Nothing
R/modGBtree.R
In FIESTA: Forest Inventory Estimation and Analysis
Defines functions
modGBtree
Documented in
modGBtree
#' Green-Book module - Generate tree estimates.
#'
#' Generates tree and or seedling estimates by domain and/or tree domain (and
#' estimation unit). Calculations are based on Scott et al. 2005 ('the
#' green-book') for mapped forest inventory plots. The non-ratio estimator for
#' estimating tree attributes by stratum and domain is used. Plots that are
#' totally nonsampled are excluded from estimation dataset. Next, an adjustment
#' factor is calculated by strata to adjust for nonsampled (nonresponse)
#' conditions that have proportion less than 1. Attributes adjusted to a
#' per-acre value are summed by plot, divided by the adjustment factor, and
#' averaged by stratum. Strata means are combined using the strata weights and
#' then expanded to using the total land area in the population.
#'
#' If variables are NULL, then it will prompt user to input variables.
#'
#' Necessary variables:\cr \tabular{llll}{ \tab \bold{Data} \tab
#' \bold{Variable} \tab \bold{Description}\cr \tab tree \tab tuniqueid \tab
#' Unique identifier for each plot, to link to pltassgn (ex. PLT_CN).\cr \tab
#' \tab CONDID \tab Unique identifier of each condition on plot, to link to
#' cond. Set CONDID=1, if only 1 condition per plot.\cr \tab \tab TPA_UNADJ
#' \tab Number of trees per acre each sample tree represents (ex. DESIGNCD=1:
#' TPA_UNADJ=6.018046 for trees on subplot; 74.965282 for trees on
#' microplot).\cr \tab cond \tab cuniqueid \tab Unique identifier for each
#' plot, to link to pltassgn (ex. PLT_CN).\cr \tab \tab CONDID \tab Unique
#' identfier of each condition on plot. Set CONDID=1, if only 1 condition per
#' plot.\cr \tab \tab CONDPROP_UNADJ \tab Unadjusted proportion of condition on
#' each plot. Set CONDPROP_UNADJ=1, if only 1 condition per plot.\cr \tab \tab
#' COND_STATUS_CD \tab Status of each forested condition on plot (i.e.
#' accessible forest, nonforest, water, etc.)\cr \tab \tab NF_COND_STATUS_CD
#' \tab If ACI=TRUE. Status of each nonforest condition on plot (i.e.
#' accessible nonforest, nonsampled nonforest)\cr \tab \tab SITECLCD \tab If
#' landarea=TIMBERLAND. Measure of site productivity.\cr \tab \tab RESERVCD
#' \tab If landarea=TIMBERLAND. Reserved status.\cr \tab \tab SUBPROP_UNADJ
#' \tab Unadjusted proportion of subplot conditions on each plot. Set
#' SUBPROP_UNADJ=1, if only 1 condition per subplot.\cr \tab \tab
#' MICRPROP_UNADJ \tab If microplot tree attributes. Unadjusted proportion of
#' microplot conditions on each plot. Set MICRPROP_UNADJ=1, if only 1 condition
#' per microplot.\cr \tab \tab MACRPROP_UNADJ \tab If macroplot tree
#' attributes. Unadjusted proportion of macroplot conditions on each plot. Set
#' MACRPROP_UNADJ=1, if only 1 condition per macroplot.\cr \tab pltassgn \tab
#' puniqueid \tab Unique identifier for each plot, to link to cond (ex. CN).\cr
#' \tab \tab STATECD \tab Identifies state each plot is located in.\cr \tab
#' \tab INVYR \tab Identifies inventory year of each plot.\cr \tab \tab
#' PLOT_STATUS_CD \tab Status of each plot (i.e. sampled, nonsampled). If not
#' included, all plots are assumed as sampled.\cr }
#'
#' For available reference tables: sort(unique(FIESTAutils::ref_codes$VARIABLE)) \cr
#'
#' @param GBpopdat List. Population data objects returned from
#' FIESTA::modGBpop().
#' @param estvar String. Name of the tree-level estimate variable (e.g.,
#' 'VOLCFNET').
#' @param estvar.filter String. A tree-level filter for estvar. Must be R
#' syntax (e.g., 'STATUSCD == 1').
#' @param estseed String. Use seedling data only or add to tree data. Seedling
#' estimates are only for counts (estvar='TPA_UNADJ')-('none', 'only', 'add').
#' @param woodland String. If woodland = 'Y', include woodland tree species
#' where measured. If woodland = 'N', only include timber species. See
#' FIESTA::ref_species$WOODLAND ='Y/N'. If woodland = 'only', only include
#' woodland species.
#' @param landarea String. The condition-level filter for defining land area
#' ('ALL', 'FOREST', 'TIMBERLAND'). If landarea='FOREST', COND_STATUS_CD = 1;
#' if landarea='TIMBERLAND', SITECLCD in(1:6) & RESERVCD = 0.
#' @param pcfilter String. A filter for plot or cond attributes (including
#' pltassgn). Must be R logical syntax.
#' @param rowvar String. Optional. Name of domain variable to group estvar by
#' for rows in table output. Rowvar must be included in an input data frame
#' (i.e., plt, cond, tree). If no rowvar is included, an estimate is returned
#' for the total estimation unit. Include colvar for grouping by 2 variables.
#' @param colvar String. Optional. If rowvar != NULL, name of domain variable
#' to group estvar by for columns in table output. Colvar must be included in
#' an input data frame (i.e., plt, cond, tree).
#' @param sumunits Logical. If TRUE, estimation units are summed and returned
#' in one table.
#' @param returntitle Logical. If TRUE, returns title(s) of the estimation
#' table(s).
#' @param savedata Logical. If TRUE, saves table(s) to outfolder.
#' @param table_opts List. See help(table_options()) for a list of
#' options.
#' @param title_opts List. See help(title_options()) for a list of options.
#' @param savedata_opts List. See help(savedata_options()) for a list
#' of options. Only used when savedata = TRUE.
#' @param gui Logical. If gui, user is prompted for parameters.
#' @param ... Parameters for modGBpop() if GBpopdat is NULL.
#' @return A list with estimates with percent sampling error for rowvar (and
#' colvar). If sumunits=TRUE or unitvar=NULL and colvar=NULL, one data frame
#' is returned. Otherwise, a list object is returned with the following
#' information. If savedata=TRUE, all data frames are written to outfolder.
#'
#' \item{est}{ Data frame. Tree estimates by rowvar, colvar (and estimation
#' unit). If sumunits=TRUE or one estimation unit and colvar=NULL, estimates
#' and percent sampling error are in one data frame. } \item{pse}{ Data frame.
#' Percent sampling errors (Confidence level 68%) for estimates by rowvar and
#' colvar (and estimation unit). Note: for 95% confidence level, multiply
#' percent sampling error by 1.96. } \item{titlelst}{ List with 1 or 2 string
#' vectors. If returntitle=TRUE a list with table title(s). The list contains
#' one title if est and pse are in the same table and two titles if est and pse
#' are in separate tables. } \item{raw}{ List of data frames. If rawdata=TRUE,
#' a list including the processing data used for estimation including: number
#' of plots and conditions; stratification information; and 1 to 8 tables with
#' calculated values for table cells and totals (See processing data below). }
#'
#' Raw data
#'
#' \item{plotsampcnt}{ Table. Number of plots by plot status (ex. sampled
#' forest on plot, sampled nonforest, nonsampled). } \item{condsampcnt}{ DF.
#' Number of conditions by condition status (forest land, nonforest land,
#' noncensus water, census water, nonsampled). } \item{unitarea}{ DF. Area by
#' estimation unit. } \item{expcondtab}{ DF. Condition-level area expansion
#' factors. } \item{tdomdat}{ DF. Final data table used for estimation. }
#'
#' \item{stratdat}{ Data frame. Strata information by estimation unit. }
#' \tabular{lll}{ \tab \bold{Variable} \tab \bold{Description}\cr \tab unitvar
#' \tab estimation unit \cr \tab strvar \tab stratum value \cr \tab strwtvar
#' \tab number of pixels by strata and estimation unit \cr \tab n.strata \tab
#' number of plots in strata (after totally nonsampled plots removed) \cr \tab
#' n.total \tab number of plots for estimation unit \cr \tab strwt \tab
#' proportion of area (or plots) by strata and estimation unit (i.e., strata
#' weight) \cr \tab CONDPROP_UNADJ_SUM \tab summed condition proportion by
#' strata and estimation unit \cr \tab CONDPROP_ADJFAC \tab adjusted condition
#' proportion by strata after nonsampled plots removed \cr }
#'
#' \item{processing data}{ Data frames. Separate data frames containing
#' calculated variables used in estimation process. The number of processing
#' tables depends on the input parameters. The tables include: total by
#' estimation unit (unit.totest); rowvar totals (unit.rowest), and if colvar is
#' not NULL, colvar totals, (unit.colvar); and a combination of rowvar and
#' colvar (unit.grpvar). If sumunits=TRUE, the raw data for the summed
#' estimation units are also included (totest, rowest, colest, grpest,
#' respectively). These tables do not included estimate proportions (nhat and
#' nhat.var).
#'
#' The data frames include the following information: \tabular{lll}{ \tab
#' \bold{Variable} \tab \bold{Description}\cr \tab nhat \tab estimated
#' proportion of trees \cr \tab nhat.var \tab variance estimate of estimated
#' proportion of trees \cr \tab NBRPLT.gt0 \tab Number of non-zero plots used
#' in estimates \cr \tab ACRES \tab total area for estimation unit \cr \tab est
#' \tab estimated area of trees nhat*ACRES \cr \tab est.var \tab variance
#' estimate of estimated area of trees nhat.var*areavar^2 \cr \tab est.se \tab
#' standard error of estimated area of trees sqrt(est.var) \cr \tab est.cv \tab
#' coefficient of variation of estimated area of trees est.se/est \cr \tab pse
#' \tab percent sampling error of estimate est.cv*100 \cr \tab CI99left \tab
#' left tail of 99 percent confidence interval for estimated area \cr \tab
#' CI99right \tab right tail of 99 percent confidence interval for estimated
#' area \cr \tab CI95left \tab left tail of 95 percent confidence interval for
#' estimated area \cr \tab CI95right \tab right tail of 95 percent confidence
#' interval for estimated area \cr \tab CI67left \tab left tail of 67 percent
#' confidence interval for estimated area \cr \tab CI67right \tab right tail of
#' 67 percent confidence interval for estimated area \cr } }
#'
#' Table(s) are also written to outfolder.
#' @note
#'
#' ADJUSTMENT FACTOR:\cr The adjustment factor is necessary to account for
#' nonsampled conditions. It is calculated for each estimation unit by strata.
#' by summing the unadjusted proportions of the subplot, microplot, and
#' macroplot (i.e. *PROP_UNADJ) and dividing by the number of plots in the
#' strata/estimation unit).
