GCD: Global Charcoal Database

#' Extraction methods
#' 
#' Charcoal extractions methods present in the database
#' 
#' 
#' @name charcoal_methods
#' @docType data
#' @format A data frame with 13 observations on the following 3 variables.
#' \describe{\item{ID_METHOD}{a factor with levels \code{ACID}
#' \code{CPRO} \code{GRAV} \code{HNPK} \code{HVLQ} \code{IMAG} \code{NOTK}
#' \code{OPPF} \code{OTHE} \code{POLS} \code{SIEV} \code{SIPO} \code{THSL}}
#' \item{METHOD}{a factor with levels \code{Acidification of sample
#' using gas chromatography to measure elemental carbon (Verardo etal 1990)}
#' \code{charcoal part Ided as opaque phytoclasts/pyrofusinite in palynofacies
#' anlaysis} \code{Charcoal part. Identified in thin slides (soil
#' micromorphology)} \code{Charcoal particles identified by imaging software}
#' \code{Charcoal separated by heavy liquid preparation} \code{Cumulative
#' probability (95\% confidence interval) alluvial soil charcoal}
#' \code{GRAVIMETRIC chemical assay (Winkler method)} \code{Hand picked
#' charcoal from soil samples} \code{Not known} \code{Other} \code{Pollen
#' slide} \code{Sieved} \code{Sieved + Pollslide}} \item{METH_CODE}{a
#' numeric vector}}
#' @keywords datasets
#' @examples
#' 
#' data(charcoal_methods)
#' ## maybe str(charcoal_methods) ; plot(charcoal_methods) ...
#' 
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#' Charcoal units
#' 
#' Charcoal units used in GCD
#' 
#' 
#' @name charcoal_units
#' @docType data
#' @format A data frame with 169 observations on the following 4 variables.
#' \describe{ \item{unit}{a factor with levels \code{\%125} \code{\%DWT}
#' \code{\%TOF} \code{\%WTO} \code{100P} \code{1012} \code{1220} \code{1422}
#' \code{1424} \code{3869} \code{5015} \code{5075} \code{6914} \code{7510}
#' \code{7738} \code{7PRA} \code{8POS} \code{ABSC} \code{ARCC} \code{AREA}
#' \code{ARPG} \code{BCCT} \code{C004} \code{C010} \code{C01K} \code{C040}
#' \code{C100} \code{C120} \code{C125} \code{C140} \code{C150} \code{C180}
#' \code{C250} \code{C65X} \code{CARE} \code{CCMY} \code{CG2M} \code{CHCO}
#' \code{CHRX} \code{CM10} \code{CMGR} \code{CMML} \code{COML} \code{CP20}
#' \code{CPAR} \code{CPRA} \code{DC13} \code{FRAG} \code{G05I} \code{G10I}
#' \code{G250} \code{GCHG} \code{GCMY} \code{GRG1} \code{GRGR} \code{GRPC}
#' \code{GT05} \code{GT10} \code{GT12} \code{GT15} \code{GT18} \code{GT1M}
#' \code{GT24} \code{GT25} \code{GT2X} \code{GT30} \code{GT38} \code{GT50}
#' \code{GT53} \code{GT5C} \code{LT12} \code{LT13} \code{LT18} \code{LT1M}
#' \code{LT25} \code{LT40} \code{M2GR} \code{M2ML} \code{MCM3} \code{MM2C}
#' \code{MM2G} \code{MMDW} \code{MMML} \code{MT10} \code{MULT} \code{NOTK}
#' \code{ORDI} \code{OTHE} \code{PCM1} \code{PCMY} \code{PHYT} \code{PP25}
#' \code{PP51} \code{PP52} \code{PPML} \code{PPOL} \code{PRAB} \code{PROB}
#' \code{PTC0} \code{PTC2} \code{PTC3} \code{PTCT} \code{PX25} \code{SQC0}
#' \code{SQCU} \code{SQCY} \code{SQG1} \code{SQG5} \code{SQL5} \code{TOCA}
#' \code{TOM1} \code{TOM2} \code{TOM3} \code{TOM4} \code{TOM5} \code{TOM6}
#' \code{TOM7} \code{TOM8} \code{TOM9} \code{TOMX} \code{TOTA} \code{UCMY}
#' \code{V025} \code{V100} \code{V125} \code{V255} \code{V501} \code{X01K}
#' \code{X105} \code{X106} \code{X120} \code{X125} \code{X150} \code{X15G}
#' \code{X160} \code{X180} \code{X18C} \code{X20P} \code{X250} \code{X25P}
#' \code{X310} \code{X37P} \code{X459} \code{X500} \code{X50U} \code{X512}
#' \code{X515} \code{X520} \code{X53C} \code{X550} \code{X55P} \code{X55U}
#' \code{XA1K} \code{XARE} \code{XARP} \code{XARS} \code{XC25} \code{XCM3}
#' \code{XCOP} \code{XFML} \code{XFRG} \code{XFRP} \code{XFRS} \code{XIMG}
#' \code{XPEA} \code{XPEE} \code{XPIX} \code{XRIF}} \item{qtype}{a
#' factor with levels \code{C0P0} \code{CONC} \code{INFL} \code{NOTK}
#' \code{OTHE} \code{SOIL}} \item{type}{a character vector}
#' \item{code}{a numeric vector} }
#' @keywords datasets
#' @examples
#' 
#' data(charcoal_methods)
#' ## maybe str(charcoal_methods) ; plot(charcoal_methods) ...
