# FIESTA - Model-Assisted Estimators

## Model-Assisted (MA) module overview

`FIESTA`’s Model-Assisted (MA) module calculates population estimates and their sampling errors by taking advantage of available model-assisted survey estimators from the `mase` R package (McConville, et al. 2018). These estimators can use a variety of auxiliary data to build models and predict over a response variable of interest, while using a bias-correction term so that the bias of the model does not depend on model mis-specification.

Functions in `FIESTA` used for fitting model-assisted estimators include the `modMAarea` function for area estimates and `modMAtree` for tree estimates. The `modMApop` function is used to get population data needed for model-assisted estimation. Below is a description and table of contents for the sections related to these functions:

FUNCTION | DESCRIPTION
--- | ---
modMApop | Creates population data for model-assisted estimation.
modMAarea | Produces area level estimates through model-assisted estimation.
modMAtree | Produces tree level estimates through model-assisted estimation.

## Objective of tutorial

The main objective of this tutorial is to demonstrate how to use `FIESTA` for generating estimates using estimators from `mase`. The model-assisted estimators can be used with FIA’s standard state-level population data (i.e, Evaluation) from the FIA database (FIADB) and also population data from a custom boundary.

The following examples are for generating estimates and estimated variances using standard FIA Evaluation data from FIA’s National database, with custom Estimation unit and Stratification information. The examples use data from three inventory years of field measurements in the state of Wyoming, from FIADB_1.7.2.00, last updated June 20, 2018, downloaded on June 25, 2018 and stored as internal data objects in `FIESTA`.

## Example data - Wyoming (WY), Inventory Years 2011-2012

View MA Example Data

Data Frame | Description
--- | ---
WYplt | WY plot-level data
WYcond | WY condition-level data
WYtree | WY tree-level data

External data | Description
--- | ---
WYbighorn_adminbnd.shp | Polygon shapefile of WY Bighorn National Forest Administrative boundary*
WYbighorn_districtbnd.shp | Polygon shapefile of WY Bighorn National Forest District boundaries**
WYbighorn_forest_nonforest_250m.tif | GeoTIFF raster of predicted forest/nonforest (1/0) for stratification***
WYbighorn_dem_250m.img | Erdas Imagine raster of elevation change, in meters****

*USDA Forest Service, Automated Lands Program (ALP). 2018. S_USA.AdministrativeForest (http://data.fs.usda.gov/geodata/edw). Description: An area encompassing all the National Forest System lands administered by an administrative unit. The area encompasses private lands, other governmental agency lands, and may contain National Forest System lands within the proclaimed boundaries of another administrative unit. All National Forest System lands fall within one and only one Administrative Forest Area.

**USDA Forest Service, Automated Lands Program (ALP). 2018. S_USA.RangerDistrict (http://data.fs.usda.gov/geodata/edw). Description: A depiction of the boundary that encompasses a Ranger District.

***Based on MODIS-based classified map resampled from 250m to 500m resolution and reclassified from 3 to 2 classes: 1:forest; 2:nonforest. Projected in Albers Conical Equal Area, Datum NAD27 (Ruefenacht et al. 2008). Clipped to extent of WYbighorn_adminbnd.shp.

****USGS National Elevation Dataset (NED), resampled from 30m resolution to 250m. Projected in Albers Conical Equal Area, Datum NAD27 (U.S. Geological Survey 2017). Clipped to boundary of WYbighorn_adminbnd.shp.

### Set up

First, you’ll need to load the `FIESTA` library:

    library(FIESTA)

Next, you’ll need to set up an “outfolder”. This is just a file path to a folder where you’d like `FIESTA` to send your data output. For our purposes in this vignette, we have saved our outfolder file path as the `outfolder` object in a temporary directory. We also set a few default options preferred for this vignette.

    outfolder <- tempdir()

### Get data for examples

View Getting Data

Now that we’ve loaded `FIESTA` and setup our outfolder, we can retrieve the data needed to run the examples. First, we point to some external data and predictor layers stored in `FIESTA` and derive new predictor layers using the `terra` package.

