R/modMAtree.R
In USDAForestService/FIESTA: Forest Inventory Estimation and Analysis
Defines functions
modMAtree
Documented in
modMAtree
#' Model-Assisted module - Generate model-assisted tree estimates.
#'
#' Generates tree estimates by estimation unit. Estimates are calculated from
#' McConville et al. (2018)'s mase R package.
#'
#' 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 (e.g. 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 (e.g., 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
#' identifier 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 }
#'
#' Reference names are available for the following variables: \cr ADFORCD,
#' AGENTCD, CCLCD, DECAYCD, DSTRBCD, KINDCD, OWNCD, OWNGRPCD, FORTYPCD,
#' FLDTYPCD, FORTYPCDCALC, TYPGRPCD, FORINDCD, RESERVCD, LANDCLCD, STDSZCD,
#' FLDSZCD, PHYSCLCD, MIST_CL_CD, PLOT_STATUS_CD, STATECD, TREECLCD, TRTCD,
#' SPCD, SPGRPCD
#'
#' @param MApopdat List. Population data objects returned from modMApop().
#' @param MAmethod String. mase (i.e., model-assisted) method to use
#' ('greg', 'gregEN', 'ratio').
#' @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 estvar.derive List. A derivation of a tree variable to estimate.
#' Must be a named list with one element (e.g.,
#' list(SDI='SUM(POWER(DIA/10,1.605) * TPA_UNADJ)'). Set estvar = NULL.
#' @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 prednames String vector. Name(s) of predictor variables to include in
#' model.
#' @param modelselect Logical. If TRUE, an elastic net regression model is fit
#' to the entire plot level data, and the variables selected in that model are
#' used for the proceeding estimation.
#' @param FIA Logical. If TRUE, the finite population term is removed from
#' estimator to match FIA estimates.
#' @param bootstrap Logical. If TRUE, returns bootstrap variance estimates,
#' otherwise uses Horvitz-Thompson estimator under simple random sampling
#' without replacement.
#' @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 modelselect_bydomain Logical. If TRUE, modelselection will occur at
#' the domain level as specified by rowvar and/or colvar and not at the level of
#' the entire sample.
#' @param ... Parameters for modMApop() if MApopdat is NULL.
#' @return If FIA=TRUE or unitvar=NULL and colvar=NULL, one data frame is
#' returned with tree estimates and percent sample errors. Otherwise, a list is
#' returned with tree estimates in one data frame (est) and percent sample
#' errors in another data frame (est.pse). If rawdata=TRUE, another list is
#' returned including raw data used in the estimation process. If
#' addtitle=TRUE and returntitle=TRUE, the title for est/pse is returned. If
#' savedata=TRUE, all data frames are written to outfolder.
#'
#' \item{est}{ Data frame. Tree estimates by rowvar, colvar (and estimation
#' unit). If FIA=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 for estimates by rowvar and colvar (and estimation
#' unit). } \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: number of plots by plot status, if in dataset (plotsampcnt);
#' number of conditions by condition status (condsampcnt); data used for
#' post-stratification (stratdat); and 1-8 tables with calculated variables
#' used for processing estimates and percent sampling error for table cell
#' values 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{stratdat}{ Data frame. Strata information by estimation unit. }
#' \tabular{lll}{ \tab \bold{Variable} \tab \bold{Description}\cr \tab ESTUNIT
#' \tab estimation unit\cr \tab STRATA \tab strata \cr \tab ACRES \tab area by
#' strata for estimation unit\cr \tab n.strata \tab number of plots in strata
#' (and estimation unit) \cr \tab n.total \tab number of plots for estimation
#' unit \cr \tab TOTACRES \tab total area for estimation unit \cr \tab strwt
#' \tab proportion of area (or number of plots) by strata (strata weight) \cr
#' \tab expfac.strata \tab expansion factor (in area unit (e.g., acres) by
#' strata (areavar/n.strata) \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 FIA=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 estimated variance of estimated
#' proportion of trees \cr \tab ACRES \tab total area for estimation unit \cr
#' \tab est \tab estimated area of trees nhat*ACRES \cr \tab est.var \tab
#' estimated variance 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.
#'
#' autoxreduce:\cr If MAmethod='GREG', and autoxreduce=TRUE, and there is an
#' error because of multicolinearity, a variable reduction method is applied to
#' remove correlated variables. The method used is based on the
#' variance-inflation factor (vif) from a linear model. The vif estimates how
#' much the variance of each x variable is inflated due to mulitcolinearity in
#' the model.