#' 
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#' GCD: Global Charcoal Database data
#' 
#' The GCD package provides Global Charcoal Database data updated at regular
#' intervals to be used in cunjuction with the paleofire package.
#' 
#' \tabular{ll}{ Package: \tab GCD\cr Type: \tab Package\cr Version: \tab
#' 4.0.0\cr Date: \tab 2018-03-01\cr License: \tab GPL (>=2)\cr }
#' 
#' @name GCD-package
#' @aliases GCD GCD-package
#' @docType package
#' @section Author(s): Global Paleofire Working Group <paleofire gmail.com>
#' @seealso \url{http://paleofire.org}
#' @references Power, M., J. Marlon, P. Bartlein, and S. Harrison. 2010. Fire
#' history and the Global Charcoal Database: a new tool for hypothesis testing
#' and data exploration. Palaeogeography, Palaeoclimatology, Palaeoecology
#' 291:52-59.
#' @concept  fire 
#' @concept global 
#' @concept charcoal 
#' @concept sediments 
#' @concept paleo
#' @examples
#' 
#' rm(list=ls())
#' 
#' library(GCD)
#' 
#' ## Charcoal data:
#' 
#' data(paleofiredata)
#' head(paleofiredata)
#' 
#' 
#' ## Associated sites informations:
#' 
#' data(paleofiresites)
#' head(paleofiresites)
#' 
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#' Internal GCD Data
#' 
#' Internal GCD Data
#' 
#' 
#' @aliases Internal PNV_L12 PNV_RF99  pub_key release
#' @name GCD-internal
NULL


#' GCD Charcoal data
#' 
#' Charcoal series from the Global Charcoal Database
#' 
#' 
#' @name paleofiredata
#' @docType data
#' @format A data frame with 134269 observations on the following 4 variables.
#' \describe{ \item{ID_SITE}{a numeric vector} \item{DEPTH}{a
#' numeric vector} \item{EST_AGE}{a numeric vector}
#' \item{QUANTITY}{a numeric vector} \item{METHOD}{a factor
#' with levels \code{ACID} \code{CPRO} \code{GRAV} \code{HNPK} \code{HVLQ}
#' \code{IMAG} \code{NOTK} \code{OREC} \code{OTHE} \code{POLS} \code{SIEV} }
#' \item{UNIT}{a factor see \code{\link{paleofiresites}} for details}
#' \item{TYPE}{a factor with levels \code{C0P0} \code{CONC} \code{INFL}
#' \code{NOTK} \code{OTHE} \code{SOIL}} }
#' @keywords datasets
#' @examples
#' 
#' data(paleofiredata)
#' ## maybe str(paleofiredata) ; plot(paleofiredata) ...