    # File names for external spatial data
    WYbhfn <- system.file("extdata", "sp_data/WYbighorn_adminbnd.shp",
                          package = "FIESTA")
    WYbhdistfn <- system.file("extdata", "sp_data/WYbighorn_districtbnd.shp",
                              package = "FIESTA")

    ## predictor variables
    fornffn <- system.file("extdata", "sp_data/WYbighorn_forest_nonforest_250m.tif",
                           package = "FIESTA")
    demfn <- system.file("extdata", "sp_data/WYbighorn_dem_250m.img",
                         package = "FIESTA")

    # Derive new predictor layers from dem
    library(terra)
    dem <- rast(demfn)
    slpfn <- paste0(outfolder, "/WYbh_slp.img")
    slp <- terra::terrain(dem,
                          v = "slope",
                          unit = "degrees",
                          filename = slpfn,
                          overwrite = TRUE)
    aspfn <- paste0(outfolder, "/WYbh_asp.img")
    asp <- terra::terrain(dem,
                          v = "aspect",
                          unit = "degrees",
                          filename = aspfn,
                          overwrite = TRUE)

Next, we can get our FIA plot data and set up our auxiliary data. We can get our FIA plot data with the `spMakeSpatialPoints` function from `FIESTA`. For more information on how to use this function, please see the `sp` vignette included with `FIESTA` (link).

    WYspplt <- spMakeSpatialPoints(
      xyplt = WYplt,
      xy.uniqueid = "CN",
      xvar = "LON_PUBLIC",
      yvar = "LAT_PUBLIC",
      xy.crs = 4269
    )

    rastlst.cont <- c(demfn, slpfn, aspfn)
    rastlst.cont.name <- c("dem", "slp", "asp")
    rastlst.cat <- fornffn
    rastlst.cat.name <- "fornf"

Next, we must generate dataset for model-assisted estimation. We can do this with the `spGetAuxiliary` function from `FIESTA`. Again, see the `sp` vignette for further information on this function.

    modeldat <- spGetAuxiliary(
      xyplt = WYspplt,
      uniqueid = "CN",
      unit_layer = WYbhfn,
      unitvar = NULL,
      rastlst.cont = rastlst.cont,
      rastlst.cont.name = rastlst.cont.name,
      rastlst.cat = rastlst.cat,
      rastlst.cat.name = rastlst.cat.name,
      rastlst.cont.stat = "mean",
      asptransform = TRUE,
      rast.asp = aspfn,
      keepNA = FALSE,
      showext = FALSE,
      savedata = FALSE)

    str(modeldat, max.level = 1)

output

    ## List of 12
    ##  $ unitvar       : chr "ONEUNIT"
    ##  $ pltassgn      :'data.frame':  56 obs. of  25 variables:
    ##  $ pltassgnid    : chr "CN"
    ##  $ unitarea      :'data.frame':  1 obs. of  2 variables:
    ##  $ areavar       : chr "ACRES_GIS"
    ##  $ unitzonal     :'data.frame':  1 obs. of  8 variables:
    ##  $ inputdf       :Classes 'data.table' and 'data.frame': 5 obs. of  7 variables:
    ##   ..- attr(*, ".internal.selfref")=<externalptr>
    ##  $ prednames     : chr [1:5] "dem" "slp" "asp_cos" "asp_sin" ...
    ##  $ zonalnames    : chr [1:7] "dem" "slp" "asp_cos" "asp_sin" ...
    ##  $ predfac       : chr "fornf"
    ##  $ npixelvar     : chr "npixels"
    ##  $ predfac.levels:List of 1

## Examples

### `modMApop`

#### Example 1: Creating our population dataset with `modMApop`

View Example

We can create our population data for model-assisted estimation. To do so, we use the `modMApop` function in `FIESTA`. We must assign our population tables with the `popTabs` argument (and unique identifiers for these tables with the `popTabIDs` argument if they are not the default), the plot assignment with the `pltassgn` argument, and in auxiliary dataset we just created with the `auxdat` argument. The `spGetAuxiliary` function has done much of the hard work for us so far, so we can just run a simple call to `modMApop`:

    MApopdat <- modMApop(popTabs = list(tree = WYtree, cond = WYcond),
                         pltassgn = WYpltassgn,
                         auxdat = modeldat)