#'
#' An adjustment factor is determined for each tree based on the size of the
#' plot it was measured on. This is identified using TPA_UNADJ as follows:
#'
#' \tabular{llr}{ \tab \bold{PLOT SIZE} \tab \bold{TPA_UNADJ} \cr \tab SUBPLOT
#' \tab 6.018046 \cr \tab MICROPLOT \tab 74.965282 \cr \tab MACROPLOT \tab
#' 0.999188 \cr }
#'
#' If ACI=FALSE, only nonsampled forest conditions are accounted for in the
#' adjustment factor. \cr If ACI=TRUE, the nonsampled nonforest conditions are
#' removed as well and accounted for in adjustment factor. This is if you are
#' interested in estimates for all lands or nonforest lands in the
#' All-Condition-Inventory.
#'
#' sumunits:\cr An estimation unit is a population, or area of interest, with
#' known area and number of plots. Individual counties or combined
#' Super-counties are common estimation units for FIA. An estimation unit may
#' also be a subpopulation of a larger population (e.g., Counties within a
#' State). Subpopulations are mutually exclusive and independent within a
#' population, therefore estimated totals and variances are additive. For
#' example, State-level estimates are generated by summing estimates from all
#' subpopulations within the State (Bechtold and Patterson. 2005. Chapter 2).
#' Each plot must be assigned to only one estimation unit.
#'
#' If sumunits=TRUE, estimates are generated by estimation unit, summed
#' together, and returned as one estimate. If rawdata=TRUE, estimates by
#' individual estimation unit are also returned.
#'
#' If sumunits=FALSE, estimates are generated and returned by estimation unit
#' as one data frame. If savedata=TRUE, a separate file is written for each
#' estimation unit.
#'
#' stratcombine:\cr If TRUE and less than 2 plots in any one estimation unit,
#' all estimation units with 10 or less plots are combined. The current method
#' for combining is to group the estimation unit with less than 10 plots with
#' the estimation unit following in consecutive order (numeric or
#' alphabetical), restrained by survey unit (UNITCD) if included in dataset,
#' and continuing until the number of plots equals 10. If there are no
#' estimation units following in order, it is combined with the estimation unit
#' previous in order.
#'
#' rowlut/collut:\cr There are several objectives for including rowlut/collut
#' look-up tables: 1) to include descriptive names that match row/column codes
#' in the input table; 2) to use number codes that match row/column names in
#' the input table for ordering rows; 3) to add rows and/or columns with 0
#' values for consistency. No duplicate names are allowed.
#'
#' Include 2 columns in the table:\cr 1-the merging variable with same name as
#' the variable in the input merge table;\cr 2-the ordering or descriptive
#' variable.\cr If the ordering variable is the rowvar/colvar in the input
#' table and the descriptive variable is in rowlut/collut, set
#' row.orderby/col.orderby equal to rowvar/colvar. If the descriptive variable
#' is the rowvar/colvar in the input table, and the ordering code variable is
#' in rowlut/collut, set row.orderby/col.orderby equal to the variable name of
#' the code variable in rowlut/collut.
#'
#' UNITS:\cr The following variables are converted from pounds (from FIA
#' database) to short tons by multiplying the variable by 0.0005. DRYBIO_AG,
#' DRYBIO_BG, DRYBIO_WDLD_SPP, DRYBIO_SAPLING, DRYBIO_STUMP, DRYBIO_TOP,
#' DRYBIO_BOLE, DRYBIOT, DRYBIOM, DRYBIOTB, JBIOTOT, CARBON_BG, CARBON_AG
#'
#' MORTALITY:\cr For Interior-West FIA, mortality estimates are mainly based on
#' whether a tree has died within the last 5 years of when the plot was
#' measured. If a plot was remeasured, mortality includes trees that were alive
#' the previous visit but were dead in the next visit. If a tree was standing
#' the previous visit, but was not standing in the next visit, no diameter was
#' collected (DIA = NA) but the tree is defined as mortality.
#'
#' Common tree filters: \cr
#'
#' \tabular{llr}{ \tab \bold{FILTER} \tab \bold{DESCRIPTION} \cr \tab "STATUSCD
#' == 1" \tab Live trees \cr \tab "STATUSCD == 2" \tab Dead trees \cr \tab
#' "TPAMORT_UNADJ > 0" \tab Mortality trees \cr \tab "STATUSCD == 2 & DIA >=
#' 5.0" \tab Dead trees >= 5.0 inches diameter \cr \tab "STATUSCD == 2 &
#' AGENTCD == 30" \tab Dead trees from fire \cr }
#' @author Tracey S. Frescino, Paul L. Patterson, Elizabeth A. Freeman
#' @references Scott, Charles T.; Bechtold, William A.; Reams, Gregory A.;
#' Smith, William D.; Westfall, James A.; Hansen, Mark H.; Moisen, Gretchen G.
#' 2005. Sample-based estimators used by the Forest Inventory and Analysis
#' national information management system. Gen. Tech. Rep. SRS-80. Asheville,
#' NC: U.S. Department of Agriculture, Forest Service, Southern Research
#' Station, p.53-77.
#' @keywords data
#' @examples
#' \donttest{
#' GBpopdat <- modGBpop(
#' popTabs = list(cond = FIESTA::WYcond,
#' tree = FIESTA::WYtree,
#' seed = FIESTA::WYseed),
#' popTabIDs = list(cond = "PLT_CN"),
#' pltassgn = FIESTA::WYpltassgn,
#' pltassgnid = "CN",
#' pjoinid = "PLT_CN",
#' unitarea = FIESTA::WYunitarea,
#' unitvar = "ESTN_UNIT",
#' strata = TRUE,
#' stratalut = WYstratalut,
#' strata_opts = strata_options(getwt = TRUE)
#' )
#'
#' tree1.1 <- modGBtree(
#' GBpopdat = GBpopdat, # pop - population calculations
#' landarea = "FOREST", # est - forest land filter
#' sumunits = TRUE, # est - sum estimation units to population
#' estvar = "VOLCFNET", # est - net cubic-foot volume
#' estvar.filter = "STATUSCD == 1", # est - live trees only
#' returntitle = TRUE # out - return title information
#' )
#' str(tree1.1, max.level = 1)
#'
#' tree1.2 <- modGBtree(
#' GBpopdat = GBpopdat, # pop - population calculations
#' landarea = "FOREST", # est - forest land filter
#' sumunits = TRUE, # est - sum estimation units to population
#' estvar = "VOLCFNET", # est - net cubic-foot volume
#' estvar.filter = "STATUSCD == 1", # est - live trees only
#' rowvar = "FORTYPCD", # est - row domain
#' returntitle = TRUE # out - return title information
#' )
#' str(tree1.2, max.level = 1)
#' }
#' @export modGBtree
modGBtree <- function(GBpopdat,
estvar,
estvar.filter = NULL,
estseed = "none",
woodland = "Y",
landarea = "FOREST",
pcfilter = NULL,
rowvar = NULL,
colvar = NULL,
sumunits = TRUE,
returntitle = FALSE,
savedata = FALSE,
table_opts = NULL,
title_opts = NULL,
savedata_opts = NULL,
gui = FALSE,
...){
##################################################################################
## DESCRIPTION:
## Generates estimates of trees by domain using non-ratio estimators.
##################################################################################
## CHECK GUI - IF NO ARGUMENTS SPECIFIED, ASSUME GUI=TRUE
if (nargs() == 0 && is.null(GBpopdat)) {
gui <- TRUE
}
## If gui.. set variables to NULL
if (gui) {
landarea=strvar=areavar=sumunits=adjplot=strata=getwt=cuniqueid=ACI=
tuniqueid=savedata=addtitle=returntitle=rawdata=rawonly=unitvar <- NULL
#if (!row.FIAname) row.FIAname <- NULL
#if (!col.FIAname) col.FIAname <- NULL
}
## Set parameter
esttype <- "TREE"
parameters <- FALSE
returnlst <- list()
rawdata <- TRUE
## Set global variables
ONEUNIT=n.total=n.strata=strwt=TOTAL <- NULL
##################################################################
## CHECK PARAMETER NAMES
##################################################################
## Check input parameters
input.params <- names(as.list(match.call()))[-1]
formallst <- c(names(formals(modGBtree)),
names(formals(modGBpop)))
if (!all(input.params %in% formallst)) {
miss <- input.params[!input.params %in% formallst]
stop("invalid parameter: ", toString(miss))
}
## Check parameter lists
pcheck.params(input.params, table_opts=table_opts, title_opts=title_opts,
savedata_opts=savedata_opts)
## Set savedata defaults
savedata_defaults_list <- formals(savedata_options)[-length(formals(savedata_options))]
for (i in 1:length(savedata_defaults_list)) {
assign(names(savedata_defaults_list)[[i]], savedata_defaults_list[[i]])
}
## Set user-supplied savedata values
if (length(savedata_opts) > 0) {
if (!savedata) {
message("savedata=FALSE with savedata parameters... no data are saved")
}
for (i in 1:length(savedata_opts)) {
if (names(savedata_opts)[[i]] %in% names(savedata_defaults_list)) {
assign(names(savedata_opts)[[i]], savedata_opts[[i]])
} else {
stop(paste("Invalid parameter: ", names(savedata_opts)[[i]]))
}
}
}
## Set table defaults
table_defaults_list <- formals(table_options)[-length(formals(table_options))]
for (i in 1:length(table_defaults_list)) {
assign(names(table_defaults_list)[[i]], table_defaults_list[[i]])
}
## Set user-supplied table values
if (length(table_opts) > 0) {
for (i in 1:length(table_opts)) {
if (names(table_opts)[[i]] %in% names(table_defaults_list)) {
assign(names(table_opts)[[i]], table_opts[[i]])
} else {
stop(paste("Invalid parameter: ", names(table_opts)[[i]]))
}
}
}
## Set title defaults
title_defaults_list <- formals(title_options)[-length(formals(title_options))]
for (i in 1:length(title_defaults_list)) {
assign(names(title_defaults_list)[[i]], title_defaults_list[[i]])
}