#' 
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#' GCD sites information
#' 
#' Sites description and features
#' 
#' \describe{l12 levels}\code{0= Water} \cr \code{1= Boreal forest} \cr
#' \code{2= Desert vegetation} \cr \code{3= Grassland and dry shrubland} \cr
#' \code{4= Savannas abd dry woodlands} \cr \code{5= Temperate forest}\cr
#' \code{6= Tropical forest}\cr \code{7= Tundra}\cr \code{8= Warm temperate}\cr
#' \code{9= Warm desert}\cr \code{10= Cold desert}\cr
#' 
#' \describe{rf99 levels} \code{0= Water} \cr \code{1= Tropical Evergreen
#' Forest/Woodland}\cr \code{2= Tropical Deciduous Forest/Woodland}\cr \code{3=
#' Temperate Broadleaf Evergreen Forest/Woodland}\cr \code{4= Temperate
#' Needleleaf Evergreen Forest/Woodland}\cr \code{5= Temperate Deciduous
#' Forest/Woodland}\cr \code{6= Boreal Evergreen Forest/Woodland}\cr \code{7=
#' Boreal Deciduous Forest/Woodland}\cr \code{8= Evergreen/Deciduous Mixed
#' Forest/Woodland}\cr \code{9= Savanna}\cr \code{10= Grassland/Steppe}\cr
#' \code{11= Dense Shrubland}\cr \code{12= Open Shrubland}\cr \code{13=
#' Tundra}\cr \code{14= Desert}\cr \code{15= Polar Desert/Rock/Ice}\cr
#' 
#' @name paleofiresites
#' @docType data
#' @format A data frame with 881 observations on the following 17 variables.
#' \describe{
#'   \item{\code{id_site}}{sites primary key from GCD v4.x.x}
#'  \item{\code{id_site_old}}{sites primary key from GCD v3.x.x, deprecated}
#'   \item{\code{pref_units}}{a factor, see help("charcoal_units") and data("charcoal_units") for details}
#'   \item{\code{site_name}}{a character vector}
#'   \item{\code{lat}}{a numeric vector}
#'   \item{\code{long}}{a numeric vector}
#'   \item{\code{elevation}}{a numeric vector of elevations}
#'   \item{\code{country}}{a character vector}
#'   \item{\code{continent}}{a factor with levels \code{Africa} \code{Antarctica} \code{Asia} \code{Australia} \code{Europe} \code{North America} \code{South America}}
#'   \item{\code{ISO3}}{ISO3 code by country}
#'   \item{\code{num_dating}}{a numeric vector}
#'   \item{\code{min_est_age}}{a numeric vector}
#'   \item{\code{max_est_age}}{a numeric vector}
#'   \item{\code{num_samp}}{a numeric vector}
#'   \item{\code{has_depth}}{factor indicating presence of depths associated to ages}
#'   \item{\code{date_int}}{a numeric vector, interval in years between two dates}
#'   \item{\code{qtype}}{a factor, see help("charcoal_units") and data("charcoal_units") for details}
#'   \item{\code{water_depth}}{a numeric vector}
#'   \item{\code{depo_context}}{a character vector, see help("depo_contex") and data("depo_contex") for details}
#'   \item{\code{id_site_type}}{a character vector, see help("site_type") and data("site_type") for details}
#'   \item{\code{id_basin_size}}{a character vector, see help("basin_size") and data("basin_size") for details}
#'   \item{\code{id_lands_desc}}{a character vector, see help("lands_desc") and data("lands_desc") for details}
#'   \item{\code{l12}}{a numeric vector, Levavasseur et al. 2012}
#'   \item{\code{rf99}}{a numeric vector, Ramankutty et al. 1999}
#'   \item{\code{gcd_version}}{main GCD releases}
#'   \item{\code{num_version}}{a numeric vector: version number 401 meaning 4.0.1}
#'   \item{\code{update_date}}{date of data update in the GCD}
#' }
#' 
#' @references Ramankutty, N., and J.A. Foley (1999). Estimating historical
#' changes in global land cover: croplands from 1700 to 1992, Global
#' Biogeochemical Cycles 13(4), 997-1027.\cr \cr Levavasseur, G., M. Vrac, D.
#' M. Roche, and D. Paillard. 2012. Statistical modelling of a new global
#' potential vegetation distribution. Environmental Research Letters 7:044019.
#' @keywords datasets
#' @examples
#' 
#' data(paleofiresites)
#' ## maybe str(paleofiresites) ; plot(paleofiresites) ...
#' 
NULL

#' Date table
#' 
#' Table with the dating information contained in GCD
#' 
#' 
#' @name date
#' @docType data
#' @format A data frame with 4872 observations on the following 8 variables.