#'
#' 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
#' @references Kelly McConville, Becky Tang, George Zhu, Shirley Cheung, and
#' Sida Li (2018). mase: Model-Assisted Survey Estimation. R package version
#' 0.1.2 https://cran.r-project.org/package=mase
#' @keywords data
#' @examples
#' \donttest{
#' # Set up population dataset (see ?modMApop() for more information)
#' MApopdat <- modMApop(popTabs = list(tree = FIESTA::WYtree,
#' cond = FIESTA::WYcond),
#' pltassgn = FIESTA::WYpltassgn,
#' pltassgnid = "CN",
#' unitarea = FIESTA::WYunitarea,
#' unitvar = "ESTN_UNIT",
#' unitzonal = FIESTA::WYunitzonal,
#' prednames = c("dem", "tcc", "tpi", "tnt"),
#' predfac = "tnt")
#'
#' # Use GREG Estimator to Estimate cubic foot volume of live trees in our
#' # population
#' mod1 <- modMAtree(MApopdat = MApopdat,
#' MAmethod = "greg",
#' estvar = "VOLCFNET",
#' estvar.filter = "STATUSCD == 1")
#'
#' str(mod1)
#' }
#' @export modMAtree
modMAtree <- function(MApopdat,
MAmethod,
estvar,
estvar.filter = NULL,
estvar.derive = NULL,
estseed = "none",
woodland = "Y",
landarea = "FOREST",
pcfilter = NULL,
rowvar = NULL,
colvar = NULL,
prednames = NULL,
modelselect = FALSE,
FIA = TRUE,
bootstrap = FALSE,
returntitle = FALSE,
savedata = FALSE,
table_opts = NULL,
title_opts = NULL,
savedata_opts = NULL,
modelselect_bydomain = FALSE,
...){
##################################################################################
## DESCRIPTION:
## Generates model-assisted estimates by domain (and estimation unit)
##################################################################################
gui <- FALSE
## If gui.. set variables to NULL
if (gui) {
tree=landarea=strvar=areavar <- NULL
if (!row.FIAname) row.FIAname <- NULL
if (!col.FIAname) col.FIAname <- NULL
}
## Set parameters
esttype <- "TREE"
popType <- "VOL"
rawdata <- TRUE
sumunits <- FALSE
returnlst <- list()
## Set global variables
ONEUNIT=n.total=n.strata=strwt=TOTAL=domclassify<- NULL
##################################################################
## CHECK PARAMETER NAMES
##################################################################
## Check input parameters
input.params <- names(as.list(match.call()))[-1]
formallst <- c(names(formals(modMAtree)),
names(formals(modMApop)))
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 = input.params,
title_opts = title_opts,
table_opts = table_opts,
savedata_opts = savedata_opts)
## Check parameter option lists
optslst <- pcheck.opts(optionlst = list(
title_opts = title_opts,
table_opts = table_opts,
savedata_opts = savedata_opts))
title_opts <- optslst$title_opts
table_opts <- optslst$table_opts
savedata_opts <- optslst$savedata_opts
for (i in 1:length(title_opts)) {
assign(names(title_opts)[[i]], title_opts[[i]])
}
for (i in 1:length(table_opts)) {
assign(names(table_opts)[[i]], table_opts[[i]])
}
##################################################################
## CHECK PARAMETER INPUTS
##################################################################
## Check MAmethod
MAmethodlst <- c("greg", "gregEN", "ratio")
MAmethod <- pcheck.varchar(var2check=MAmethod, varnm="MAmethod", gui=gui,
checklst=MAmethodlst, caption="MAmethod", multiple=FALSE, stopifnull=TRUE)
if (MAmethod %in% c("greg", "gregEN")) {
predselectlst <- list()
}
###################################################################################
## Check data and generate population information
###################################################################################
list.items <- c("pltcondx", "cuniqueid", "condid",
"treex", "tuniqueid",
"unitarea", "unitvar", "unitlut", "npixels",
"npixelvar", "plotsampcnt", "condsampcnt")
MApopdat <- pcheck.object(MApopdat, "MApopdat", list.items=list.items)
if (is.null(MApopdat)) return(NULL)
pltidsadj <- MApopdat$pltidsadj
pltcondx <- MApopdat$pltcondx
cuniqueid <- MApopdat$cuniqueid
pltassgnid <- MApopdat$pltassgnid
condid <- MApopdat$condid
treex <- MApopdat$treex
seedx <- MApopdat$seedx
if (is.null(treex) && is.null(seedx)) {
stop("must include tree data for tree estimates")
}
tuniqueid <- MApopdat$tuniqueid
ACI <- MApopdat$ACI
pltassgnx <- MApopdat$pltassgnx
unitarea <- MApopdat$unitarea
areavar <- MApopdat$areavar
areaunits <- MApopdat$areaunits
unitvar <- MApopdat$unitvar
unitlut <- MApopdat$unitlut
unitvars <- MApopdat$unitvars
npixels <- MApopdat$npixels
npixelvar <- MApopdat$npixelvar
expcondtab <- MApopdat$expcondtab
plotsampcnt <- MApopdat$plotsampcnt
condsampcnt <- MApopdat$condsampcnt
states <- MApopdat$states
invyrs <- MApopdat$invyrs
predfac <- MApopdat$predfac
adj <- MApopdat$adj
popdatindb <- MApopdat$popdatindb
pop_fmt <- MApopdat$pop_fmt
pop_dsn <- MApopdat$pop_dsn
pop_schema <- MApopdat$pop_schema
popconn <- MApopdat$popconn
dbqueries <- MApopdat$dbqueries
dbqueriesWITH <- MApopdat$dbqueriesWITH
adjcase <- MApopdat$adjcase
pltidsid <- MApopdat$pjoinid
pltassgnid <- MApopdat$pltassgnid
pltcondflds <- MApopdat$pltcondflds
if (MAmethod %in% c("greg", "gregEN", "ratio")) {
if (is.null(prednames)) {
prednames <- MApopdat$prednames
} else {
if (!all(prednames %in% MApopdat$prednames)) {
if (any(prednames %in% MApopdat$predfac)) {
predfacnames <- prednames[prednames %in% MApopdat$predfac]
for (nm in predfacnames) {
