R/lichen.R

In EZtune: Tunes AdaBoost, Elastic Net, Support Vector Machines, and Gradient Boosting Machines

#' Lichen data from the Current Vegetation Survey
#'
#' Data were collected between 1993 and 1999 as part of the Lichen Air Quality
#' surveys on public lands in Oregon and southern Washington. Observations
#' were obtained from 1-acre (0.4 ha) plots at Current Vegetation Survey
#' (CVS) sites. Indicator variables denote the presences and absences of 7
#' lichen species. Data for each sampled plot include the topographic
#' variables elevation, aspect, and slope; bioclimatic predictors
#' including maximum, minimum, daily, and average temperatures, relative
#' humidity precipitation, evapotranspiration, and vapor pressure; and
#' vegetation variables including the average age of the dominant conifer
#' and percent conifer cover. The data in lichenTest were collected from
#' half-acre plots at CVS sites in the same geographical region and contains
#' many of the same variables, including presences and absences for the 7
#' lichen species. As such, it is a good test dataset for predictive methods
#' applied to the Lichen Air Quality data.
#'
#' @format A data frame with 840 observations and 40 variables. One variable
#' is a location identifier, 7 (coded as 0 and 1) identify the presence or
#' absence of a type of lichen species, and 32 are characteristics of the
#' survey site where the data were collected.
#'
#' There were 12 monthly values in the original data for each of the
#' bioclimatic predictors. Principal components analyses suggested that
#' for each of these predictors 2 principal components explained the vast
#' majority (95.0\%-99.5\%) of the total variability. Based on these analyses,
#' indices were created for each set of bioclimatic predictors. The variables
#' with the suffix Ave in the variable name are the average of 12 monthly
#' variables. The variables with the suffix Diff are contrasts between the
#' sum of the April-September monthly values and the sum of the
#' October-December and January-March monthly values, divided by 12. Roughly
#' speaking, these are summer-to-winter contrasts.
#'
#' The variables are summarized as follows:
#' \describe{
#' \item{PlotNum}{Identifier of the section of forest from which the data were collected.}
#' \item{LobaOreg}{Lobaria oregana (Absent = 0, Present = 1)}
#' \item{LobaPulm}{Lobaria pulmonaria (Absent = 0, Present = 1)}
#' \item{NephBell}{Nephroma bellum (Absent = 0, Present = 1)}
#' \item{NephHelv}{Nephroma helveticum (Absent = 0, Present = 1)}
#' \item{PseuAnom}{Pseudocyphellaria anomala (Absent = 0, Present = 1)}
#' \item{PseuAnth}{Pseudocyphellaria anthraspis (Absent = 0, Present = 1)}
#' \item{PseuCroc}{Pseudocyphellaria crocata (Absent = 0, Present = 1)}
#' \item{EvapoTransAve}{Average monthly potential evapotranspiration in mm}
#' \item{EvapoTransDiff}{Summer-to-winter difference in monthly potential evapotranspiration in mm}
#' \item{MoistIndexAve}{Average monthly moisture index in cm}
#' \item{MoistIndexDiff}{Summer-to-winter difference in monthly monthly moisture index in cm}
#' \item{PrecipAve}{Average monthly precipitation in cm}
#' \item{PrecipDiff}{Summer-to-winter difference in monthly precipitation in cm}
#' \item{RelHumidAve}{Average monthly relative humidity in percent}
#' \item{RelHumidDiff}{Summer-to-winter difference in monthly relative humidity in percent}
#' \item{PotGlobRadAve}{Average monthly potential global radiation in kJ}
#' \item{PotGlobRadDiff}{Summer-to-winter difference in monthly potential global radiation in kJ}
#' \item{AveTempAve}{Average monthly average temperature in degrees Celsius}
#' \item{AveTempDiff}{Summer-to-winter difference in monthly average temperature in degrees Celsius}
#' \item{MaxTempAve}{Average monthly maximum temperature in degrees Celsius}
#' \item{MaxTempDiff}{Summer-to-winter difference in monthly maximum temperature in degrees Celsius}
#' \item{MinTempAve}{Average monthly minimum temperature in degrees Celsius}
#' \item{MinTempDiff}{Summer-to-winter difference in monthly minimum temperature in degrees Celsius}
#' \item{DayTempAve}{Mean average daytime temperature in degrees Celsius}
#' \item{DayTempDiff}{Summer-to-winter difference in average daytime temperature in degrees Celsius}
#' \item{AmbVapPressAve}{Average monthly average ambient vapor pressure in Pa}
#' \item{AmbVapPressDiff}{Summer-to-winter difference in monthly average ambient vapor pressure in Pa}
#' \item{SatVapPressAve}{Average monthly average saturated vapor pressure in Pa}
#' \item{SatVapPressDiff}{Summer-to-winter difference in monthly average saturated vapor pressure in Pa}
#' \item{Aspect}{Aspect in degrees}
#' \item{TransAspect}{Transformed Aspect: TransAspect=(1-cos(Aspect))/2}
#' \item{Elevation}{Elevation in meters}
#' \item{Slope}{Percent slope}
#' \item{ReserveStatus}{Reserve Status (Reserve, Matrix)}
#' \item{StandAgeClass}{Stand Age Class (< 80 years, 80+ years)}
#' \item{ACONIF}{Average age of the dominant conifer in years}
#' \item{PctVegCov}{Percent vegetation cover}
#' \item{PctConifCov}{Percent conifer cover}
#' \item{PctBroadLeafCov}{Percent broadleaf cover}
#' \item{TreeBiomass}{Live tree (> 1inch DBH) biomass, above ground, dry weight.}
#' }
#' @source Cutler, D. Richard., Thomas C. Edwards Jr., Karen H. Beard,
#' Adele Cutler, Kyle T. Hess, Jacob Gibson, and Joshua J. Lawler. 2007.
#' Random Forests for Classification in Ecology. Ecology 88(11): 2783-2792.
"lichen"