## Set user-supplied title values
if (length(title_opts) > 0) {
for (i in 1:length(title_opts)) {
if (names(title_opts)[[i]] %in% names(title_defaults_list)) {
assign(names(title_opts)[[i]], title_opts[[i]])
} else {
stop(paste("Invalid parameter: ", names(title_opts)[[i]]))
}
}
}
##################################################################
## CHECK PARAMETER INPUTS
##################################################################
list.items <- c("condx", "pltcondx", "treex", "cuniqueid", "condid",
"tuniqueid", "ACI.filter", "unitarea", "unitvar", "stratalut",
"strvar", "plotsampcnt", "condsampcnt")
GBpopdat <- pcheck.object(GBpopdat, "GBpopdat", list.items=list.items)
if (is.null(GBpopdat)) return(NULL)
condx <- GBpopdat$condx
pltcondx <- GBpopdat$pltcondx
treex <- GBpopdat$treex
seedx <- GBpopdat$seedx
if (is.null(treex) && is.null(seedx)) {
stop("must include tree data for tree estimates")
}
cuniqueid <- GBpopdat$cuniqueid
condid <- GBpopdat$condid
tuniqueid <- GBpopdat$tuniqueid
ACI.filter <- GBpopdat$ACI.filter
unitarea <- GBpopdat$unitarea
areavar <- GBpopdat$areavar
areaunits <- GBpopdat$areaunits
unitvar <- GBpopdat$unitvar
unitvars <- GBpopdat$unitvars
stratalut <- GBpopdat$stratalut
strvar <- GBpopdat$strvar
expcondtab <- GBpopdat$expcondtab
plotsampcnt <- GBpopdat$plotsampcnt
condsampcnt <- GBpopdat$condsampcnt
states <- GBpopdat$states
invyrs <- GBpopdat$invyrs
stratcombinelut <- GBpopdat$stratcombinelut
strwtvar <- GBpopdat$strwtvar
adj <- GBpopdat$adj
strunitvars <- c(unitvar, strvar)
strata <- GBpopdat$strata
pop_fmt <- GBpopdat$pop_fmt
pop_dsn <- GBpopdat$pop_dsn
########################################
## Check area units
########################################
unitchk <- pcheck.areaunits(unitarea=unitarea, areavar=areavar,
areaunits=areaunits, metric=metric)
unitarea <- unitchk$unitarea
areavar <- unitchk$areavar
areaunits <- unitchk$outunits
if (is.null(key(unitarea))) {
setkeyv(unitarea, unitvar)
}
###################################################################################
## Check parameters and apply plot and condition filters
###################################################################################
estdat <- check.estdata(esttype=esttype, pop_fmt=pop_fmt, pop_dsn=pop_dsn,
pltcondf=pltcondx, cuniqueid=cuniqueid, condid=condid,
treex=treex, seedx=seedx, estseed=estseed, woodland=woodland,
sumunits=sumunits, landarea=landarea, ACI.filter=ACI.filter,
pcfilter=pcfilter, allin1=allin1,
estround=estround, pseround=pseround, divideby=divideby,
addtitle=addtitle, returntitle=returntitle,
rawdata=rawdata, rawonly=rawonly, savedata=savedata,
outfolder=outfolder, overwrite_dsn=overwrite_dsn,
overwrite_layer=overwrite_layer, outfn.pre=outfn.pre,
outfn.date=outfn.date, append_layer=append_layer,
raw_fmt=raw_fmt, raw_dsn=raw_dsn, gui=gui)
if (is.null(estdat)) return(NULL)
pltcondf <- estdat$pltcondf
cuniqueid <- estdat$cuniqueid
treef <- estdat$treef
seedf <- estdat$seedf
tuniqueid <- estdat$tuniqueid
estseed <- estdat$estseed
woodland <- estdat$woodland
sumunits <- estdat$sumunits
landarea <- estdat$landarea
allin1 <- estdat$allin1
estround <- estdat$estround
pseround <- estdat$pseround
divideby <- estdat$divideby
addtitle <- estdat$addtitle
returntitle <- estdat$returntitle
rawdata <- estdat$rawdata
rawonly <- estdat$rawonly
savedata <- estdat$savedata
outfolder <- estdat$outfolder
overwrite_layer <- estdat$overwrite_layer
append_layer <- estdat$append_layer
raw_fmt <- estdat$raw_fmt
raw_dsn <- estdat$raw_dsn
rawfolder <- estdat$rawfolder
conn <- estdat$conn
if ("STATECD" %in% names(pltcondf)) {
states <- pcheck.states(sort(unique(pltcondf$STATECD)))
}
if ("INVYR" %in% names(pltcondf)) {
invyr <- sort(unique(pltcondf$INVYR))
}
#############################################################################
### Check row and column data
#############################################################################
rowcolinfo <- check.rowcol(gui=gui, esttype=esttype, conn=conn,
treef=treef, seedf=seedf,
condf=pltcondf, cuniqueid=cuniqueid,
tuniqueid=tuniqueid, estseed=estseed,
rowvar=rowvar, colvar=colvar,
row.FIAname=row.FIAname, col.FIAname=col.FIAname,
row.orderby=row.orderby, col.orderby=col.orderby,
row.add0=row.add0, col.add0=col.add0,
title.rowvar=title.rowvar, title.colvar=title.colvar,
rowlut=rowlut, collut=collut, rowgrp=rowgrp,
rowgrpnm=rowgrpnm, rowgrpord=rowgrpord,
landarea=landarea, states=states)
treef <- rowcolinfo$treef
seedf <- rowcolinfo$seedf
condf <- rowcolinfo$condf
uniquerow <- rowcolinfo$uniquerow
uniquecol <- rowcolinfo$uniquecol
domainlst <- rowcolinfo$domainlst
rowvar <- rowcolinfo$rowvar
colvar <- rowcolinfo$colvar
row.orderby <- rowcolinfo$row.orderby
col.orderby <- rowcolinfo$col.orderby
row.add0 <- rowcolinfo$row.add0
col.add0 <- rowcolinfo$col.add0
title.rowvar <- rowcolinfo$title.rowvar
title.colvar <- rowcolinfo$title.colvar
rowgrpnm <- rowcolinfo$rowgrpnm
title.rowgrp <- rowcolinfo$title.rowgrp
bytdom <- rowcolinfo$bytdom
tdomvar <- rowcolinfo$tdomvar
tdomvar2 <- rowcolinfo$tdomvar2
grpvar <- rowcolinfo$grpvar
#rm(rowcolinfo)
## Generate a uniquecol for estimation units
if (!sumunits && colvar == "NONE") {
uniquecol <- data.table(unitarea[[unitvar]])
setnames(uniquecol, unitvar)
uniquecol[[unitvar]] <- factor(uniquecol[[unitvar]])
}
###############################################################################
### Get estimation data from tree table
###############################################################################
adjtree <- ifelse(adj %in% c("samp", "plot"), TRUE, FALSE)
treedat <- check.tree(gui=gui, treef=treef, seedf=seedf, estseed=estseed,
bycond=TRUE, condf=condf, bytdom=bytdom,
tuniqueid=tuniqueid, cuniqueid=cuniqueid,
esttype=esttype, estvarn=estvar, estvarn.filter=estvar.filter,
esttotn=TRUE, tdomvar=tdomvar, tdomvar2=tdomvar2,
adjtree=adjtree, metric=metric, woodland=woodland)
if (is.null(treedat)) return(NULL)
tdomdat <- treedat$tdomdat
if (rowvar != "TOTAL") {
#if (!row.add0) {
if (any(is.na(tdomdat[[rowvar]]))) {
if (!row.FIAname) {
rval <- ifelse (any(!is.na(tdomdat[[rowvar]]) & tdomdat[[rowvar]] == 0), max(tdomdat[[rowvar]], na.rm=TRUE), 0)
tdomdat[is.na(tdomdat[[rowvar]]), rowvar] <- rval
levels(uniquerow[[rowvar]]) <- c(levels(uniquerow[[rowvar]]), as.character(rval))
uniquerow[is.na(uniquerow[[rowvar]]), rowvar] <- as.character(rval)
} else {
tdomdat <- tdomdat[!is.na(tdomdat[[rowvar]]), ]
}
}
#}
if (colvar != "NONE") {
#if (!col.add0) {
if (any(is.na(tdomdat[[colvar]]))) {
if (!col.FIAname) {
cval <- ifelse (any(!is.na(tdomdat[[colvar]]) & tdomdat[[colvar]] == 0), max(tdomdat[[colvar]], na.rm=TRUE), 0)
tdomdat[is.na(tdomdat[[colvar]]), colvar] <- cval
levels(uniquecol[[colvar]]) <- c(levels(uniquecol[[colvar]]), as.character(cval))
uniquecol[is.na(uniquecol[[colvar]]), colvar] <- as.character(cval)
} else {
tdomdat <- tdomdat[!is.na(tdomdat[[colvar]]), ]
}
}
#}
}
}
## Merge tdomdat with condx
xchk <- check.matchclass(condx, tdomdat, c(cuniqueid, condid))
condx <- xchk$tab1
tdomdat <- xchk$tab2
tdomdat <- merge(condx, tdomdat, by=c(cuniqueid, condid))
estvar <- treedat$estvar
estvar.name <- treedat$estvar.name
estvar.filter <- treedat$estvar.filter
tdomvarlst <- treedat$tdomvarlst
estunits <- treedat$estunits
###############################################################################
### Get titles for output tables
###############################################################################
alltitlelst <- check.titles(dat=tdomdat, esttype=esttype,
estseed=estseed, woodland=woodland,
sumunits=sumunits, title.main=title.main, title.ref=title.ref,
title.rowvar=title.rowvar, title.rowgrp=title.rowgrp,
title.colvar=title.colvar, title.unitvar=title.unitvar,
title.filter=title.filter, title.unitsn=estunits,
title.estvarn=title.estvar,
unitvar=unitvar, rowvar=rowvar, colvar=colvar,
estvarn=estvar, estvarn.filter=estvar.filter,
addtitle=addtitle, returntitle=returntitle,
rawdata=rawdata, states=states, invyrs=invyrs,
landarea=landarea, pcfilter=pcfilter, allin1=allin1,
divideby=divideby, outfn.pre=outfn.pre)
title.unitvar <- alltitlelst$title.unitvar
title.est <- alltitlelst$title.est
title.pse <- alltitlelst$title.pse
title.estpse <- alltitlelst$title.estpse
title.ref <- alltitlelst$title.ref
outfn.estpse <- alltitlelst$outfn.estpse
outfn.param <- alltitlelst$outfn.param
if (rawdata) {
outfn.rawdat <- alltitlelst$outfn.rawdat
}
############################################################################
## GENERATE ESTIMATES
############################################################################
unit_totest=unit_rowest=unit_colest=unit_grpest=rowunit=totunit=tdomdattot <- NULL
addtotal <- ifelse(((rowvar == "TOTAL" || length(unique(tdomdat[[rowvar]])) > 1) ||
(!is.null(tdomvarlst) && length(tdomvarlst) > 1)), TRUE, FALSE)
stratalut <- setDT(stratalut)
## Note: tdomdat is the summed response by condition (not domain)
#if (addtotal) {
## Get estimate for total
tdomdattot <- tdomdat[, lapply(.SD, sum, na.rm=TRUE),
by=c(strunitvars, cuniqueid, "TOTAL"), .SDcols=estvar.name]
unit_totest <- GBest.pbar(sumyn = estvar.name,
ysum = tdomdattot,