Note that the `modMApop` function returns a list with lots of information and data for us to use. For a quick look at what this list includes we can use the `str` function:

    str(MApopdat, max.level = 1)

output

    ## List of 26
    ##  $ module     : chr "MA"
    ##  $ popType    : chr "VOL"
    ##  $ condx      :Classes 'data.table' and 'data.frame':    66 obs. of  17 variables:
    ##   ..- attr(*, "sorted")= chr [1:2] "PLT_CN" "CONDID"
    ##   ..- attr(*, ".internal.selfref")=<externalptr>
    ##  $ pltcondx   :Classes 'data.table' and 'data.frame':    66 obs. of  29 variables:
    ##   ..- attr(*, ".internal.selfref")=<externalptr>
    ##   ..- attr(*, "sorted")= chr [1:2] "PLT_CN" "CONDID"
    ##  $ cuniqueid  : chr "PLT_CN"
    ##  $ condid     : chr "CONDID"
    ##  $ ACI.filter : chr "COND_STATUS_CD == 1"
    ##  $ unitarea   :Classes 'data.table' and 'data.frame':    1 obs. of  2 variables:
    ##   ..- attr(*, ".internal.selfref")=<externalptr>
    ##   ..- attr(*, "sorted")= chr "ONEUNIT"
    ##  $ areavar    : chr "ACRES_GIS"
    ##  $ areaunits  : chr "acres"
    ##  $ unitvar    : chr "ONEUNIT"
    ##  $ unitvars   : chr "ONEUNIT"
    ##  $ unitlut    :Classes 'data.table' and 'data.frame':    1 obs. of  7 variables:
    ##   ..- attr(*, ".internal.selfref")=<externalptr>
    ##   ..- attr(*, "sorted")= chr "ONEUNIT"
    ##  $ plotsampcnt:'data.frame': 2 obs. of  3 variables:
    ##  $ condsampcnt:'data.frame': 4 obs. of  3 variables:
    ##  $ npixels    :Classes 'data.table' and 'data.frame':    1 obs. of  2 variables:
    ##   ..- attr(*, ".internal.selfref")=<externalptr>
    ##  $ npixelvar  : chr "npixels"
    ##  $ states     : chr "Wyoming"
    ##  $ invyrs     :List of 1
    ##  $ estvar.area: chr "CONDPROP_ADJ"
    ##  $ adj        : chr "plot"
    ##  $ treex      :Classes 'data.table' and 'data.frame':    1691 obs. of  21 variables:
    ##   ..- attr(*, ".internal.selfref")=<externalptr>
    ##   ..- attr(*, "sorted")= chr "PLT_CN"
    ##  $ tuniqueid  : chr "PLT_CN"
    ##  $ adjtree    : logi FALSE
    ##  $ prednames  : chr [1:5] "dem" "slp" "asp_cos" "asp_sin" ...
    ##  $ predfac    : chr "fornf"

Now that we’ve created our population dataset, we can move on to estimation.

### `modMAarea`

#### Example 2: Area of forest land, Wyoming, 2011-2013

View Example

In this example, we look at estimating the area of forest land in Wyoming from 2011 to 2013 summed to the population unit (`sumunit = TRUE`) with the generalized regression estimator (`MAmethod = "greg"`). `FIESTA` returns raw data for area of forest land, Wyoming, 2011-2013 (sum estimation units).

    area1 <- modMAarea(
      MApopdat = MApopdat, # pop - population calculations for WY, post-stratification
      MAmethod = "greg", # est - model-assisted method
      landarea = "FOREST", # est - forest land filter
      )

We can look at the structure of this output with `str` and the estimates below. Note that again `FIESTA` outputs a list.