prednames[prednames == nm] <- MApopdat$prednames[grepl(nm, MApopdat$prednames)]
}
} else {
stop("invalid prednames... must be in: ", toString(MApopdat$prednames))
}
}
}
}
if (popdatindb) {
if (is.null(popconn) || !DBI::dbIsValid(popconn)) {
if (!is.null(pop_dsn)) {
if (pop_fmt == "sqlite") {
popconn <- DBtestSQLite(pop_dsn, dbconnopen = TRUE)
}
} else {
stop("invalid database connection")
}
}
#pltcondx <- dbqueries$pltcondx
pltcondxWITHqry <- dbqueriesWITH$pltcondxWITH
pltcondxadjWITHqry <- dbqueriesWITH$pltcondxadjWITH
} else {
pltcondxWITHqry <- NULL
pltcondxWITHqry=pltcondxadjWITHqry <- NULL
}
########################################
## Check area units
########################################
unitchk <- pcheck.areaunits(unitarea=unitarea, areavar=areavar,
areaunits=areaunits, metric=metric)
unitarea <- unitchk$unitarea
areavar <- unitchk$areavar
areaunits <- unitchk$outunits
if (is.null(key(unitarea))) {
setkeyv(unitarea, unitvar)
}
###################################################################################
## Check parameters and apply plot and condition filters
###################################################################################
estdat <-
check.estdata(esttype = esttype,
popType = popType,
popdatindb = popdatindb,
popconn = popconn, pop_schema = pop_schema,
pltcondx = pltcondx,
pltcondflds = pltcondflds,
totals = totals,
pop_fmt=pop_fmt, pop_dsn=pop_dsn,
landarea = landarea,
ACI = ACI,
pcfilter = pcfilter,
allin1 = allin1, divideby = divideby,
estround = estround, pseround = pseround,
returntitle = returntitle,
rawonly = rawonly,
savedata = savedata,
savedata_opts = savedata_opts,
gui = gui)
if (is.null(estdat)) return(NULL)
esttype <- estdat$esttype
totals <- estdat$totals
landarea <- estdat$landarea
allin1 <- estdat$allin1
divideby <- estdat$divideby
estround <- estdat$estround
pseround <- estdat$pseround
addtitle <- estdat$addtitle
returntitle <- estdat$returntitle
rawonly <- estdat$rawonly
savedata <- estdat$savedata
outfolder <- estdat$outfolder
overwrite_layer <- estdat$overwrite_layer
outfn.pre <- estdat$outfn.pre
outfn.date <- estdat$outfn.date
append_layer = estdat$append_layer
rawfolder <- estdat$rawfolder
raw_fmt <- estdat$raw_fmt
raw_dsn <- estdat$raw_dsn
pcwhereqry <- estdat$where.qry
SCHEMA. <- estdat$SCHEMA.
pltcondflds <- estdat$pltcondflds
###################################################################################
## Check parameter inputs and tree filters
###################################################################################
estdatVOL <-
check.estdataVOL(esttype = esttype,
popdatindb = popdatindb,
popconn = popconn,
cuniqueid = cuniqueid, condid = condid,
treex = treex, seedx = seedx,
tuniqueid = tuniqueid,
estseed = estseed,
woodland = woodland,
gui = gui)
treex <- estdatVOL$treex
treeflds <- estdatVOL$treeflds
tuniqueid <- estdatVOL$tuniqueid
estseed <- estdatVOL$estseed
woodland <- estdatVOL$woodland
seedx <- estdatVOL$seedx
seedflds <- estdatVOL$seedflds
###################################################################################
### Check row and column data
###################################################################################
rowcolinfo <-
check.rowcol(esttype = esttype,
popType = popType,
popdatindb = popdatindb,
popconn = popconn, SCHEMA. = SCHEMA.,
pltcondx = pltcondx,
pltcondflds = pltcondflds,
withqry = pltcondxWITHqry,
estseed = estseed,
treex = treex, treeflds = treeflds,
seedx = seedx, seedflds = seedflds,
cuniqueid = cuniqueid, condid = condid,
rowvar = rowvar, colvar = colvar,
row.FIAname = row.FIAname, col.FIAname = col.FIAname,
row.orderby = row.orderby, col.orderby = col.orderby,
row.classify = row.classify, col.classify = col.classify,
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, title.rowgrp = NULL,
whereqry = pcwhereqry)
uniquerow <- rowcolinfo$uniquerow
uniquecol <- rowcolinfo$uniquecol
domainlst <- rowcolinfo$domainlst
rowvar <- rowcolinfo$rowvar
colvar <- rowcolinfo$colvar
rowvarnm <- rowcolinfo$rowvarnm
colvarnm <- rowcolinfo$colvarnm
row.orderby <- rowcolinfo$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$title.rowgrp
grpvar <- rowcolinfo$grpvar
bytdom <- rowcolinfo$bytdom
bypcdom <- rowcolinfo$bypcdom
tdomvar <- rowcolinfo$tdomvar
tdomvar2 <- rowcolinfo$tdomvar2
classifyrow <- rowcolinfo$classifyrow
classifycol <- rowcolinfo$classifycol
#rm(rowcolinfo)
## if classified columns, create domclassify list for summarizing tree data
if (any(!is.null(classifyrow), !is.null(classifycol))) {
domclassify <- list()
if (!is.null(classifyrow)) {
domclassify[[rowvar]] <- classifyrow$row.classify
}
if (!is.null(classifycol)) {
domclassify[[colvar]] <- classifycol$col.classify
}
}
#################################################################################
### GET ESTIMATION DATA FROM TREE TABLE
#################################################################################
adjtree <- ifelse(adj %in% c("samp", "plot"), TRUE, FALSE)
if (popdatindb) {
pltidsWITHqry <- dbqueriesWITH$pltcondxadjWITH
} else {
pltidsWITHqry <- NULL
}
treedat <-
check.tree(treex = treex,
seedx = seedx,
estseed = estseed,
bycond = TRUE,
condx = pltcondx,
tuniqueid = tuniqueid, cuniqueid = cuniqueid,
esttype = esttype,