esttype = esttype,
uniqueid = cuniqueid,
stratalut = stratalut,
unitvar = unitvar,
strvar = strvar,
domain = "TOTAL")
tabs <- check.matchclass(unitarea, unit_totest, unitvar)
unitarea <- tabs$tab1
unit_totest <- tabs$tab2
setkeyv(unit_totest, unitvar)
unit_totest <- unit_totest[unitarea, nomatch=0]
if (totals) {
unit_totest <- getpse(unit_totest, areavar=areavar, esttype=esttype)
} else {
unit_totest <- getpse(unit_totest, esttype=esttype)
}
#}
## Get row, column, cell estimate and merge area if row or column in cond table
if (rowvar != "TOTAL") {
tdomdatsum <- tdomdat[, lapply(.SD, sum, na.rm=TRUE),
by=c(strunitvars, cuniqueid, rowvar), .SDcols=estvar.name]
tdomdatsum <- tdomdatsum[!is.na(tdomdatsum[[rowvar]]),]
unit_rowest <- GBest.pbar(sumyn = estvar.name,
ysum = tdomdatsum,
uniqueid = cuniqueid,
stratalut = stratalut,
unitvar = unitvar,
strvar = strvar,
domain = rowvar)
if (colvar != "NONE") {
tdomdatsum <- tdomdat[, lapply(.SD, sum, na.rm=TRUE),
by=c(strunitvars, cuniqueid, colvar), .SDcols=estvar.name]
tdomdatsum <- tdomdatsum[!is.na(tdomdatsum[[colvar]]),]
unit_colest <- GBest.pbar(sumyn = estvar.name,
ysum = tdomdatsum,
uniqueid = cuniqueid,
stratalut = stratalut,
unitvar = unitvar,
strvar = strvar,
domain = colvar)
tdomdatsum <- tdomdat[, lapply(.SD, sum, na.rm=TRUE),
by=c(strunitvars, cuniqueid, grpvar), .SDcols=estvar.name]
unit_grpest <- GBest.pbar(sumyn =estvar.name,
ysum = tdomdatsum,
uniqueid = cuniqueid,
stratalut = stratalut,
unitvar = unitvar,
strvar = strvar,
domain = grpvar)
}
}
###################################################################################
## Check add0 and Add area
###################################################################################
if (!sumunits && nrow(unitarea) > 1) col.add0 <- TRUE
if (!is.null(unit_rowest)) {
unit_rowest <- add0unit(x=unit_rowest, xvar=rowvar,
uniquex=uniquerow, unitvar=unitvar,
xvar.add0=row.add0)
tabs <- check.matchclass(unitarea, unit_rowest, unitvar)
unitarea <- tabs$tab1
unit_rowest <- tabs$tab2
if (!is.null(row.orderby) && row.orderby != "NONE") {
setorderv(unit_rowest, c(row.orderby))
}
setkeyv(unit_rowest, unitvar)
unit_rowest <- unit_rowest[unitarea, nomatch=0]
if (totals) {
unit_rowest <- getpse(unit_rowest, areavar=areavar, esttype=esttype)
} else {
unit_rowest <- getpse(unit_rowest, esttype=esttype)
}
setkeyv(unit_rowest, c(unitvar, rowvar))
}
if (!is.null(unit_colest)) {
unit_colest <- add0unit(x=unit_colest, xvar=colvar,
uniquex=uniquecol, unitvar=unitvar,
xvar.add0=col.add0)
tabs <- check.matchclass(unitarea, unit_colest, unitvar)
unitarea <- tabs$tab1
unit_colest <- tabs$tab2
if (!is.null(col.orderby) && col.orderby != "NONE") {
setorderv(unit_colest, c(col.orderby))
}
setkeyv(unit_colest, unitvar)
unit_colest <- unit_colest[unitarea, nomatch=0]
if (totals) {
unit_colest <- getpse(unit_colest, areavar=areavar, esttype=esttype)
} else {
unit_colest <- getpse(unit_colest, esttype=esttype)
}
setkeyv(unit_colest, c(unitvar, colvar))
}
if (!is.null(unit_grpest)) {
unit_grpest <- add0unit(x=unit_grpest, xvar=rowvar,
uniquex=uniquerow, unitvar=unitvar,
xvar.add0=row.add0, xvar2=colvar,
uniquex2=uniquecol, xvar2.add0=col.add0)
tabs <- check.matchclass(unitarea, unit_grpest, unitvar)
unitarea <- tabs$tab1
unit_grpest <- tabs$tab2
if (!is.null(row.orderby) && row.orderby != "NONE") {
if (!is.null(col.orderby) && col.orderby != "NONE") {
setorderv(unit_grpest, c(row.orderby, col.orderby))
} else {
setorderv(unit_grpest, c(row.orderby))
}
} else if (!is.null(col.orderby) && col.orderby != "NONE") {
setorderv(unit_grpest, c(col.orderby))
}
setkeyv(unit_grpest, unitvar)
unit_grpest <- unit_grpest[unitarea, nomatch=0]
if (totals) {
unit_grpest <- getpse(unit_grpest, areavar=areavar, esttype=esttype)
} else {
unit_grpest <- getpse(unit_grpest, esttype=esttype)
}
setkeyv(unit_grpest, c(unitvar, rowvar, colvar))
}
###################################################################################
## Get row and column totals for units if sumunits=FALSE
###################################################################################
## For sumunits=FALSE, get estimation unit totals
if (!sumunits && (length(unique(unitarea[[unitvar]])) > 1 && rowvar != "TOTAL")) {
## AGGREGATE UNIT stratalut FOR ROWVAR and GRAND TOTAL
stratalut2 <- data.table(stratalut, ONEUNIT=1)
strunitvars2 <- c("ONEUNIT", strvar)
stratalut2 <- stratalut2[, lapply(.SD, sum, na.rm=TRUE),
by=strunitvars2, .SDcols=c(strwtvar, "n.strata")]
stratalut2[, strwt:=prop.table(get(strwtvar)), by="ONEUNIT"]
stratalut2[, n.total := sum(n.strata)]
setkeyv(stratalut2, strunitvars2)
unitarea2 <- data.table(unitarea, ONEUNIT=1)
unitarea2 <- unitarea2[, lapply(.SD, sum, na.rm=TRUE), by="ONEUNIT",
.SDcols=areavar]
setkey(unitarea2, "ONEUNIT")
tdomdat[, ONEUNIT := 1]
## Calculate unit totals for rowvar
tdomdatsum <- tdomdat[, lapply(.SD, sum, na.rm=TRUE),
by=c(strunitvars2, tuniqueid, rowvar), .SDcols=estvar.name]
rowunit <- GBest.pbar(sumyn = estvar.name,
ysum = tdomdatsum,
esttype = esttype,
uniqueid = tuniqueid,
stratalut = stratalut2,
unitvar = "ONEUNIT",
strvar = strvar,
domain = rowvar)
rowunit <- add0unit(x=rowunit, xvar=rowvar,
uniquex=uniquerow, unitvar="ONEUNIT",
xvar.add0=row.add0)
tabs <- check.matchclass(unitarea2, rowunit, "ONEUNIT")
unitarea2 <- tabs$tab1
rowunit <- tabs$tab2
setkeyv(rowunit, "ONEUNIT")
rowunit <- rowunit[unitarea2, nomatch=0]
if (totals) {
rowunit <- getpse(rowunit, areavar=areavar, esttype=esttype)
} else {
rowunit <- getpse(rowunit, esttype=esttype)
}
setkeyv(rowunit, c("ONEUNIT", rowvar))
## Calculate grand total for all units
tdomdatsum <- tdomdat[, lapply(.SD, sum, na.rm=TRUE),
by=c(strunitvars2, tuniqueid, "TOTAL"), .SDcols=estvar.name]
totunit <- GBest.pbar(sumyn = estvar.name,
ysum = tdomdatsum,
esttype = esttype,
uniqueid = tuniqueid,
stratalut = stratalut2,
unitvar = "ONEUNIT",
strvar = strvar,
domain = "TOTAL")
tabs <- check.matchclass(unitarea2, totunit, "ONEUNIT")
unitarea2 <- tabs$tab1
totunit <- tabs$tab2
setkeyv(totunit, "ONEUNIT")
totunit <- totunit[unitarea2, nomatch=0]
if (totals) {
totunit <- getpse(totunit, areavar=areavar, esttype=esttype)
} else {
totunit <- getpse(totunit, esttype=esttype)
}
}
###################################################################################
## GENERATE OUTPUT TABLES
###################################################################################
message("getting output...")
estnm <- "est"
tabs <- est.outtabs(esttype=esttype, sumunits=sumunits, areavar=areavar,
unitvar=unitvar, unitvars=unitvars, unit_totest=unit_totest,
unit_rowest=unit_rowest, unit_colest=unit_colest, unit_grpest=unit_grpest,
rowvar=rowvar, colvar=colvar, uniquerow=uniquerow, uniquecol=uniquecol,
rowgrp=rowgrp, rowgrpnm=rowgrpnm, rowunit=rowunit, totunit=totunit,
allin1=allin1, savedata=savedata, addtitle=addtitle, title.ref=title.ref,
title.colvar=title.colvar, title.rowvar=title.rowvar, title.rowgrp=title.rowgrp,
title.unitvar=title.unitvar, title.estpse=title.estpse, title.est=title.est,
title.pse=title.pse, rawdata=rawdata, rawonly=rawonly, outfn.estpse=outfn.estpse,
outfolder=outfolder, outfn.date=outfn.date, overwrite=overwrite_layer,
estnm=estnm, estround=estround, pseround=pseround, divideby=divideby,
returntitle=returntitle, estnull=estnull, psenull=psenull, raw.keep0=raw.keep0)
est2return <- tabs$tabest
pse2return <- tabs$tabpse
if (!is.null(est2return)) {
returnlst$est <- setDF(est2return)
}
if (!is.null(pse2return)) {
returnlst$pse <- setDF(pse2return)
}
if(returntitle) {
returnlst$titlelst <- alltitlelst
}
if (rawdata) {
rawdat <- tabs$rawdat
rawdat$domdat <- setDF(tdomdat)
rawdat$estvar <- estvar.name
rawdat$estvar.filter <- estvar.filter
if (savedata) {
if (!is.null(title.estpse)) {
title.raw <- paste(title.estpse, title.ref)
} else {
title.raw <- title.est
}
for (i in 1:length(rawdat)) {
tabnm <- names(rawdat[i])
rawtab <- rawdat[[i]]
outfn.rawtab <- paste0(outfn.rawdat, "_", tabnm)
if (tabnm %in% c("plotsampcnt", "condsampcnt", "stratcombinelut")) {
write2csv(rawtab, outfolder=rawfolder, outfilenm=outfn.rawtab,
outfn.date=outfn.date, overwrite=overwrite_layer)
} else if (is.data.frame(rawtab)) {
if (raw_fmt != "csv") {
out_layer <- tabnm
} else {
out_layer <- outfn.rawtab
}
datExportData(rawtab,
savedata_opts=list(outfolder=rawfolder,
out_fmt=raw_fmt,
out_dsn=raw_dsn,
out_layer=out_layer,
overwrite_layer=overwrite_layer,
append_layer=append_layer,
add_layer=TRUE)
)
}
}
}
rawdat$module <- "GB"
rawdat$esttype <- esttype
rawdat$GBmethod <- ifelse(strata, "PS", "HT")
rawdat$estvar <- estvar
rawdat$estvar.filter <- estvar.filter
if (!is.null(rowvar)) rawdat$rowvar <- rowvar
if (!is.null(colvar)) rawdat$colvar <- colvar
rawdat$areaunits <- areaunits
rawdat$estunits <- estunits
returnlst$raw <- rawdat
}
if ("STATECD" %in% names(pltcondf)) {
returnlst$statecd <- sort(unique(pltcondf$STATECD))
}
if ("INVYR" %in% names(pltcondf)) {
returnlst$invyr <- sort(unique(pltcondf$INVYR))
}
return(returnlst)
}
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Defines functions modGBtree
Documented in modGBtree
#' Green-Book module - Generate tree estimates.