    str(area1, max.level = 2)

output

    ## List of 4
    ##  $ est    :Classes 'data.table' and 'data.frame':    1 obs. of  3 variables:
    ##   ..$ ONEUNIT               : num 1
    ##   ..$ Estimate              : num 660395
    ##   ..$ Percent Sampling Error: num 9.42
    ##   ..- attr(*, ".internal.selfref")=<externalptr>
    ##   ..- attr(*, "sorted")= chr "ONEUNIT"
    ##  $ raw    :List of 9
    ##   ..$ unit_totest  :'data.frame':    1 obs. of  18 variables:
    ##   ..$ domdat       :'data.frame':    66 obs. of  19 variables:
    ##   ..$ module       : chr "MA"
    ##   ..$ esttype      : chr "AREA"
    ##   ..$ MAmethod     : chr "greg"
    ##   ..$ predselectlst:List of 1
    ##   ..$ rowvar       : chr "TOTAL"
    ##   ..$ colvar       : chr "NONE"
    ##   ..$ areaunits    : chr "acres"
    ##  $ statecd: int 56
    ##  $ invyr  : int [1:3] 2011 2012 2013

    area1$est

output

    ##    ONEUNIT Estimate Percent Sampling Error
    ## 1:       1 660395.1                   9.42

#### Example 3: Area of forest land, Wyoming, 2011-2013, using the Elastic Net for variable selection

View Example

Here, we fit the same model as the above example, but rather than using `"greg"` are our model-assisted method, we can use `"gregEN"` where the EN stands for “elastic net”. The elastic net performs variable selection for us, grabbing predictors it finds to be most useful in the model.

    area2 <- modMAarea(
      MApopdat = MApopdat, # pop - population calculations for WY, post-stratification
      MAmethod = "gregEN", # est - model-assisted method
      landarea = "FOREST", # est - forest land filter
      )

We can again see that the structure of the list is very similar to that in the above example:

    str(area2, max.level = 2)

output

    ## List of 4
    ##  $ est    :Classes 'data.table' and 'data.frame':    1 obs. of  3 variables:
    ##   ..$ ONEUNIT               : num 1
    ##   ..$ Estimate              : num 666699
    ##   ..$ Percent Sampling Error: num 10.2
    ##   ..- attr(*, ".internal.selfref")=<externalptr>
    ##   ..- attr(*, "sorted")= chr "ONEUNIT"
    ##  $ raw    :List of 9
    ##   ..$ unit_totest  :'data.frame':    1 obs. of  18 variables:
    ##   ..$ domdat       :'data.frame':    66 obs. of  19 variables:
    ##   ..$ module       : chr "MA"
    ##   ..$ esttype      : chr "AREA"
    ##   ..$ MAmethod     : chr "gregEN"
    ##   ..$ predselectlst:List of 1
    ##   ..$ rowvar       : chr "TOTAL"
    ##   ..$ colvar       : chr "NONE"
    ##   ..$ areaunits    : chr "acres"
    ##  $ statecd: int 56
    ##  $ invyr  : int [1:3] 2011 2012 2013

However now the `raw` list has an item call `predselectlst`. We can look at this item now:

    area2$raw$predselectlst$totest

output

    ##    ONEUNIT TOTAL           dem slp asp_cos asp_sin fornf2
    ## 1:       1     1 -0.0002550206   0       0       0      0

Notably, we can see that `dem`, `slp`, `asp_cos`, and `asp_sin` were removed from the model.

#### Example 4: Area by forest type on forest land, Wyoming, 2011-2013

View Example

In this example, we look at adding rows to the output and include returntitle=TRUE to return title information.

    area3 <- modMAarea(
        MApopdat = MApopdat,         # pop - population calculations for WY, post-stratification
        MAmethod = "greg",           # est - model-assisted method
        landarea = "FOREST",         # est - forest land filter
        rowvar = "FORTYPCD",         # est - row domain
        returntitle = TRUE           # out - return title information
        )

Again, we can look at the contents of the output list. The output now includes titlelst, a list of associated titles.

    str(area3, max.level = 1)

output

    ## List of 5
    ##  $ est     :'data.frame':    8 obs. of  3 variables:
    ##  $ titlelst:List of 9
    ##  $ raw     :List of 10
    ##  $ statecd : int 56
    ##  $ invyr   : int [1:3] 2011 2012 2013

And the estimates:

    ## Estimate and percent sampling error of estimate
    area3$est

output

    ##   Forest type Estimate Percent Sampling Error
    ## 1         201  42653.6                  60.56
    ## 2         265  47917.2                  67.78
    ## 3         266  71039.9                  43.05
    ## 4         268  39520.3                   68.8
    ## 5         281 407596.6                  16.05
    ## 6         901  24905.9                  78.03
    ## 7         999  26761.6                  63.54
    ## 8       Total 660395.1                   9.42