estvarn = estvar,
estvarn.filter = estvar.filter,
estvarn.derive = estvar.derive,
esttotn = TRUE,
bydomainlst = c(domainlst, "TOTAL"),
tdomvar = tdomvar, tdomvar2 = tdomvar2,
adjtree = adjtree,
adjvar = "tadjfac",
metric = metric,
woodland = woodland,
ACI = ACI,
domclassify = domclassify,
dbconn = popconn, schema = pop_schema,
pltidsWITHqry = pltidsWITHqry,
pcwhereqry = pcwhereqry,
pltidsid = pltidsid,
bytdom = bytdom,
gui = gui)
if (is.null(treedat)) stop(NULL)
tdomdat <- treedat$tdomdat
estvar <- treedat$estvar
estvar.name <- treedat$estvar.name
estvar.filter <- treedat$estvar.filter
tdomvarlst <- treedat$tdomvarlst
estunits <- treedat$estunits
treeqry <- treedat$treeqry
classifynmlst <- treedat$classifynmlst
## If classified rowvar or colvar, get class names
if (!is.null(classifynmlst)) {
if (!is.null(classifynmlst[[rowvar]])) {
rowvar <- classifynmlst[[rowvar]]
}
if (!is.null(classifynmlst[[colvar]])) {
colvar <- classifynmlst[[colvar]]
}
if (!is.null(grpvar)) {
grpvar <- c(rowvar, colvar)
}
}
#################################################################################
### GET TITLES FOR OUTPUT TABLES
#################################################################################
alltitlelst <-
check.titles(dat = tdomdat,
esttype = esttype,
estseed = estseed,
woodland = woodland,
sumunits = sumunits,
title.main = title.main,
title.ref = title.ref,
title.rowvar = title.rowvar,
title.rowgrp = title.rowgrp,
title.colvar = title.colvar,
title.unitvar = title.unitvar,
title.filter = title.filter,
title.unitsn = estunits,
title.estvarn = title.estvar,
unitvar = unitvar,
rowvar = rowvar, colvar = colvar,
estvarn = estvar,
estvarn.filter = estvar.filter,
addtitle = addtitle,
returntitle = returntitle,
rawdata = rawdata,
states = states, invyrs = invyrs,
landarea = landarea,
pcfilter =pcfilter,
allin1 = allin1,
divideby = divideby,
outfn.pre = outfn.pre)
title.unitvar <- alltitlelst$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$outfn.rawdat
outfn.rawdat <- paste0(outfn.rawdat, "_modMA_mase", "_", MAmethod)
}
## Append name of package and method to outfile name
outfn.estpse <- paste0(outfn.estpse, "_modMA_mase", "_", MAmethod)
#################################################################################
## GENERATE ESTIMATES
#################################################################################
estdat <-
getMAestimates(esttype = esttype,
domdatn = tdomdat,
uniqueid = pltassgnid,
estvarn.name = estvar.name,
rowvar = rowvar, colvar = colvar,
grpvar = grpvar,
MAmethod = MAmethod,
modelselect = modelselect,
prednames = prednames,
FIA = FIA,
bootstrap = bootstrap,
pltassgnx = pltassgnx,
unitarea = unitarea,
unitvar = unitvar,
areavar = areavar,
unitlut = unitlut,
npixels = npixels,
totals = totals,
uniquerow = uniquerow,
uniquecol = uniquecol,
row.orderby = row.orderby,
col.orderby = col.orderby,
row.add0 = row.add0,
col.add0 = col.add0,
row.NAname = row.NAname,
col.NAname = col.NAname)
if (is.null(estdat)) stop()
unit_totest <- estdat$unit_totest
unit_rowest <- estdat$unit_rowest
unit_colest <- estdat$unit_colest
unit_grpest <- estdat$unit_grpest
predselectlst <- estdat$predselectlst
predselect.overall <- estdat$predselect.overall
unit_weights <- estdat$unit_weights
###############################################################################
## 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 = rowvarnm, colvar = colvarnm,
uniquerow = uniquerow, uniquecol = uniquecol,
rowgrp = rowgrp, rowgrpnm = rowgrpnm,
allin1 = allin1,
savedata = savedata, addtitle = addtitle,
title.ref = title.ref,
title.rowvar = title.rowvar, title.colvar = title.colvar,
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 (!row.add0 && any(est2return$Total == "--")) {
est2return <- est2return[est2return$Total != "--",]
}
if (!is.null(est2return)) {
if (!row.add0 && any(est2return$Total == "--")) {
est2return <- est2return[est2return$Total != "--",]
}
returnlst$est <- setDF(est2return)
}
if (!is.null(pse2return)) {
if (!row.add0 && any(pse2return$Total == "--")) {
pse2return <- pse2return[pse2return$Total != "--",]
}
returnlst$pse <- setDF(pse2return)
}
if(returntitle) {
returnlst$titlelst <- alltitlelst
}
if (rawdata) {
rawdat <- tabs$rawdat
rawdat$domdat <- setDF(tdomdat)
rawdat$plotweights <- unit_weights
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])
if (!tabnm %in% c(estvar, prednames)) {
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$module <- "MA"
rawdat$esttype <- "TREE"
rawdat$MAmethod <- MAmethod
rawdat$predselect.overall <- predselect.overall
rawdat$predselectlst <- predselectlst
rawdat$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
}
returnlst$statecd <- sort(pcheck.states(states, statereturn = "VALUE"))
returnlst$states <- states
returnlst$invyr <- sort(unique(unlist(invyrs)))
return(returnlst)
}
USDAForestService/FIESTA documentation built on April 5, 2025, 4:13 a.m.
R Package Documentation
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Defines functions modMAtree
Documented in modMAtree
#' Model-Assisted module - Generate model-assisted tree estimates.
#'
#' Generates tree estimates by estimation unit. Estimates are calculated from
#' McConville et al. (2018)'s mase R package.