#'
#' Generates tree and or seedling estimates by domain and/or tree domain (and
#' estimation unit). Calculations are based on Scott et al. 2005 ('the
#' green-book') for mapped forest inventory plots. The non-ratio estimator for
#' estimating tree attributes by stratum and domain is used. Plots that are
#' totally nonsampled are excluded from estimation dataset. Next, an adjustment
#' factor is calculated by strata to adjust for nonsampled (nonresponse)
#' conditions that have proportion less than 1. Attributes adjusted to a
#' per-acre value are summed by plot, divided by the adjustment factor, and
#' averaged by stratum. Strata means are combined using the strata weights and
#' then expanded to using the total land area in the population.
#'
#' If variables are NULL, then it will prompt user to input variables.
#'
#' Necessary variables:\cr \tabular{llll}{ \tab \bold{Data} \tab
#' \bold{Variable} \tab \bold{Description}\cr \tab tree \tab tuniqueid \tab
#' Unique identifier for each plot, to link to pltassgn (ex. PLT_CN).\cr \tab
#' \tab CONDID \tab Unique identifier of each condition on plot, to link to
#' cond. Set CONDID=1, if only 1 condition per plot.\cr \tab \tab TPA_UNADJ
#' \tab Number of trees per acre each sample tree represents (ex. DESIGNCD=1:
#' TPA_UNADJ=6.018046 for trees on subplot; 74.965282 for trees on
#' microplot).\cr \tab cond \tab cuniqueid \tab Unique identifier for each
#' plot, to link to pltassgn (ex. PLT_CN).\cr \tab \tab CONDID \tab Unique
#' identfier of each condition on plot. Set CONDID=1, if only 1 condition per
#' plot.\cr \tab \tab CONDPROP_UNADJ \tab Unadjusted proportion of condition on
#' each plot. Set CONDPROP_UNADJ=1, if only 1 condition per plot.\cr \tab \tab
#' COND_STATUS_CD \tab Status of each forested condition on plot (i.e.
#' accessible forest, nonforest, water, etc.)\cr \tab \tab NF_COND_STATUS_CD
#' \tab If ACI=TRUE. Status of each nonforest condition on plot (i.e.
#' accessible nonforest, nonsampled nonforest)\cr \tab \tab SITECLCD \tab If
#' landarea=TIMBERLAND. Measure of site productivity.\cr \tab \tab RESERVCD
#' \tab If landarea=TIMBERLAND. Reserved status.\cr \tab \tab SUBPROP_UNADJ
#' \tab Unadjusted proportion of subplot conditions on each plot. Set
#' SUBPROP_UNADJ=1, if only 1 condition per subplot.\cr \tab \tab
#' MICRPROP_UNADJ \tab If microplot tree attributes. Unadjusted proportion of
#' microplot conditions on each plot. Set MICRPROP_UNADJ=1, if only 1 condition
#' per microplot.\cr \tab \tab MACRPROP_UNADJ \tab If macroplot tree
#' attributes. Unadjusted proportion of macroplot conditions on each plot. Set
#' MACRPROP_UNADJ=1, if only 1 condition per macroplot.\cr \tab pltassgn \tab
#' puniqueid \tab Unique identifier for each plot, to link to cond (ex. CN).\cr
#' \tab \tab STATECD \tab Identifies state each plot is located in.\cr \tab
#' \tab INVYR \tab Identifies inventory year of each plot.\cr \tab \tab
#' PLOT_STATUS_CD \tab Status of each plot (i.e. sampled, nonsampled). If not
#' included, all plots are assumed as sampled.\cr }
#'
#' For available reference tables: sort(unique(FIESTAutils::ref_codes$VARIABLE)) \cr
#'
#' @param GBpopdat List. Population data objects returned from
#' FIESTA::modGBpop().
#' @param estvar String. Name of the tree-level estimate variable (e.g.,
#' 'VOLCFNET').
#' @param estvar.filter String. A tree-level filter for estvar. Must be R
#' syntax (e.g., 'STATUSCD == 1').
#' @param estseed String. Use seedling data only or add to tree data. Seedling
#' estimates are only for counts (estvar='TPA_UNADJ')-('none', 'only', 'add').
#' @param woodland String. If woodland = 'Y', include woodland tree species
#' where measured. If woodland = 'N', only include timber species. See
#' FIESTA::ref_species$WOODLAND ='Y/N'. If woodland = 'only', only include
#' woodland species.
#' @param landarea String. The condition-level filter for defining land area
#' ('ALL', 'FOREST', 'TIMBERLAND'). If landarea='FOREST', COND_STATUS_CD = 1;
#' if landarea='TIMBERLAND', SITECLCD in(1:6) & RESERVCD = 0.
#' @param pcfilter String. A filter for plot or cond attributes (including
#' pltassgn). Must be R logical syntax.
#' @param rowvar String. Optional. Name of domain variable to group estvar by
#' for rows in table output. Rowvar must be included in an input data frame
#' (i.e., plt, cond, tree). If no rowvar is included, an estimate is returned
#' for the total estimation unit. Include colvar for grouping by 2 variables.
#' @param colvar String. Optional. If rowvar != NULL, name of domain variable
#' to group estvar by for columns in table output. Colvar must be included in
#' an input data frame (i.e., plt, cond, tree).
#' @param sumunits Logical. If TRUE, estimation units are summed and returned
#' in one table.
#' @param returntitle Logical. If TRUE, returns title(s) of the estimation
#' table(s).
#' @param savedata Logical. If TRUE, saves table(s) to outfolder.
#' @param table_opts List. See help(table_options()) for a list of
#' options.
#' @param title_opts List. See help(title_options()) for a list of options.
#' @param savedata_opts List. See help(savedata_options()) for a list
#' of options. Only used when savedata = TRUE.
#' @param gui Logical. If gui, user is prompted for parameters.
#' @param ... Parameters for modGBpop() if GBpopdat is NULL.
#' @return A list with estimates with percent sampling error for rowvar (and
#' colvar). If sumunits=TRUE or unitvar=NULL and colvar=NULL, one data frame
#' is returned. Otherwise, a list object is returned with the following
#' information. If savedata=TRUE, all data frames are written to outfolder.
#'
#' \item{est}{ Data frame. Tree estimates by rowvar, colvar (and estimation
#' unit). If sumunits=TRUE or one estimation unit and colvar=NULL, estimates
#' and percent sampling error are in one data frame. } \item{pse}{ Data frame.
#' Percent sampling errors (Confidence level 68%) for estimates by rowvar and
#' colvar (and estimation unit). Note: for 95% confidence level, multiply
#' percent sampling error by 1.96. } \item{titlelst}{ List with 1 or 2 string
#' vectors. If returntitle=TRUE a list with table title(s). The list contains
#' one title if est and pse are in the same table and two titles if est and pse
#' are in separate tables. } \item{raw}{ List of data frames. If rawdata=TRUE,
#' a list including the processing data used for estimation including: number
#' of plots and conditions; stratification information; and 1 to 8 tables with
#' calculated values for table cells and totals (See processing data below). }
#'
#' Raw data
#'
#' \item{plotsampcnt}{ Table. Number of plots by plot status (ex. sampled
#' forest on plot, sampled nonforest, nonsampled). } \item{condsampcnt}{ DF.
#' Number of conditions by condition status (forest land, nonforest land,
#' noncensus water, census water, nonsampled). } \item{unitarea}{ DF. Area by
#' estimation unit. } \item{expcondtab}{ DF. Condition-level area expansion
#' factors. } \item{tdomdat}{ DF. Final data table used for estimation. }
#'
#' \item{stratdat}{ Data frame. Strata information by estimation unit. }
#' \tabular{lll}{ \tab \bold{Variable} \tab \bold{Description}\cr \tab unitvar
#' \tab estimation unit \cr \tab strvar \tab stratum value \cr \tab strwtvar
#' \tab number of pixels by strata and estimation unit \cr \tab n.strata \tab
#' number of plots in strata (after totally nonsampled plots removed) \cr \tab
#' n.total \tab number of plots for estimation unit \cr \tab strwt \tab
#' proportion of area (or plots) by strata and estimation unit (i.e., strata
#' weight) \cr \tab CONDPROP_UNADJ_SUM \tab summed condition proportion by
#' strata and estimation unit \cr \tab CONDPROP_ADJFAC \tab adjusted condition
#' proportion by strata after nonsampled plots removed \cr }
#'
#' \item{processing data}{ Data frames. Separate data frames containing
#' calculated variables used in estimation process. The number of processing
#' tables depends on the input parameters. The tables include: total by
#' estimation unit (unit.totest); rowvar totals (unit.rowest), and if colvar is
#' not NULL, colvar totals, (unit.colvar); and a combination of rowvar and
#' colvar (unit.grpvar). If sumunits=TRUE, the raw data for the summed
#' estimation units are also included (totest, rowest, colest, grpest,
#' respectively). These tables do not included estimate proportions (nhat and
#' nhat.var).
#'
#' The data frames include the following information: \tabular{lll}{ \tab
#' \bold{Variable} \tab \bold{Description}\cr \tab nhat \tab estimated
#' proportion of trees \cr \tab nhat.var \tab variance estimate of estimated
#' proportion of trees \cr \tab NBRPLT.gt0 \tab Number of non-zero plots used
#' in estimates \cr \tab ACRES \tab total area for estimation unit \cr \tab est
#' \tab estimated area of trees nhat*ACRES \cr \tab est.var \tab variance
#' estimate of estimated area of trees nhat.var*areavar^2 \cr \tab est.se \tab
#' standard error of estimated area of trees sqrt(est.var) \cr \tab est.cv \tab
#' coefficient of variation of estimated area of trees est.se/est \cr \tab pse
#' \tab percent sampling error of estimate est.cv*100 \cr \tab CI99left \tab
#' left tail of 99 percent confidence interval for estimated area \cr \tab
#' CI99right \tab right tail of 99 percent confidence interval for estimated
#' area \cr \tab CI95left \tab left tail of 95 percent confidence interval for
#' estimated area \cr \tab CI95right \tab right tail of 95 percent confidence
#' interval for estimated area \cr \tab CI67left \tab left tail of 67 percent
#' confidence interval for estimated area \cr \tab CI67right \tab right tail of
#' 67 percent confidence interval for estimated area \cr } }
#'
#' Table(s) are also written to outfolder.
#' @note
#'
#' ADJUSTMENT FACTOR:\cr The adjustment factor is necessary to account for
#' nonsampled conditions. It is calculated for each estimation unit by strata.
#' by summing the unadjusted proportions of the subplot, microplot, and
#' macroplot (i.e. *PROP_UNADJ) and dividing by the number of plots in the
#' strata/estimation unit).