#' \describe{ \item{ID_SITE}{a numeric vector}
#' \item{DATE_LAB_NUMBER}{a factor with many levels}
#' \item{DEPTH}{a numeric vector} \item{TICKNESS}{a numeric
#' vector} \item{AGE}{a numeric vector} \item{ERROR}{a numeric
#' vector} \item{ID_DATE_TYPE}{a numeric vector}
#' \item{ID_MAT_DATED}{a factor with levels} }
#' obtained ~~
#' @keywords datasets
#' @examples
#' 
#' data(date)
#' ## maybe str(date) ; plot(date) ...
#' 
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#' Material Dated
#' 
#' 
#' @name mat_dated
#' @docType data
#' @format A data frame with 23 observations on the following 4 variables.
#' \describe{ \item{ID_MAT_DATED}{a numeric vector}
#' \item{MAT_DATED_STANDARD_LEVEL}{a character vector}
#' \item{MAT_DATED_TYPE}{a character vector}
#' \item{MAT_DATED_HIGH_LEVEL}{a character vector} }
#' obtained ~~
#' @keywords datasets
#' @examples
#' 
#' data(mat_dated)
#' ## maybe str(mat_dated) ; plot(mat_dated) ...
#' 
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#' Type of dates in date.rda
#' 
#' 
#' 
#' @name date_type
#' @docType data
#' @format A data frame with 31 observations on the following 4 variables.
#' \describe{ \item{ID_DATE_TYPE}{a numeric vector}
#' \item{DATE_TYPE_CODE}{a character vector}
#' \item{DATE_TYPE_NAME}{a character vector}
#' \item{DATE_TYPE_NUMBER}{a numeric vector} }
#' obtained ~~
#' @keywords datasets
#' @examples
#' 
#' data(date_type)
#' ## maybe str(date_type) ; plot(date_type) ...
#' 
NULL



#' Depositional contexts
#' 

#' @name depo_context
#' @docType data
#' @format A data frame with 17 observations on the following 4 variables.
#' \describe{ \item{ID_DEPO_CONTEXT}{a numeric vector}
#' \item{DEPO_CONTEXT_CODE}{a character vector}
#' \item{DEPO_CONTEXT_NAME}{a character vector}
#' \item{DEPO_CONTEXT_NUMBER}{a numeric vector} }
#' @keywords datasets
#' @examples
#' 
#' data(depo_context)
#' ## maybe str(depo_context) ; plot(depo_context) ...
#' 
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#' Type of sites
#' 
#' @name site_type
#' @docType data
#' @format A data frame with 53 observations on the following 4 variables.
#' \describe{ \item{ID_SITE_TYPE}{a numeric vector}
#' \item{SITE_TYPE_LEVEL}{a character vector}
#' \item{SITE_TYPE_DESC}{a character vector}
#' \item{SITE_TYPE_HIGH_LEVEL}{a character vector} }
#' @keywords datasets
#' @examples
#' 
#' data(site_type)
#' ## maybe str(site_type) ; plot(site_type) ...
#' 
NULL


#' Landscape description elements
#' 
#' 
#' @name lands_desc
#' @docType data
#' @format A data frame with 20 observations on the following 3 variables.
#' \describe{ \item{ID_LANDS_DESC}{a numeric vector}
#' \item{LANDS_DESC_CODE}{a character vector}
#' \item{LANDS_DESC_NAME}{a character vector} }
#' @keywords datasets
#' @examples
#' 
#' data(lands_desc)
#' ## maybe str(lands_desc) ; plot(lands_desc) ...
#' 
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#' Basin size
#' 
#' @name basin_size
#' @docType data
#' @format A data frame with 7 observations on the following 5 variables.
#' \describe{ \item{ID_BASIN_SIZE}{a numeric vector}
#' \item{BASIN_SIZE_CODE}{a character vector}
#' \item{BASIN_SIZE_DESC}{a character vector}
#' \item{BASIN_SIZE_RANGE_MIN}{a character vector}
#' \item{BASIN_SIZE_RANGE_MAX}{a character vector} }
#' @keywords datasets
#' @examples
#' 
#' data(basin_size)
#' ## maybe str(basin_size) ; plot(basin_size) ...
#' 
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