#'
#' 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 (e.g. 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 (e.g., 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
#' identifier 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 }
#'
#' Reference names are available for the following variables: \cr ADFORCD,
#' AGENTCD, CCLCD, DECAYCD, DSTRBCD, KINDCD, OWNCD, OWNGRPCD, FORTYPCD,
#' FLDTYPCD, FORTYPCDCALC, TYPGRPCD, FORINDCD, RESERVCD, LANDCLCD, STDSZCD,
#' FLDSZCD, PHYSCLCD, MIST_CL_CD, PLOT_STATUS_CD, STATECD, TREECLCD, TRTCD,
#' SPCD, SPGRPCD
#'
#' @param MApopdat List. Population data objects returned from modMApop().
#' @param MAmethod String. mase (i.e., model-assisted) method to use
#' ('greg', 'gregEN', 'ratio').
#' @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 estvar.derive List. A derivation of a tree variable to estimate.
#' Must be a named list with one element (e.g.,
#' list(SDI='SUM(POWER(DIA/10,1.605) * TPA_UNADJ)'). Set estvar = NULL.
#' @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 prednames String vector. Name(s) of predictor variables to include in
#' model.
#' @param modelselect Logical. If TRUE, an elastic net regression model is fit
#' to the entire plot level data, and the variables selected in that model are
#' used for the proceeding estimation.
#' @param FIA Logical. If TRUE, the finite population term is removed from
#' estimator to match FIA estimates.
#' @param bootstrap Logical. If TRUE, returns bootstrap variance estimates,
#' otherwise uses Horvitz-Thompson estimator under simple random sampling
#' without replacement.
#' @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 modelselect_bydomain Logical. If TRUE, modelselection will occur at
#' the domain level as specified by rowvar and/or colvar and not at the level of
#' the entire sample.
#' @param ... Parameters for modMApop() if MApopdat is NULL.
#' @return If FIA=TRUE or unitvar=NULL and colvar=NULL, one data frame is
#' returned with tree estimates and percent sample errors. Otherwise, a list is
#' returned with tree estimates in one data frame (est) and percent sample
#' errors in another data frame (est.pse). If rawdata=TRUE, another list is
#' returned including raw data used in the estimation process. If
#' addtitle=TRUE and returntitle=TRUE, the title for est/pse is returned. If
#' savedata=TRUE, all data frames are written to outfolder.
#'
#' \item{est}{ Data frame. Tree estimates by rowvar, colvar (and estimation
#' unit). If FIA=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 for estimates by rowvar and colvar (and estimation
#' unit). } \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: number of plots by plot status, if in dataset (plotsampcnt);
#' number of conditions by condition status (condsampcnt); data used for
#' post-stratification (stratdat); and 1-8 tables with calculated variables
#' used for processing estimates and percent sampling error for table cell
#' values 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{stratdat}{ Data frame. Strata information by estimation unit. }
#' \tabular{lll}{ \tab \bold{Variable} \tab \bold{Description}\cr \tab ESTUNIT
#' \tab estimation unit\cr \tab STRATA \tab strata \cr \tab ACRES \tab area by
#' strata for estimation unit\cr \tab n.strata \tab number of plots in strata
#' (and estimation unit) \cr \tab n.total \tab number of plots for estimation
#' unit \cr \tab TOTACRES \tab total area for estimation unit \cr \tab strwt
#' \tab proportion of area (or number of plots) by strata (strata weight) \cr
#' \tab expfac.strata \tab expansion factor (in area unit (e.g., acres) by
#' strata (areavar/n.strata) \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 FIA=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 estimated variance of estimated
#' proportion of trees \cr \tab ACRES \tab total area for estimation unit \cr
#' \tab est \tab estimated area of trees nhat*ACRES \cr \tab est.var \tab
#' estimated variance 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.
#'
#' autoxreduce:\cr If MAmethod='GREG', and autoxreduce=TRUE, and there is an
#' error because of multicolinearity, a variable reduction method is applied to
#' remove correlated variables. The method used is based on the
#' variance-inflation factor (vif) from a linear model. The vif estimates how
#' much the variance of each x variable is inflated due to mulitcolinearity in
#' the model.
#'
#' 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
#' @references Kelly McConville, Becky Tang, George Zhu, Shirley Cheung, and
#' Sida Li (2018). mase: Model-Assisted Survey Estimation. R package version
#' 0.1.2 https://cran.r-project.org/package=mase
#' @keywords data
#' @examples
#' \donttest{
#' # Set up population dataset (see ?modMApop() for more information)
#' MApopdat <- modMApop(popTabs = list(tree = FIESTA::WYtree,
#' cond = FIESTA::WYcond),
#' pltassgn = FIESTA::WYpltassgn,
#' pltassgnid = "CN",
#' unitarea = FIESTA::WYunitarea,
#' unitvar = "ESTN_UNIT",
#' unitzonal = FIESTA::WYunitzonal,
#' prednames = c("dem", "tcc", "tpi", "tnt"),
#' predfac = "tnt")
#'
#' # Use GREG Estimator to Estimate cubic foot volume of live trees in our
#' # population
#' mod1 <- modMAtree(MApopdat = MApopdat,
#' MAmethod = "greg",
#' estvar = "VOLCFNET",
#' estvar.filter = "STATUSCD == 1")
#'
#' str(mod1)
#' }
#' @export modMAtree
modMAtree <- function(MApopdat,
MAmethod,
estvar,
estvar.filter = NULL,
estvar.derive = NULL,
estseed = "none",
woodland = "Y",
landarea = "FOREST",
pcfilter = NULL,
rowvar = NULL,
colvar = NULL,
prednames = NULL,
modelselect = FALSE,
FIA = TRUE,
bootstrap = FALSE,
returntitle = FALSE,
savedata = FALSE,
table_opts = NULL,
title_opts = NULL,
savedata_opts = NULL,
modelselect_bydomain = FALSE,
...){