Along with raw data and titles:

    ## Raw data (list object) for estimate
    raw3 <- area3$raw      # extract raw data list object from output
    names(raw3)

output

    ##  [1] "unit_totest"   "unit_rowest"   "domdat"        "module"
    ##  [5] "esttype"       "MAmethod"      "predselectlst" "rowvar"
    ##  [9] "colvar"        "areaunits"

    head(raw3$unit_totest) # estimates by estimation unit (i.e., ESTN_UNIT)

output

    ##   ONEUNIT      nhat    nhat.var NBRPLT NBRPLT.gt0 ACRES_GIS AREAUSED      est
    ## 1       1 0.5936603 0.003129767     56         37   1112412  1112412 660395.1
    ##      est.var   est.se     est.cv      pse CI99left CI99right CI95left CI95right
    ## 1 3872964796 62233.15 0.09423624 9.423624 500093.1    820697 538420.4  782369.8
    ##   CI68left CI68right
    ## 1 598506.8  722283.3

    raw3$totest            # estimates for population (i.e., WY)

output

    ## NULL

    head(raw3$unit_rowest) # estimates by row, by estimation unit (i.e., ESTN_UNIT)

output

    ##   ONEUNIT Forest type       nhat     nhat.var NBRPLT NBRPLT.gt0 ACRES_GIS
    ## 1       1         201 0.03834336 0.0005392280     56          2   1112412
    ## 2       1         265 0.04307505 0.0008523855     56          4   1112412
    ## 3       1         266 0.06386110 0.0007557639     56          5   1112412
    ## 4       1         268 0.03552668 0.0005973938     56          3   1112412
    ## 5       1         281 0.36640782 0.0034566717     56         23   1112412
    ## 6       1         901 0.02238906 0.0003052203     56          1   1112412
    ##   AREAUSED       est    est.var   est.se    est.cv      pse CI99left CI99right
    ## 1  1112412  42653.63  667273775 25831.64 0.6056142 60.56142      0.0 109191.53
    ## 2  1112412  47917.21 1054793996 32477.59 0.6777855 67.77855      0.0 131573.95
    ## 3  1112412  71039.88  935228490 30581.51 0.4304836 43.04836      0.0 149812.62
    ## 4  1112412  39520.32  739251639 27189.18 0.6879799 68.79799      0.0 109555.01
    ## 5  1112412 407596.59 4277497216 65402.58 0.1604591 16.04591 239130.7 576062.46
    ## 6  1112412  24905.87  377698351 19434.46 0.7803167 78.03167      0.0  74965.72
    ##    CI95left CI95right   CI68left CI68right
    ## 1      0.00  93282.72  16965.145  68342.11
    ## 2      0.00 111572.13  15619.617  80214.81
    ## 3  11101.23 130978.53  40627.860 101451.90
    ## 4      0.00  92810.14  12481.820  66558.81
    ## 5 279409.89 535783.28 342556.478 472636.70
    ## 6      0.00  62996.71   5579.111  44232.62

    head(raw3$rowest)      # estimates by row for population (i.e., WY)

output

    ## NULL

    ## Titles (list object) for estimate
    titlelst3 <- area3$titlelst
    names(titlelst3)

output

    ## [1] "title.estpse"  "title.unitvar" "title.ref"     "outfn.estpse"
    ## [5] "outfn.rawdat"  "outfn.param"   "title.rowvar"  "title.row"
    ## [9] "title.unitsn"

    titlelst3

output

    ## $title.estpse
    ## [1] "Area, in acres, and percent sampling error on forest land by forest type"
    ##
    ## $title.unitvar
    ## [1] "ONEUNIT"
    ##
    ## $title.ref
    ## [1] ", 2011-2013"
    ##
    ## $outfn.estpse
    ## [1] "area_FORTYPCD_forestland"
    ##
    ## $outfn.rawdat
    ## [1] "area_FORTYPCD_forestland_rawdata"
    ##
    ## $outfn.param
    ## [1] "area_FORTYPCD_forestland_parameters"
    ##
    ## $title.rowvar
    ## [1] "Forest type"
    ##
    ## $title.row
    ## [1] "Area, in acres, on forest land by forest type; , 2011-2013"
    ##
    ## $title.unitsn
    ## [1] "acres"

#### Example 5: Area by forest type and stand-size class on forest land, Wyoming, 2011-2013

View Example

In this example, we look at adding rows and columns to output, including FIA names. We also output estimates and percent standard error in the same cell with the `allin1` argument in `table_options` and save data to an outfolder with the `outfolder` argument in `savedata_options`.