#'
#' An adjustment factor is determined for each tree based on the size of the
#' plot it was measured on. This is identified using TPA_UNADJ as follows:
#'
#' \tabular{llr}{ \tab \bold{PLOT SIZE} \tab \bold{TPA_UNADJ} \cr \tab SUBPLOT
#' \tab 6.018046 \cr \tab MICROPLOT \tab 74.965282 \cr \tab MACROPLOT \tab
#' 0.999188 \cr }
#'
#' If ACI=FALSE, only nonsampled forest conditions are accounted for in the
#' adjustment factor. \cr If ACI=TRUE, the nonsampled nonforest conditions are
#' removed as well and accounted for in adjustment factor. This is if you are
#' interested in estimates for all lands or nonforest lands in the
#' All-Condition-Inventory.
#'
#' sumunits:\cr An estimation unit is a population, or area of interest, with
#' known area and number of plots. Individual counties or combined
#' Super-counties are common estimation units for FIA. An estimation unit may
#' also be a subpopulation of a larger population (e.g., Counties within a
#' State). Subpopulations are mutually exclusive and independent within a
#' population, therefore estimated totals and variances are additive. For
#' example, State-level estimates are generated by summing estimates from all
#' subpopulations within the State (Bechtold and Patterson. 2005. Chapter 2).
#' Each plot must be assigned to only one estimation unit.
#'
#' If sumunits=TRUE, estimates are generated by estimation unit, summed
#' together, and returned as one estimate. If rawdata=TRUE, estimates by
#' individual estimation unit are also returned.
#'
#' If sumunits=FALSE, estimates are generated and returned by estimation unit
#' as one data frame. If savedata=TRUE, a separate file is written for each
#' estimation unit.
#'
#' stratcombine:\cr If TRUE and less than 2 plots in any one estimation unit,
#' all estimation units with 10 or less plots are combined. The current method
#' for combining is to group the estimation unit with less than 10 plots with
#' the estimation unit following in consecutive order (numeric or
#' alphabetical), restrained by survey unit (UNITCD) if included in dataset,
#' and continuing until the number of plots equals 10. If there are no
#' estimation units following in order, it is combined with the estimation unit
#' previous in order.
#'
#' rowlut/collut:\cr There are several objectives for including rowlut/collut
#' look-up tables: 1) to include descriptive names that match row/column codes
#' in the input table; 2) to use number codes that match row/column names in
#' the input table for ordering rows; 3) to add rows and/or columns with 0
#' values for consistency. No duplicate names are allowed.
#'
#' Include 2 columns in the table:\cr 1-the merging variable with same name as
#' the variable in the input merge table;\cr 2-the ordering or descriptive
#' variable.\cr If the ordering variable is the rowvar/colvar in the input
#' table and the descriptive variable is in rowlut/collut, set
#' row.orderby/col.orderby equal to rowvar/colvar. If the descriptive variable
#' is the rowvar/colvar in the input table, and the ordering code variable is
#' in rowlut/collut, set row.orderby/col.orderby equal to the variable name of
#' the code variable in rowlut/collut.
#'
#' UNITS:\cr The following variables are converted from pounds (from FIA
#' database) to short tons by multiplying the variable by 0.0005. DRYBIO_AG,
#' DRYBIO_BG, DRYBIO_WDLD_SPP, DRYBIO_SAPLING, DRYBIO_STUMP, DRYBIO_TOP,
#' DRYBIO_BOLE, DRYBIOT, DRYBIOM, DRYBIOTB, JBIOTOT, CARBON_BG, CARBON_AG
#'
#' MORTALITY:\cr For Interior-West FIA, mortality estimates are mainly based on
#' whether a tree has died within the last 5 years of when the plot was
#' measured. If a plot was remeasured, mortality includes trees that were alive
#' the previous visit but were dead in the next visit. If a tree was standing
#' the previous visit, but was not standing in the next visit, no diameter was
#' collected (DIA = NA) but the tree is defined as mortality.
#'
#' Common tree filters: \cr
#'
#' \tabular{llr}{ \tab \bold{FILTER} \tab \bold{DESCRIPTION} \cr \tab "STATUSCD
#' == 1" \tab Live trees \cr \tab "STATUSCD == 2" \tab Dead trees \cr \tab
#' "TPAMORT_UNADJ > 0" \tab Mortality trees \cr \tab "STATUSCD == 2 & DIA >=
#' 5.0" \tab Dead trees >= 5.0 inches diameter \cr \tab "STATUSCD == 2 &
#' AGENTCD == 30" \tab Dead trees from fire \cr }
#' @author Tracey S. Frescino, Paul L. Patterson, Elizabeth A. Freeman
#' @references Scott, Charles T.; Bechtold, William A.; Reams, Gregory A.;
#' Smith, William D.; Westfall, James A.; Hansen, Mark H.; Moisen, Gretchen G.
#' 2005. Sample-based estimators used by the Forest Inventory and Analysis
#' national information management system. Gen. Tech. Rep. SRS-80. Asheville,
#' NC: U.S. Department of Agriculture, Forest Service, Southern Research
#' Station, p.53-77.
#' @keywords data
#' @examples
#' \donttest{
#' GBpopdat <- modGBpop(
#' popTabs = list(cond = FIESTA::WYcond,
#' tree = FIESTA::WYtree,
#' seed = FIESTA::WYseed),
#' popTabIDs = list(cond = "PLT_CN"),
#' pltassgn = FIESTA::WYpltassgn,
#' pltassgnid = "CN",
#' pjoinid = "PLT_CN",
#' unitarea = FIESTA::WYunitarea,
#' unitvar = "ESTN_UNIT",
#' strata = TRUE,
#' stratalut = WYstratalut,
#' strata_opts = strata_options(getwt = TRUE)
#' )
#'
#' tree1.1 <- modGBtree(
#' GBpopdat = GBpopdat, # pop - population calculations
#' landarea = "FOREST", # est - forest land filter
#' sumunits = TRUE, # est - sum estimation units to population
#' estvar = "VOLCFNET", # est - net cubic-foot volume
#' estvar.filter = "STATUSCD == 1", # est - live trees only
#' returntitle = TRUE # out - return title information
#' )
#' str(tree1.1, max.level = 1)
#'
#' tree1.2 <- modGBtree(
#' GBpopdat = GBpopdat, # pop - population calculations
#' landarea = "FOREST", # est - forest land filter
#' sumunits = TRUE, # est - sum estimation units to population
#' estvar = "VOLCFNET", # est - net cubic-foot volume
#' estvar.filter = "STATUSCD == 1", # est - live trees only
#' rowvar = "FORTYPCD", # est - row domain
#' returntitle = TRUE # out - return title information
#' )
#' str(tree1.2, max.level = 1)
#' }
#' @export modGBtree
modGBtree <- function(GBpopdat,
estvar,
estvar.filter = NULL,
estseed = "none",
woodland = "Y",
landarea = "FOREST",
pcfilter = NULL,
rowvar = NULL,
colvar = NULL,
sumunits = TRUE,
returntitle = FALSE,
savedata = FALSE,
table_opts = NULL,
title_opts = NULL,
savedata_opts = NULL,
gui = FALSE,
...){
##################################################################################
## DESCRIPTION:
## Generates estimates of trees by domain using non-ratio estimators.
##################################################################################
## CHECK GUI - IF NO ARGUMENTS SPECIFIED, ASSUME GUI=TRUE
if (nargs() == 0 && is.null(GBpopdat)) {
gui <- TRUE
}
## If gui.. set variables to NULL
if (gui) {
landarea=strvar=areavar=sumunits=adjplot=strata=getwt=cuniqueid=ACI=
tuniqueid=savedata=addtitle=returntitle=rawdata=rawonly=unitvar <- NULL
#if (!row.FIAname) row.FIAname <- NULL
#if (!col.FIAname) col.FIAname <- NULL
}
## Set parameter
esttype <- "TREE"
parameters <- FALSE
returnlst <- list()
rawdata <- TRUE
## Set global variables
ONEUNIT=n.total=n.strata=strwt=TOTAL <- NULL
##################################################################
## CHECK PARAMETER NAMES
##################################################################
## Check input parameters
input.params <- names(as.list(match.call()))[-1]
formallst <- c(names(formals(modGBtree)),
names(formals(modGBpop)))
if (!all(input.params %in% formallst)) {
miss <- input.params[!input.params %in% formallst]
stop("invalid parameter: ", toString(miss))
}
## Check parameter lists
pcheck.params(input.params, table_opts=table_opts, title_opts=title_opts,
savedata_opts=savedata_opts)
## Set savedata defaults
savedata_defaults_list <- formals(savedata_options)[-length(formals(savedata_options))]
for (i in 1:length(savedata_defaults_list)) {
assign(names(savedata_defaults_list)[[i]], savedata_defaults_list[[i]])
}
## Set user-supplied savedata values
if (length(savedata_opts) > 0) {
if (!savedata) {
message("savedata=FALSE with savedata parameters... no data are saved")
}
for (i in 1:length(savedata_opts)) {
if (names(savedata_opts)[[i]] %in% names(savedata_defaults_list)) {
assign(names(savedata_opts)[[i]], savedata_opts[[i]])
} else {
stop(paste("Invalid parameter: ", names(savedata_opts)[[i]]))
}
}
}
## Set table defaults
table_defaults_list <- formals(table_options)[-length(formals(table_options))]
for (i in 1:length(table_defaults_list)) {
assign(names(table_defaults_list)[[i]], table_defaults_list[[i]])
}
## Set user-supplied table values
if (length(table_opts) > 0) {
for (i in 1:length(table_opts)) {
if (names(table_opts)[[i]] %in% names(table_defaults_list)) {
assign(names(table_opts)[[i]], table_opts[[i]])
} else {
stop(paste("Invalid parameter: ", names(table_opts)[[i]]))
}
}
}
## Set title defaults
title_defaults_list <- formals(title_options)[-length(formals(title_options))]
for (i in 1:length(title_defaults_list)) {
assign(names(title_defaults_list)[[i]], title_defaults_list[[i]])