##################################################################################
## DESCRIPTION:
## Generates model-assisted estimates by domain (and estimation unit)
##################################################################################
gui <- FALSE
## If gui.. set variables to NULL
if (gui) {
tree=landarea=strvar=areavar <- NULL
if (!row.FIAname) row.FIAname <- NULL
if (!col.FIAname) col.FIAname <- NULL
}
## Set parameters
esttype <- "TREE"
popType <- "VOL"
rawdata <- TRUE
sumunits <- FALSE
returnlst <- list()
## Set global variables
ONEUNIT=n.total=n.strata=strwt=TOTAL=domclassify<- NULL
##################################################################
## CHECK PARAMETER NAMES
##################################################################
## Check input parameters
input.params <- names(as.list(match.call()))[-1]
formallst <- c(names(formals(modMAtree)),
names(formals(modMApop)))
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 = input.params,
title_opts = title_opts,
table_opts = table_opts,
savedata_opts = savedata_opts)
## Check parameter option lists
optslst <- pcheck.opts(optionlst = list(
title_opts = title_opts,
table_opts = table_opts,
savedata_opts = savedata_opts))
title_opts <- optslst$title_opts
table_opts <- optslst$table_opts
savedata_opts <- optslst$savedata_opts
for (i in 1:length(title_opts)) {
assign(names(title_opts)[[i]], title_opts[[i]])
}
for (i in 1:length(table_opts)) {
assign(names(table_opts)[[i]], table_opts[[i]])
}
##################################################################
## CHECK PARAMETER INPUTS
##################################################################
## Check MAmethod
MAmethodlst <- c("greg", "gregEN", "ratio")
MAmethod <- pcheck.varchar(var2check=MAmethod, varnm="MAmethod", gui=gui,
checklst=MAmethodlst, caption="MAmethod", multiple=FALSE, stopifnull=TRUE)
if (MAmethod %in% c("greg", "gregEN")) {
predselectlst <- list()
}
###################################################################################
## Check data and generate population information
###################################################################################
list.items <- c("pltcondx", "cuniqueid", "condid",
"treex", "tuniqueid",
"unitarea", "unitvar", "unitlut", "npixels",
"npixelvar", "plotsampcnt", "condsampcnt")
MApopdat <- pcheck.object(MApopdat, "MApopdat", list.items=list.items)
if (is.null(MApopdat)) return(NULL)
pltidsadj <- MApopdat$pltidsadj
pltcondx <- MApopdat$pltcondx
cuniqueid <- MApopdat$cuniqueid
pltassgnid <- MApopdat$pltassgnid
condid <- MApopdat$condid
treex <- MApopdat$treex
seedx <- MApopdat$seedx
if (is.null(treex) && is.null(seedx)) {
stop("must include tree data for tree estimates")
}
tuniqueid <- MApopdat$tuniqueid
ACI <- MApopdat$ACI
pltassgnx <- MApopdat$pltassgnx
unitarea <- MApopdat$unitarea
areavar <- MApopdat$areavar
areaunits <- MApopdat$areaunits
unitvar <- MApopdat$unitvar
unitlut <- MApopdat$unitlut
unitvars <- MApopdat$unitvars
npixels <- MApopdat$npixels
npixelvar <- MApopdat$npixelvar
expcondtab <- MApopdat$expcondtab
plotsampcnt <- MApopdat$plotsampcnt
condsampcnt <- MApopdat$condsampcnt
states <- MApopdat$states
invyrs <- MApopdat$invyrs
predfac <- MApopdat$predfac
adj <- MApopdat$adj
popdatindb <- MApopdat$popdatindb
pop_fmt <- MApopdat$pop_fmt
pop_dsn <- MApopdat$pop_dsn
pop_schema <- MApopdat$pop_schema
popconn <- MApopdat$popconn
dbqueries <- MApopdat$dbqueries
dbqueriesWITH <- MApopdat$dbqueriesWITH
adjcase <- MApopdat$adjcase
pltidsid <- MApopdat$pjoinid
pltassgnid <- MApopdat$pltassgnid
pltcondflds <- MApopdat$pltcondflds
if (MAmethod %in% c("greg", "gregEN", "ratio")) {
if (is.null(prednames)) {
prednames <- MApopdat$prednames
} else {
if (!all(prednames %in% MApopdat$prednames)) {
if (any(prednames %in% MApopdat$predfac)) {
predfacnames <- prednames[prednames %in% MApopdat$predfac]
for (nm in predfacnames) {
prednames[prednames == nm] <- MApopdat$prednames[grepl(nm, MApopdat$prednames)]
}
} else {
stop("invalid prednames... must be in: ", toString(MApopdat$prednames))
}
}
}
}
if (popdatindb) {
if (is.null(popconn) || !DBI::dbIsValid(popconn)) {
if (!is.null(pop_dsn)) {
if (pop_fmt == "sqlite") {
popconn <- DBtestSQLite(pop_dsn, dbconnopen = TRUE)
}
} else {
stop("invalid database connection")
}
}
#pltcondx <- dbqueries$pltcondx
pltcondxWITHqry <- dbqueriesWITH$pltcondxWITH
pltcondxadjWITHqry <- dbqueriesWITH$pltcondxadjWITH
} else {
pltcondxWITHqry <- NULL
pltcondxWITHqry=pltcondxadjWITHqry <- NULL
}
########################################
## Check area units
########################################
unitchk <- pcheck.areaunits(unitarea=unitarea, areavar=areavar,
areaunits=areaunits, metric=metric)
unitarea <- unitchk$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,
popType = popType,
popdatindb = popdatindb,
popconn = popconn, pop_schema = pop_schema,
pltcondx = pltcondx,
pltcondflds = pltcondflds,
totals = totals,
pop_fmt=pop_fmt, pop_dsn=pop_dsn,
landarea = landarea,
ACI = ACI,
pcfilter = pcfilter,
allin1 = allin1, divideby = divideby,
estround = estround, pseround = pseround,
returntitle = returntitle,
rawonly = rawonly,
savedata = savedata,
savedata_opts = savedata_opts,
gui = gui)
if (is.null(estdat)) return(NULL)
esttype <- estdat$esttype
totals <- estdat$totals
landarea <- estdat$landarea
allin1 <- estdat$allin1
divideby <- estdat$divideby
estround <- estdat$estround
pseround <- estdat$pseround
addtitle <- estdat$addtitle
returntitle <- estdat$returntitle
rawonly <- estdat$rawonly
savedata <- estdat$savedata
outfolder <- estdat$outfolder
overwrite_layer <- estdat$overwrite_layer
outfn.pre <- estdat$outfn.pre
outfn.date <- estdat$outfn.date
append_layer = estdat$append_layer
rawfolder <- estdat$rawfolder
raw_fmt <- estdat$raw_fmt
raw_dsn <- estdat$raw_dsn
pcwhereqry <- estdat$where.qry
SCHEMA. <- estdat$SCHEMA.
