciation_glacial: glaciation status during the Late Wisconsin glaciation,
#' where 'Glaciated' where the whole zone was glaciated, 'Not_Glaciated' where the whole zone
#' was not glaciated, and 'Partially_Glaciated' where a part of the zone was glaciated
#' \item wlconnections_allwetlands_*: the wetland polygons that intersect or are
#' within 30 m buffer around a lake shoreline, measured as count, area (ha), or sum of
#' shoreline length (km) that intersects or touches wetland polygons
#' (* = count, contributing_area_ha, shoreline_km).
#' \item wlconnections_forestedwetlands_count: the forested wetland polygons that intersect or are
#' within 30 m buffer around a lake shoreline, measured as count, area (ha), or sum of
#' shoreline length (km) that intersects or touches wetland polygons
#' (* = count, contributing_area_ha, shoreline_km).
#' \item wlconnections_scrubshrubwetlands_count: the scrub-shrub wetland polygons that intersect or are
#' within 30 m buffer around a lake shoreline, measured as count, area (ha), or sum of
#' shoreline length (km) that intersects or touches wetland polygons
#' (* = count, contributing_area_ha, shoreline_km).
#' \item wlconnections_openwaterwetlands_count: the open water wetland polygons that intersect or are
#' within 30 m buffer around a lake shoreline, measured as count, area (ha), or sum of
#' shoreline length (km) that intersects or touches wetland polygons
#' (* = count, contributing_area_ha, shoreline_km).
#' \item wlconnections_otherwetlands_count: the other-wetland polygons that intersect or are
#' within 30 m buffer around a lake shoreline, measured as count, area (ha), or sum of
#' shoreline length (km) that intersects or touches wetland polygons
#' (* = count, contributing_area_ha, shoreline_km).
#' \item lakeconnection: connectivity of focal lake to upstream
#' features (DR_LakeStream = drainage lake with an upstream lake,
#' DR_Stream = drainage lake with upstream stream,
#' Headwater = lake with outlet but no inlet,
#' Isolated = lake with no inlets or outlets)
#' }
#'
#' @docType data
#' @keywords datasets
#' @name lagoslakes
#' @aliases lakes.geo
#' @references Soranno et al. (2017) \doi{10.1093/gigascience/gix101}
NULL
#' LAGOSNE sources
#'
#' A dataset identifying the sources of limnological data in LAGOSNE.
#'
#' @format A data frame with observations of 19 variables:
#' \itemize{
#' \item programid: unique LAGOSNE program identifier
#' \item programname: name of the sampling/monitoring program that
#' collected the data
#' \item metadataid: unique metadata identifier associated with
#' \item sourceid
#' \item sourcename
#' \item composite
#' \item programtype: categorical description of the type of sampling
#' /monitoring effort
#' \item fundingsource
#' \item labtype
#' \item programlink
#' \item programstatus
#' \item dataprovider
#' \item organization
#' \item sourcedescription
#' \item beg_yr
#' \item end_yr
#' \item state_name
#' \item lakecount
#' \item variable_list
#' }
#' @docType data
#' @keywords datasets
#' @name lagos_source_program
#' @aliases programs lagos.source.programs source.programs lagos.source lagos_source_program
#' @references Soranno et al. (2017) \doi{10.1093/gigascience/gix101}
NULL
#' The spatial extent of LAGOSNE data
#'
#' A dataset containing the spatial extent of LAGOSNE data.
#'
#' @name lg_extent
#' @format A single sf polygon
#' @docType data
#' @keywords data
NULL
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