}
## Set user-supplied title values
if (length(title_opts) > 0) {
for (i in 1:length(title_opts)) {
if (names(title_opts)[[i]] %in% names(title_defaults_list)) {
assign(names(title_opts)[[i]], title_opts[[i]])
} else {
stop(paste("Invalid parameter: ", names(title_opts)[[i]]))
}
}
}
##################################################################
## CHECK PARAMETER INPUTS
##################################################################
list.items <- c("condx", "pltcondx", "treex", "cuniqueid", "condid",
"tuniqueid", "ACI.filter", "unitarea", "unitvar", "stratalut",
"strvar", "plotsampcnt", "condsampcnt")
GBpopdat <- pcheck.object(GBpopdat, "GBpopdat", list.items=list.items)
if (is.null(GBpopdat)) return(NULL)
condx <- GBpopdat$condx
pltcondx <- GBpopdat$pltcondx
treex <- GBpopdat$treex
seedx <- GBpopdat$seedx
if (is.null(treex) && is.null(seedx)) {
stop("must include tree data for tree estimates")
}
cuniqueid <- GBpopdat$cuniqueid
condid <- GBpopdat$condid
tuniqueid <- GBpopdat$tuniqueid
ACI.filter <- GBpopdat$ACI.filter
unitarea <- GBpopdat$unitarea
areavar <- GBpopdat$areavar
areaunits <- GBpopdat$areaunits
unitvar <- GBpopdat$unitvar
unitvars <- GBpopdat$unitvars
stratalut <- GBpopdat$stratalut
strvar <- GBpopdat$strvar
expcondtab <- GBpopdat$expcondtab
plotsampcnt <- GBpopdat$plotsampcnt
condsampcnt <- GBpopdat$condsampcnt
states <- GBpopdat$states
invyrs <- GBpopdat$invyrs
stratcombinelut <- GBpopdat$stratcombinelut
strwtvar <- GBpopdat$strwtvar
adj <- GBpopdat$adj
strunitvars <- c(unitvar, strvar)
strata <- GBpopdat$strata
pop_fmt <- GBpopdat$pop_fmt
pop_dsn <- GBpopdat$pop_dsn
########################################
## Check area units
########################################
unitchk <- pcheck.areaunits(unitarea=unitarea, areavar=areavar,
areaunits=areaunits, metric=metric)
unitarea <- unitchk$unitarea
areavar <- unitchk$areavar
areaunits <- unitchk$outunits
if (is.null(key(unitarea))) {
setkeyv(unitarea, unitvar)
}
###################################################################################
## Check parameters and apply plot and condition filters
###################################################################################
estdat <- check.estdata(esttype=esttype, pop_fmt=pop_fmt, pop_dsn=pop_dsn,
pltcondf=pltcondx, cuniqueid=cuniqueid, condid=condid,
treex=treex, seedx=seedx, estseed=estseed, woodland=woodland,
sumunits=sumunits, landarea=landarea, ACI.filter=ACI.filter,
pcfilter=pcfilter, allin1=allin1,
estround=estround, pseround=pseround, divideby=divideby,
addtitle=addtitle, returntitle=returntitle,
rawdata=rawdata, rawonly=rawonly, savedata=savedata,
outfolder=outfolder, overwrite_dsn=overwrite_dsn,
overwrite_layer=overwrite_layer, outfn.pre=outfn.pre,
outfn.date=outfn.date, append_layer=append_layer,
raw_fmt=raw_fmt, raw_dsn=raw_dsn, gui=gui)
if (is.null(estdat)) return(NULL)
pltcondf <- estdat$pltcondf
cuniqueid <- estdat$cuniqueid
treef <- estdat$treef
seedf <- estdat$seedf
tuniqueid <- estdat$tuniqueid
estseed <- estdat$estseed
woodland <- estdat$woodland
sumunits <- estdat$sumunits
landarea <- estdat$landarea
allin1 <- estdat$allin1
estround <- estdat$estround
pseround <- estdat$pseround
divideby <- estdat$divideby
addtitle <- estdat$addtitle
returntitle <- estdat$returntitle
rawdata <- estdat$rawdata
rawonly <- estdat$rawonly
savedata <- estdat$savedata
outfolder <- estdat$outfolder
overwrite_layer <- estdat$overwrite_layer
append_layer <- estdat$append_layer
raw_fmt <- estdat$raw_fmt
raw_dsn <- estdat$raw_dsn
rawfolder <- estdat$rawfolder
conn <- estdat$conn
if ("STATECD" %in% names(pltcondf)) {
states <- pcheck.states(sort(unique(pltcondf$STATECD)))
}
if ("INVYR" %in% names(pltcondf)) {
invyr <- sort(unique(pltcondf$INVYR))
}
#############################################################################
### Check row and column data
#############################################################################
rowcolinfo <- check.rowcol(gui=gui, esttype=esttype, conn=conn,
treef=treef, seedf=seedf,
condf=pltcondf, cuniqueid=cuniqueid,
tuniqueid=tuniqueid, estseed=estseed,
rowvar=rowvar, colvar=colvar,
row.FIAname=row.FIAname, col.FIAname=col.FIAname,
row.orderby=row.orderby, col.orderby=col.orderby,
row.add0=row.add0, col.add0=col.add0,
title.rowvar=title.rowvar, title.colvar=title.colvar,
rowlut=rowlut, collut=collut, rowgrp=rowgrp,
rowgrpnm=rowgrpnm, rowgrpord=rowgrpord,
landarea=landarea, states=states)
treef <- rowcolinfo$treef
seedf <- rowcolinfo$seedf
condf <- rowcolinfo$condf
uniquerow <- rowcolinfo$uniquerow
uniquecol <- rowcolinfo$uniquecol
domainlst <- rowcolinfo$domainlst
rowvar <- rowcolinfo$rowvar
colvar <- rowcolinfo$colvar
row.orderby <- rowcolinfo$row.orderby
col.orderby <- rowcolinfo$col.orderby
row.add0 <- rowcolinfo$row.add0
col.add0 <- rowcolinfo$col.add0
title.rowvar <- rowcolinfo$title.rowvar
title.colvar <- rowcolinfo$title.colvar
rowgrpnm <- rowcolinfo$rowgrpnm
title.rowgrp <- rowcolinfo$title.rowgrp
bytdom <- rowcolinfo$bytdom
tdomvar <- rowcolinfo$tdomvar
tdomvar2 <- rowcolinfo$tdomvar2
grpvar <- rowcolinfo$grpvar
#rm(rowcolinfo)
## Generate a uniquecol for estimation units
if (!sumunits && colvar == "NONE") {
uniquecol <- data.table(unitarea[[unitvar]])
setnames(uniquecol, unitvar)
uniquecol[[unitvar]] <- factor(uniquecol[[unitvar]])
}
###############################################################################
### Get estimation data from tree table
###############################################################################
adjtree <- ifelse(adj %in% c("samp", "plot"), TRUE, FALSE)
treedat <- check.tree(gui=gui, treef=treef, seedf=seedf, estseed=estseed,
bycond=TRUE, condf=condf, bytdom=bytdom,
tuniqueid=tuniqueid, cuniqueid=cuniqueid,
esttype=esttype, estvarn=estvar, estvarn.filter=estvar.filter,
esttotn=TRUE, tdomvar=tdomvar, tdomvar2=tdomvar2,
adjtree=adjtree, metric=metric, woodland=woodland)
if (is.null(treedat)) return(NULL)
tdomdat <- treedat$tdomdat
if (rowvar != "TOTAL") {
#if (!row.add0) {
if (any(is.na(tdomdat[[rowvar]]))) {
if (!row.FIAname) {
rval <- ifelse (any(!is.na(tdomdat[[rowvar]]) & tdomdat[[rowvar]] == 0), max(tdomdat[[rowvar]], na.rm=TRUE), 0)
tdomdat[is.na(tdomdat[[rowvar]]), rowvar] <- rval
levels(uniquerow[[rowvar]]) <- c(levels(uniquerow[[rowvar]]), as.character(rval))
uniquerow[is.na(uniquerow[[rowvar]]), rowvar] <- as.character(rval)
} else {
tdomdat <- tdomdat[!is.na(tdomdat[[rowvar]]), ]
}
}
#}
if (colvar != "NONE") {
#if (!col.add0) {
if (any(is.na(tdomdat[[colvar]]))) {
if (!col.FIAname) {
cval <- ifelse (any(!is.na(tdomdat[[colvar]]) & tdomdat[[colvar]] == 0), max(tdomdat[[colvar]], na.rm=TRUE), 0)
tdomdat[is.na(tdomdat[[colvar]]), colvar] <- cval
levels(uniquecol[[colvar]]) <- c(levels(uniquecol[[colvar]]), as.character(cval))
uniquecol[is.na(uniquecol[[colvar]]), colvar] <- as.character(cval)
} else {
tdomdat <- tdomdat[!is.na(tdomdat[[colvar]]), ]
}
}
#}
}
}
## Merge tdomdat with condx
xchk <- check.matchclass(condx, tdomdat, c(cuniqueid, condid))
condx <- xchk$tab1
tdomdat <- xchk$tab2
tdomdat <- merge(condx, tdomdat, by=c(cuniqueid, condid))
estvar <- treedat$estvar
estvar.name <- treedat$estvar.name
estvar.filter <- treedat$estvar.filter
tdomvarlst <- treedat$tdomvarlst
estunits <- treedat$estunits
###############################################################################
### Get titles for output tables
###############################################################################
alltitlelst <- check.titles(dat=tdomdat, esttype=esttype,
estseed=estseed, woodland=woodland,
sumunits=sumunits, title.main=title.main, title.ref=title.ref,
title.rowvar=title.rowvar, title.rowgrp=title.rowgrp,
title.colvar=title.colvar, title.unitvar=title.unitvar,
title.filter=title.filter, title.unitsn=estunits,
title.estvarn=title.estvar,
unitvar=unitvar, rowvar=rowvar, colvar=colvar,
estvarn=estvar, estvarn.filter=estvar.filter,
addtitle=addtitle, returntitle=returntitle,
rawdata=rawdata, states=states, invyrs=invyrs,
landarea=landarea, pcfilter=pcfilter, allin1=allin1,
divideby=divideby, outfn.pre=outfn.pre)
title.unitvar <- alltitlelst$title.unitvar
title.est <- alltitlelst$title.est
title.pse <- alltitlelst$title.pse
title.estpse <- alltitlelst$title.estpse
title.ref <- alltitlelst$title.ref
outfn.estpse <- alltitlelst$outfn.estpse
outfn.param <- alltitlelst$outfn.param
if (rawdata) {
outfn.rawdat <- alltitlelst$outfn.rawdat
}
############################################################################
## GENERATE ESTIMATES
############################################################################
unit_totest=unit_rowest=unit_colest=unit_grpest=rowunit=totunit=tdomdattot <- NULL
addtotal <- ifelse(((rowvar == "TOTAL" || length(unique(tdomdat[[rowvar]])) > 1) ||
(!is.null(tdomvarlst) && length(tdomvarlst) > 1)), TRUE, FALSE)
stratalut <- setDT(stratalut)
## Note: tdomdat is the summed response by condition (not domain)
#if (addtotal) {
## Get estimate for total
tdomdattot <- tdomdat[, lapply(.SD, sum, na.rm=TRUE),
by=c(strunitvars, cuniqueid, "TOTAL"), .SDcols=estvar.name]