pltcondflds <- estdat$pltcondflds
###################################################################################
## Check parameter inputs and tree filters
###################################################################################
estdatVOL <-
check.estdataVOL(esttype = esttype,
popdatindb = popdatindb,
popconn = popconn,
cuniqueid = cuniqueid, condid = condid,
treex = treex, seedx = seedx,
tuniqueid = tuniqueid,
estseed = estseed,
woodland = woodland,
gui = gui)
treex <- estdatVOL$treex
treeflds <- estdatVOL$treeflds
tuniqueid <- estdatVOL$tuniqueid
estseed <- estdatVOL$estseed
woodland <- estdatVOL$woodland
seedx <- estdatVOL$seedx
seedflds <- estdatVOL$seedflds
###################################################################################
### Check row and column data
###################################################################################
rowcolinfo <-
check.rowcol(esttype = esttype,
popType = popType,
popdatindb = popdatindb,
popconn = popconn, SCHEMA. = SCHEMA.,
pltcondx = pltcondx,
pltcondflds = pltcondflds,
withqry = pltcondxWITHqry,
estseed = estseed,
treex = treex, treeflds = treeflds,
seedx = seedx, seedflds = seedflds,
cuniqueid = cuniqueid, condid = condid,
rowvar = rowvar, colvar = colvar,
row.FIAname = row.FIAname, col.FIAname = col.FIAname,
row.orderby = row.orderby, col.orderby = col.orderby,
row.classify = row.classify, col.classify = col.classify,
row.add0 = row.add0, col.add0 = col.add0,
title.rowvar = title.rowvar, title.colvar = title.colvar,
rowlut = rowlut, collut = collut,
rowgrp = rowgrp, rowgrpnm = rowgrpnm,
rowgrpord = rowgrpord, title.rowgrp = NULL,
whereqry = pcwhereqry)
uniquerow <- rowcolinfo$uniquerow
uniquecol <- rowcolinfo$uniquecol
domainlst <- rowcolinfo$domainlst
rowvar <- rowcolinfo$rowvar
colvar <- rowcolinfo$colvar
rowvarnm <- rowcolinfo$rowvarnm
colvarnm <- rowcolinfo$colvarnm
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
grpvar <- rowcolinfo$grpvar
bytdom <- rowcolinfo$bytdom
bypcdom <- rowcolinfo$bypcdom
tdomvar <- rowcolinfo$tdomvar
tdomvar2 <- rowcolinfo$tdomvar2
classifyrow <- rowcolinfo$classifyrow
classifycol <- rowcolinfo$classifycol
#rm(rowcolinfo)
## if classified columns, create domclassify list for summarizing tree data
if (any(!is.null(classifyrow), !is.null(classifycol))) {
domclassify <- list()
if (!is.null(classifyrow)) {
domclassify[[rowvar]] <- classifyrow$row.classify
}
if (!is.null(classifycol)) {
domclassify[[colvar]] <- classifycol$col.classify
}
}
#################################################################################
### GET ESTIMATION DATA FROM TREE TABLE
#################################################################################
adjtree <- ifelse(adj %in% c("samp", "plot"), TRUE, FALSE)
if (popdatindb) {
pltidsWITHqry <- dbqueriesWITH$pltcondxadjWITH
} else {
pltidsWITHqry <- NULL
}
treedat <-
check.tree(treex = treex,
seedx = seedx,
estseed = estseed,
bycond = TRUE,
condx = pltcondx,
tuniqueid = tuniqueid, cuniqueid = cuniqueid,
esttype = esttype,
estvarn = estvar,
estvarn.filter = estvar.filter,
estvarn.derive = estvar.derive,
esttotn = TRUE,
bydomainlst = c(domainlst, "TOTAL"),
tdomvar = tdomvar, tdomvar2 = tdomvar2,
adjtree = adjtree,
adjvar = "tadjfac",
metric = metric,
woodland = woodland,
ACI = ACI,
domclassify = domclassify,
dbconn = popconn, schema = pop_schema,
pltidsWITHqry = pltidsWITHqry,
pcwhereqry = pcwhereqry,
pltidsid = pltidsid,
bytdom = bytdom,
gui = gui)
if (is.null(treedat)) stop(NULL)
tdomdat <- treedat$tdomdat
estvar <- treedat$estvar
estvar.name <- treedat$estvar.name
estvar.filter <- treedat$estvar.filter
tdomvarlst <- treedat$tdomvarlst
estunits <- treedat$estunits
treeqry <- treedat$treeqry
classifynmlst <- treedat$classifynmlst
## If classified rowvar or colvar, get class names
if (!is.null(classifynmlst)) {
if (!is.null(classifynmlst[[rowvar]])) {
rowvar <- classifynmlst[[rowvar]]
}
if (!is.null(classifynmlst[[colvar]])) {
colvar <- classifynmlst[[colvar]]
}
if (!is.null(grpvar)) {
grpvar <- c(rowvar, colvar)
}
}
#################################################################################
### 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
outfn.rawdat <- paste0(outfn.rawdat, "_modMA_mase", "_", MAmethod)
}
