R: Model-Assisted module - Generate population data for MA...

modMApop {FIESTA}

R Documentation

Model-Assisted module - Generate population data for MA module.

Description

Generates population data for generating model-assisted estimation. Plots that are totally nonsampled are excluded from estimation dataset. Next, an adjustment factor is calculated by strata (if MAmethod="PS") or by estimation unit 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 and/or estimation unit. Note: population data must be generated by MA method.

Usage

modMApop(
  popType = "VOL",
  popTabs = popTables(),
  popTabIDs = popTableIDs(),
  popFilter = popFilters(),
  pltassgn = NULL,
  pltassgnid = "PLT_CN",
  dsn = NULL,
  pjoinid = "CN",
  areawt = "CONDPROP_UNADJ",
  adjplot = TRUE,
  unitvar = NULL,
  unitarea = NULL,
  areavar = "ACRES",
  unitzonal = NULL,
  prednames = NULL,
  predfac = NULL,
  standardize = TRUE,
  returndata = TRUE,
  savedata = FALSE,
  saveobj = FALSE,
  objnm = "MApopdat",
  unit_opts = NULL,
  savedata_opts = NULL,
  MAdata = NULL,
  pltdat = NULL,
  auxdat = NULL,
  gui = FALSE,
  ...
)

Arguments

`popType`	String. Type of evaluation(s) to include in population data. Note: currently only c('CURR', 'VOL', 'LULC') are available. See details below for descriptions of each.
`popTabs`	List of population tables the user would like returned. See help(popTables) for a list of options.
`popTabIDs`	List of unique IDs corresponding to the population tables that the user has requested. See help(popTableIDs) for a list of options.
`popFilter`	List of population filters. See help(popFilters) for a list of options.
`pltassgn`	DF/DT, Optional. R object, sf R object, comma-delimited file(.csv), layer or spatial layer in dsn, or shapefile(.shp). Plot-level assignment of estimation unit and/or strata, with one record for each plot.
`pltassgnid`	String.
`dsn`	String. Name of database where tree, cond, and plot-level tables reside. The dsn varies by driver. See gdal OGR vector formats (https://www.gdal.org/ogr_formats.html).
`pjoinid`	String. Join variable in plot to match pltassgnid. Does not need to be uniqueid. If using most current XY coordinates for plot assignments, use identifier for plot (e.g., PLOT_ID).
`areawt`	String. Name of variable for summarizing area weights (e.g., CONDPROP_UNADJ).
`adjplot`	Logical. If TRUE, adjusts for nonresponse at plot-level.
`unitvar`	String. Name of the estimation unit variable in unitarea and cond or pltassgn data frame with estimation unit assignment for each plot (e.g., 'ESTN_UNIT'). Optional if only one estimation unit.
`unitarea`	Numeric or DF. Total area by estimation unit. If only 1 estimation unit, include number of total acreage for the area of interest or a data frame with area and estimation unit. If more than one estimation unit, provide a data frame of total area by estimation unit, including unitvar and areavar.
`areavar`	String. Name of area variable in unitarea. Default="ACRES".
`unitzonal`	DF/DT. Table with zonal auxiliary information by estimation unit. For continuous data, means by estimation unit; for categorical data, proportion of class by estimation unit.
`prednames`	String vector. Name(s) of predictor variables to include in model.
`predfac`	String vector. Name(s) of prednames that are factors (i.e., categorical). Names will change in output depending on number of categories.
`standardize`	Logical. If TRUE, predictors are standardized.
`returndata`	Logical. If TRUE, returns data objects.
`savedata`	Logical. If TRUE, saves table(s) to outfolder.
`saveobj`	Logical. If TRUE, saves returned list object to outfolder.
`objnm`	String. Name of *.rds object.
`unit_opts`	List. See help(unit_options()) for a list of options.
`savedata_opts`	List. See help(savedata_options()) for a list of options. Only used when savedata = TRUE.
`MAdata`	List. Data output from FIESTA::MAdata().
`pltdat`	R List object. Output data list components from FIESTA::spGetPlots().
`auxdat`	List. Auxiliary data output from FIESTA::spGetAuxiliary().
`gui`	Logical. If gui, user is prompted for parameters.
`...`	For extendibility.

Details

If variables are NULL, then it will prompt user to input variables.