unit_totest <- GBest.pbar(sumyn = estvar.name,
ysum = tdomdattot,
esttype = esttype,
uniqueid = cuniqueid,
stratalut = stratalut,
unitvar = unitvar,
strvar = strvar,
domain = "TOTAL")
tabs <- check.matchclass(unitarea, unit_totest, unitvar)
unitarea <- tabs$tab1
unit_totest <- tabs$tab2
setkeyv(unit_totest, unitvar)
unit_totest <- unit_totest[unitarea, nomatch=0]
if (totals) {
unit_totest <- getpse(unit_totest, areavar=areavar, esttype=esttype)
} else {
unit_totest <- getpse(unit_totest, esttype=esttype)
}
#}
## Get row, column, cell estimate and merge area if row or column in cond table
if (rowvar != "TOTAL") {
tdomdatsum <- tdomdat[, lapply(.SD, sum, na.rm=TRUE),
by=c(strunitvars, cuniqueid, rowvar), .SDcols=estvar.name]
tdomdatsum <- tdomdatsum[!is.na(tdomdatsum[[rowvar]]),]
unit_rowest <- GBest.pbar(sumyn = estvar.name,
ysum = tdomdatsum,
uniqueid = cuniqueid,
stratalut = stratalut,
unitvar = unitvar,
strvar = strvar,
domain = rowvar)
if (colvar != "NONE") {
tdomdatsum <- tdomdat[, lapply(.SD, sum, na.rm=TRUE),
by=c(strunitvars, cuniqueid, colvar), .SDcols=estvar.name]
tdomdatsum <- tdomdatsum[!is.na(tdomdatsum[[colvar]]),]
unit_colest <- GBest.pbar(sumyn = estvar.name,
ysum = tdomdatsum,
uniqueid = cuniqueid,
stratalut = stratalut,
unitvar = unitvar,
strvar = strvar,
domain = colvar)
tdomdatsum <- tdomdat[, lapply(.SD, sum, na.rm=TRUE),
by=c(strunitvars, cuniqueid, grpvar), .SDcols=estvar.name]
unit_grpest <- GBest.pbar(sumyn =estvar.name,
ysum = tdomdatsum,
uniqueid = cuniqueid,
stratalut = stratalut,
unitvar = unitvar,
strvar = strvar,
domain = grpvar)
}
}
###################################################################################
## Check add0 and Add area
###################################################################################
if (!sumunits && nrow(unitarea) > 1) col.add0 <- TRUE
if (!is.null(unit_rowest)) {
unit_rowest <- add0unit(x=unit_rowest, xvar=rowvar,
uniquex=uniquerow, unitvar=unitvar,
xvar.add0=row.add0)
tabs <- check.matchclass(unitarea, unit_rowest, unitvar)
unitarea <- tabs$tab1
unit_rowest <- tabs$tab2
if (!is.null(row.orderby) && row.orderby != "NONE") {
setorderv(unit_rowest, c(row.orderby))
}
setkeyv(unit_rowest, unitvar)
unit_rowest <- unit_rowest[unitarea, nomatch=0]
if (totals) {
unit_rowest <- getpse(unit_rowest, areavar=areavar, esttype=esttype)
} else {
unit_rowest <- getpse(unit_rowest, esttype=esttype)
}
setkeyv(unit_rowest, c(unitvar, rowvar))
}
if (!is.null(unit_colest)) {
unit_colest <- add0unit(x=unit_colest, xvar=colvar,
uniquex=uniquecol, unitvar=unitvar,
xvar.add0=col.add0)
tabs <- check.matchclass(unitarea, unit_colest, unitvar)
unitarea <- tabs$tab1
unit_colest <- tabs$tab2
if (!is.null(col.orderby) && col.orderby != "NONE") {
setorderv(unit_colest, c(col.orderby))
}
setkeyv(unit_colest, unitvar)
unit_colest <- unit_colest[unitarea, nomatch=0]
if (totals) {
unit_colest <- getpse(unit_colest, areavar=areavar, esttype=esttype)
} else {
unit_colest <- getpse(unit_colest, esttype=esttype)
}
setkeyv(unit_colest, c(unitvar, colvar))
}
if (!is.null(unit_grpest)) {
unit_grpest <- add0unit(x=unit_grpest, xvar=rowvar,
uniquex=uniquerow, unitvar=unitvar,
xvar.add0=row.add0, xvar2=colvar,
uniquex2=uniquecol, xvar2.add0=col.add0)
tabs <- check.matchclass(unitarea, unit_grpest, unitvar)
unitarea <- tabs$tab1
unit_grpest <- tabs$tab2
if (!is.null(row.orderby) && row.orderby != "NONE") {
if (!is.null(col.orderby) && col.orderby != "NONE") {
setorderv(unit_grpest, c(row.orderby, col.orderby))
} else {
setorderv(unit_grpest, c(row.orderby))
}
} else if (!is.null(col.orderby) && col.orderby != "NONE") {
setorderv(unit_grpest, c(col.orderby))
}
setkeyv(unit_grpest, unitvar)
unit_grpest <- unit_grpest[unitarea, nomatch=0]
if (totals) {
unit_grpest <- getpse(unit_grpest, areavar=areavar, esttype=esttype)
} else {
unit_grpest <- getpse(unit_grpest, esttype=esttype)
}
setkeyv(unit_grpest, c(unitvar, rowvar, colvar))
}
###################################################################################
## Get row and column totals for units if sumunits=FALSE
###################################################################################
## For sumunits=FALSE, get estimation unit totals
if (!sumunits && (length(unique(unitarea[[unitvar]])) > 1 && rowvar != "TOTAL")) {
## AGGREGATE UNIT stratalut FOR ROWVAR and GRAND TOTAL
stratalut2 <- data.table(stratalut, ONEUNIT=1)
strunitvars2 <- c("ONEUNIT", strvar)
stratalut2 <- stratalut2[, lapply(.SD, sum, na.rm=TRUE),
by=strunitvars2, .SDcols=c(strwtvar, "n.strata")]
stratalut2[, strwt:=prop.table(get(strwtvar)), by="ONEUNIT"]
stratalut2[, n.total := sum(n.strata)]
setkeyv(stratalut2, strunitvars2)
unitarea2 <- data.table(unitarea, ONEUNIT=1)
unitarea2 <- unitarea2[, lapply(.SD, sum, na.rm=TRUE), by="ONEUNIT",
.SDcols=areavar]
setkey(unitarea2, "ONEUNIT")
tdomdat[, ONEUNIT := 1]
## Calculate unit totals for rowvar
tdomdatsum <- tdomdat[, lapply(.SD, sum, na.rm=TRUE),
by=c(strunitvars2, tuniqueid, rowvar), .SDcols=estvar.name]
rowunit <- GBest.pbar(sumyn = estvar.name,
ysum = tdomdatsum,
esttype = esttype,
uniqueid = tuniqueid,
stratalut = stratalut2,
unitvar = "ONEUNIT",
strvar = strvar,
domain = rowvar)
rowunit <- add0unit(x=rowunit, xvar=rowvar,
uniquex=uniquerow, unitvar="ONEUNIT",
xvar.add0=row.add0)
tabs <- check.matchclass(unitarea2, rowunit, "ONEUNIT")
unitarea2 <- tabs$tab1
rowunit <- tabs$tab2
setkeyv(rowunit, "ONEUNIT")
rowunit <- rowunit[unitarea2, nomatch=0]
if (totals) {
rowunit <- getpse(rowunit, areavar=areavar, esttype=esttype)
} else {
rowunit <- getpse(rowunit, esttype=esttype)
}
setkeyv(rowunit, c("ONEUNIT", rowvar))
## Calculate grand total for all units
tdomdatsum <- tdomdat[, lapply(.SD, sum, na.rm=TRUE),
by=c(strunitvars2, tuniqueid, "TOTAL"), .SDcols=estvar.name]
totunit <- GBest.pbar(sumyn = estvar.name,
ysum = tdomdatsum,
esttype = esttype,
uniqueid = tuniqueid,
stratalut = stratalut2,
unitvar = "ONEUNIT",
strvar = strvar,
domain = "TOTAL")
tabs <- check.matchclass(unitarea2, totunit, "ONEUNIT")
unitarea2 <- tabs$tab1
totunit <- tabs$tab2
setkeyv(totunit, "ONEUNIT")
totunit <- totunit[unitarea2, nomatch=0]
if (totals) {
totunit <- getpse(totunit, areavar=areavar, esttype=esttype)
} else {
totunit <- getpse(totunit, esttype=esttype)
}
}
###################################################################################
## GENERATE OUTPUT TABLES
###################################################################################
message("getting output...")
estnm <- "est"
tabs <- est.outtabs(esttype=esttype, sumunits=sumunits, areavar=areavar,
unitvar=unitvar, unitvars=unitvars, unit_totest=unit_totest,
unit_rowest=unit_rowest, unit_colest=unit_colest, unit_grpest=unit_grpest,
rowvar=rowvar, colvar=colvar, uniquerow=uniquerow, uniquecol=uniquecol,
rowgrp=rowgrp, rowgrpnm=rowgrpnm, rowunit=rowunit, totunit=totunit,
allin1=allin1, savedata=savedata, addtitle=addtitle, title.ref=title.ref,
title.colvar=title.colvar, title.rowvar=title.rowvar, title.rowgrp=title.rowgrp,
title.unitvar=title.unitvar, title.estpse=title.estpse, title.est=title.est,
title.pse=title.pse, rawdata=rawdata, rawonly=rawonly, outfn.estpse=outfn.estpse,
outfolder=outfolder, outfn.date=outfn.date, overwrite=overwrite_layer,
estnm=estnm, estround=estround, pseround=pseround, divideby=divideby,
returntitle=returntitle, estnull=estnull, psenull=psenull, raw.keep0=raw.keep0)
est2return <- tabs$tabest
pse2return <- tabs$tabpse
if (!is.null(est2return)) {
returnlst$est <- setDF(est2return)
}
if (!is.null(pse2return)) {
returnlst$pse <- setDF(pse2return)
}
if(returntitle) {
returnlst$titlelst <- alltitlelst
}
if (rawdata) {
rawdat <- tabs$rawdat
rawdat$domdat <- setDF(tdomdat)
rawdat$estvar <- estvar.name
rawdat$estvar.filter <- estvar.filter
if (savedata) {
if (!is.null(title.estpse)) {
title.raw <- paste(title.estpse, title.ref)
} else {
title.raw <- title.est
}
for (i in 1:length(rawdat)) {
tabnm <- names(rawdat[i])
rawtab <- rawdat[[i]]
outfn.rawtab <- paste0(outfn.rawdat, "_", tabnm)
if (tabnm %in% c("plotsampcnt", "condsampcnt", "stratcombinelut")) {
write2csv(rawtab, outfolder=rawfolder, outfilenm=outfn.rawtab,
outfn.date=outfn.date, overwrite=overwrite_layer)
} else if (is.data.frame(rawtab)) {
if (raw_fmt != "csv") {
out_layer <- tabnm
} else {
out_layer <- outfn.rawtab
}
datExportData(rawtab,
savedata_opts=list(outfolder=rawfolder,
out_fmt=raw_fmt,
out_dsn=raw_dsn,
out_layer=out_layer,
overwrite_layer=overwrite_layer,
append_layer=append_layer,
add_layer=TRUE)
)
}
}
}
rawdat$module <- "GB"
rawdat$esttype <- esttype
rawdat$GBmethod <- ifelse(strata, "PS", "HT")
rawdat$estvar <- estvar
rawdat$estvar.filter <- estvar.filter
if (!is.null(rowvar)) rawdat$rowvar <- rowvar
if (!is.null(colvar)) rawdat$colvar <- colvar
rawdat$areaunits <- areaunits
rawdat$estunits <- estunits
returnlst$raw <- rawdat
}
if ("STATECD" %in% names(pltcondf)) {
returnlst$statecd <- sort(unique(pltcondf$STATECD))
}
if ("INVYR" %in% names(pltcondf)) {
returnlst$invyr <- sort(unique(pltcondf$INVYR))
}
return(returnlst)
}
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