RSFIA: FIA Tree Mortality Analysis

#' Metadata from the FIADB pdf reference on tables and their respective column names.
#'
#' Taken from FIADB version 7.2 documentation.
#'
#' See FIA documentation for descriptions of columns, although most are self-explanatory.
#'
#' @name FIA_table_metadata
#' @docType data
#' @format A length-7 named list
#' \describe{
#'   \item{APPENDIX_D}{Forest Type Codes and Names}
#'   \item{APPENDIX_E}{Tree Species Group Codes}
#'   \item{APPENDIX_F}{Tree Species Codes, Names, and Occurrences}
#'   \item{APPENDIX_J}{Damage Codes and Thresholds}
#'   \item{APPENDIX_L}{FIA Inventories by State, Year, and Type}
#'   \item{INDEX_1}{Index of Tables}
#'   \item{INDEX_2}{Index of Column Names}
#' }
'FIA_table_metadata'
#' FIA Tree Mortality Estimates With Explanatory Variables
#'
#' See /vignettes for the process.
#'
#' This dataset includes logging and beetles, includes FIA fire
#' but not plots within fire perimeters, and only has plots in the
#' Cascades (M242) and South Rockies (M331)
#'
#' @name FIA_mortality_with_explanatory
#' @docType data
#' @format Dataframe
'FIA_mortality_with_explanatory'
#' Daymet data for fuzzy FIA plot locations
#'
#' See `Get_daymet_data.Rmd` for notes.
#'
#' @name FIA_plot_daymet
#' @docType data
#' @format data.frame
#'FIA_plot_daymet'
#' FIA weather data (DAYMET), binned by year
#'
#' See `bin_explanatory_by_year`
#'
#' Analagous to `FIA_spectrals_by_year_bin`, but for DAYMET-derived data.
#'
#' @name FIA_weather_by_year_bin
#' @docType data
#' @format data.frame
'FIA_weather_by_year_bin'
#' FIA tree-level data
#'
#' Includes all the trees used in the analysis of `Make_mortality_dataframe`
#'
#' @name FIA_mortality_TREE_level
#' @docType data
#' @format data.frame
#'FIA_mortality_TREE_level'
#' FIA species-level tree counts
#'
#' @name FIA_tree_counts
#' @docType data
#' @format data.frame
'FIA_tree_counts'
#' Outlier counts, generated on 2 Jan 2018
#' @name outlier_count_table
#' @docType data
#' @format data.frame
'outlier_count_table'
#' @name remote
#' @docType data
#' @format object of class 'remote'
#' @examples NULL
#' library(RSFIA)
#' remote <- new('remote')
#' remote@bands <- c(101L, 102L, 103L, 7L)
#' remote <- AddCoords(remote, FIA_mortality_with_explanatory$LON, FIA_mortality_with_explanatory$LAT)
#' remote@nc_dir <- '/media/bem/F_STORAGE/RSFIA_analysis'
#' remote@file_name <- 'RGI_NDVI_NDMI_MIR_2000_2015_nplots12k.nc'
#' remote@ft_dir <- '/media/bem/F_STORAGE/RSFIA_data/GEE_outputs'
#' remote@variables <- as.character(remote@bands)
#' remote <- SetupDataFile(remote)
#' t1 <- Sys.time()
#' ReadEarthEngineOutputs(remote, 'Landsat 7')
#' remote@n_fill <- length(remote@sample)
#' print(difftime(Sys.time(), t1))
'remote'
#' @name sgrid
#' @docType data
#' @format object of class 'soilgrids'
#' @examples
#' data('remote')
#' sgrid <- new('soilgrids')
#' sgrid@coords <- remote@coords
#' sgrid@sample <- remote@sample
#' sgrid@nc_dir <- '/media/bem/F_STORAGE/RSFIA_analysis'
#' sgrid@file_name <- 'soil_variables_2000_2015_nplots12k.nc'
#' sgrid <- SetupDataFile(sgrid)
#' t1 <- Sys.time()
#' sgrid <- DownloadSoilGrids(sgrid)
#' Sys.time() # took about 4 hours for 12k points
#' #use_data(sgrid)
'sgrid'
#' @name mort_response_variables
#' @docType data
#' @format object of class 'mortality'
'mort_response_variables'
#' @name daymet
#' @docType data
#' @format object of class 'daymet
#' @examples
#' dmet <- new('daymet')
#' dmet@coords <- remote@coords
#' dmet@sample <- remote@sample
#' dmet@nc_dir <- '/media/bem/F_STORAGE/RSFIA_analysis'
#' dmet@file_name <- 'daymet_2000_2015_nplots12k.nc'
#' dmet@time <- c(1980:2015)
#' dmet <- SetupDataFile(dmet)
#' dmet0 <- DownloadDaymet(dmet)
#' daymet <- dmet0
#use_data(daymet)
'daymet'
#' @name yearly_daymet
#' @docType data
#' @format object of class daymet
#' @examples
'yearly_daymet'