Necessary variables:

Data	Variable	Description
tree	tuniqueid	Unique identifier for each plot, to link to pltassgn (e.g. PLT_CN).
	CONDID	Unique identifier of each condition on plot, to link to cond. Set CONDID=1, if only 1 condition per plot.
	TPA_UNADJ	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).
cond	cuniqueid	Unique identifier for each plot, to link to pltassgn (e.g. PLT_CN).
	CONDID	Unique identifier of each condition on plot. Set CONDID=1, if only 1 condition per plot.
	CONDPROP_UNADJ	Unadjusted proportion of condition on each plot. Set CONDPROP_UNADJ=1, if only 1 condition per plot.
	COND_STATUS_CD	Status of each forested condition on plot (i.e. accessible forest, nonforest, water, etc.)
	NF_COND_STATUS_CD	If ACI=TRUE. Status of each nonforest condition on plot (i.e. accessible nonforest, nonsampled nonforest)
	SITECLCD	If landarea=TIMBERLAND. Measure of site productivity.
	RESERVCD	If landarea=TIMBERLAND. Reserved status.
	SUBPROP_UNADJ	Unadjusted proportion of subplot conditions on each plot. Set SUBPROP_UNADJ=1, if only 1 condition per subplot.
	MICRPROP_UNADJ	If microplot tree attributes. Unadjusted proportion of microplot conditions on each plot. Set MICRPROP_UNADJ=1, if only 1 condition per microplot.
	MACRPROP_UNADJ	If macroplot tree attributes. Unadjusted proportion of macroplot conditions on each plot. Set MACRPROP_UNADJ=1, if only 1 condition per macroplot.
pltassgn	puniqueid	Unique identifier for each plot, to link to cond (e.g. CN).
	STATECD	Identifies state each plot is located in.
	INVYR	Identifies inventory year of each plot.
	PLOT_STATUS_CD	Status of each plot (i.e. sampled, nonsampled). If not included, all plots are assumed as sampled.

For available reference tables: sort(unique(FIESTAutils::ref_codes$VARIABLE))

Value

A list with population data for Green-Book estimates.

`condx`	Data frame. Condition-level data including plot-level assignment of estimation unit and stratum (if strata=TRUE) and adjusted condition proportion.
`pltcondx`	Data frame. Condition-level data, merged with plot data.
`cuniqueid`	String. Unique identifier of plot in condx and pltcondx.
`condid`	String. Unique identifier of condition in condx and pltcondx.
`treex`	Data frame. If esttype='TREE', tree-level data, including sample adjustment factor.
`tuniqueid`	String. If esttype='TREE', unique identifier of plot in treex.
`ACI.filter`	String. If ACI=FALSE, ACI.filter="COND_STATUS_CD == 1" .
`unitarea`	String. Returned table of area by estimation unit.
`unitvar`	String. Variable name for estimation unit.
`expcondtab`	String. If ACI=FALSE, ACI.filter="COND_STATUS_CD == 1".
`plotsampcnt`	Data frame. Number of plots by PLOT_STATUS_CD.
`condsampcnt`	Data frame. Number of conditions by COND_STATUS_CD.
`states`	String. State names in dataset.
`invyrs`	String. Range of inventory years in dataset.

	Variable	Description
	unitvar	estimation unit
	n.total	number of plots for estimation unit
	CONDPROP_UNADJ_SUM	summed condition proportion by strata and estimation unit
	CONDPROP_ADJFAC	adjusted condition proportion by strata after nonsampled plots removed
	AREA_USED	total area of estimation unit
	expfac	strata-level expansion factor after nonsampled plots and conditions removed (AREA_USED/n.strata)
	EXPNS	strata-level area expansions (expfac * strwt)

Table(s) are also written to outfolder.

Note

ADJUSTMENT FACTOR:
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:

	PLOT SIZE	TPA_UNADJ
	SUBPLOT	6.018046
	MICROPLOT	74.965282
	MACROPLOT	0.999188

If ACI=FALSE, only nonsampled forest conditions are accounted for in the adjustment factor.
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.

unitcombine:
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.

stratcombine:
If TRUE and less than 2 plots in any one strata class within an estimation unit, all strata classes with 2 or less plots are combined. The current method for combining is to group the strata with less than 2 plots with the strata class following in consecutive order (numeric or alphabetical), restrained by estimation unit (if unitcombine=FALSE), and continuing until the number of plots equals 10. If there are no strata classes following in order, it is combined with the estimation unit previous in order.

Author(s)

Tracey S. Frescino, Paul L. Patterson

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.

Examples


# NOTE: FIA data objects used in these examples are stored in `FIESTA`, but
# can be generated for populations of interest by the user with functions in
# `FIESTA` such as `spGetPlots()`, `spGetAuxiliary()`, etc. For more
# information, see `FIESTA`'s extensive vignettes.
 
# Population data for counties in Wyoming
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")
         
# Adding seedling data as well
modMApop(popTabs = list(tree = FIESTA::WYtree,
                        cond = FIESTA::WYcond,
                        seed = FIESTA::WYseed),
         pltassgn = FIESTA::WYpltassgn,
         pltassgnid = "CN",
         unitarea = FIESTA::WYunitarea,
         unitvar = "ESTN_UNIT",
         unitzonal = FIESTA::WYunitzonal,
         prednames = c("dem", "tcc", "tpi", "tnt"),
         predfac = "tnt")

[Package FIESTA version 3.6.4 Index]