## Append name of package and method to outfile name
outfn.estpse <- paste0(outfn.estpse, "_modMA_mase", "_", MAmethod)
#################################################################################
## GENERATE ESTIMATES
#################################################################################
estdat <-
getMAestimates(esttype = esttype,
domdatn = tdomdat,
uniqueid = pltassgnid,
estvarn.name = estvar.name,
rowvar = rowvar, colvar = colvar,
grpvar = grpvar,
MAmethod = MAmethod,
modelselect = modelselect,
prednames = prednames,
FIA = FIA,
bootstrap = bootstrap,
pltassgnx = pltassgnx,
unitarea = unitarea,
unitvar = unitvar,
areavar = areavar,
unitlut = unitlut,
npixels = npixels,
totals = totals,
uniquerow = uniquerow,
uniquecol = uniquecol,
row.orderby = row.orderby,
col.orderby = col.orderby,
row.add0 = row.add0,
col.add0 = col.add0,
row.NAname = row.NAname,
col.NAname = col.NAname)
if (is.null(estdat)) stop()
unit_totest <- estdat$unit_totest
unit_rowest <- estdat$unit_rowest
unit_colest <- estdat$unit_colest
unit_grpest <- estdat$unit_grpest
predselectlst <- estdat$predselectlst
predselect.overall <- estdat$predselect.overall
unit_weights <- estdat$unit_weights
###############################################################################
## GENERATE OUTPUT TABLES
###############################################################################
message("getting output...")
estnm <- "est"
tabs <-
est.outtabs(esttype = esttype,
sumunits = sumunits, areavar = areavar,
unitvar = unitvar, unitvars = unitvars,
unit_totest = unit_totest,
unit_rowest = unit_rowest, unit_colest = unit_colest,
unit_grpest = unit_grpest,
rowvar = rowvarnm, colvar = colvarnm,
uniquerow = uniquerow, uniquecol = uniquecol,
rowgrp = rowgrp, rowgrpnm = rowgrpnm,
allin1 = allin1,
savedata = savedata, addtitle = addtitle,
title.ref = title.ref,
title.rowvar = title.rowvar, title.colvar = title.colvar,
title.rowgrp = title.rowgrp,
title.unitvar = title.unitvar, title.estpse = title.estpse,
title.est = title.est, title.pse = title.pse,
rawdata = rawdata, rawonly = rawonly,
outfn.estpse = outfn.estpse,
outfolder = outfolder, outfn.date = outfn.date,
overwrite = overwrite_layer, estnm = estnm,
estround = estround, pseround = pseround,
divideby = divideby,
returntitle = returntitle,
estnull = estnull, psenull = psenull,
raw.keep0 = raw.keep0)
est2return <- tabs$tabest
pse2return <- tabs$tabpse
if (!row.add0 && any(est2return$Total == "--")) {
est2return <- est2return[est2return$Total != "--",]
}
if (!is.null(est2return)) {
if (!row.add0 && any(est2return$Total == "--")) {
est2return <- est2return[est2return$Total != "--",]
}
returnlst$est <- setDF(est2return)
}
if (!is.null(pse2return)) {
if (!row.add0 && any(pse2return$Total == "--")) {
pse2return <- pse2return[pse2return$Total != "--",]
}
returnlst$pse <- setDF(pse2return)
}
if(returntitle) {
returnlst$titlelst <- alltitlelst
}
if (rawdata) {
rawdat <- tabs$rawdat
rawdat$domdat <- setDF(tdomdat)
rawdat$plotweights <- unit_weights
rawdat$estvar <- estvar.name
rawdat$estvar.filter <- estvar.filter
if (savedata) {
if (!is.null(title.estpse)) {
title.raw <- paste(title.estpse, title.ref)
} else {
title.raw <- title.est
}
for (i in 1:length(rawdat)) {
tabnm <- names(rawdat[i])
if (!tabnm %in% c(estvar, prednames)) {
rawtab <- rawdat[[i]]
outfn.rawtab <- paste0(outfn.rawdat, "_", tabnm)
if (tabnm %in% c("plotsampcnt", "condsampcnt", "stratcombinelut")) {
write2csv(rawtab, outfolder=rawfolder, outfilenm=outfn.rawtab,
outfn.date=outfn.date, overwrite=overwrite_layer)
} else if (is.data.frame(rawtab)) {
if (raw_fmt != "csv") {
out_layer <- tabnm
} else {
out_layer <- outfn.rawtab
}
datExportData(rawtab,
savedata_opts=list(outfolder=rawfolder,
out_fmt=raw_fmt,
out_dsn=raw_dsn,
out_layer=out_layer,
overwrite_layer=overwrite_layer,
append_layer=append_layer,
add_layer=TRUE))
}
}
}
}
rawdat$module <- "MA"
rawdat$esttype <- "TREE"
rawdat$MAmethod <- MAmethod
rawdat$predselect.overall <- predselect.overall
rawdat$predselectlst <- predselectlst
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$raw <- rawdat
}
returnlst$statecd <- sort(pcheck.states(states, statereturn = "VALUE"))
returnlst$states <- states
returnlst$invyr <- sort(unique(unlist(invyrs)))
return(returnlst)
}
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