    ## Area of forest land by forest type and stand-size class, Wyoming, 2011-2013
    area4 <- modMAarea(
        MApopdat = MApopdat,         # pop - population calculations for WY, post-stratification
        MAmethod = "greg",           # est - model-assisted method
        landarea = "FOREST",         # est - forest land filter
        rowvar = "FORTYPCD",         # est - row domain
        colvar = "STDSZCD",          # est - column domain
        savedata = TRUE,             # out - save data to outfolder
        returntitle = TRUE,          # out - return title information
        table_opts = list(
          row.FIAname = TRUE,          # table - row domain names
          col.FIAname = TRUE,          # table - column domain names
          allin1 = TRUE                # table - return output with est(pse)
          ),
        savedata_opts = list(
          outfolder = outfolder,       # save - outfolder for saving data
          outfn.pre = "WY"             # save - prefix for output files
          )
        )

    area4$est

output

    ##                         Forest type     Large diameter    Medium diameter
    ## 1:                      Douglas-fir  23,330.7 ( 79.00)        -- (    --)
    ## 2:                 Engelmann spruce  36,892.1 ( 74.16)  11,025.2 (175.15)
    ## 3: Engelmann spruce / subalpine fir  40,287.9 ( 68.99)  14,443.2 ( 66.30)
    ## 4:                    Subalpine fir  26,255.3 ( 75.29)        -- (    --)
    ## 5:                   Lodgepole pine 140,798.2 ( 33.20) 230,288.3 ( 20.42)
    ## 6:                            Aspen        -- (    --)        -- (    --)
    ## 7:                       Nonstocked        -- (    --)        -- (    --)
    ## 8:                            Total 267,564.1 ( 21.17) 255,756.7 ( 19.38)
    ##        Small diameter        Nonstocked              Total
    ## 1:  19,322.9 ( 99.12)       -- (    --)  42,653.6 ( 60.56)
    ## 2:        -- (    --)       -- (    --)  47,917.2 ( 67.78)
    ## 3:  16,308.7 ( 71.46)       -- (    --)  71,039.9 ( 43.05)
    ## 4:  13,265.0 (141.72)       -- (    --)  39,520.3 ( 68.80)
    ## 5:  36,510.1 ( 74.46)       -- (    --) 407,596.6 ( 16.05)
    ## 6:  24,905.9 ( 78.03)       -- (    --)  24,905.9 ( 78.03)
    ## 7:        -- (    --) 26,761.6 ( 63.54)  26,761.6 ( 63.54)
    ## 8: 110,312.6 ( 37.41) 26,761.6 ( 63.54) 660,395.1 (  9.42)

We can again look at the output list, estimates, raw data, and titles:

    ## Look at output list
    names(area4)

output

    ## [1] "est"      "pse"      "titlelst" "raw"      "statecd"  "invyr"

    ## Estimate and percent sampling error of estimate
    head(area4$est)

output

    ##                         Forest type     Large diameter    Medium diameter
    ## 1:                      Douglas-fir  23,330.7 ( 79.00)        -- (    --)
    ## 2:                 Engelmann spruce  36,892.1 ( 74.16)  11,025.2 (175.15)
    ## 3: Engelmann spruce / subalpine fir  40,287.9 ( 68.99)  14,443.2 ( 66.30)
    ## 4:                    Subalpine fir  26,255.3 ( 75.29)        -- (    --)
    ## 5:                   Lodgepole pine 140,798.2 ( 33.20) 230,288.3 ( 20.42)
    ## 6:                            Aspen        -- (    --)        -- (    --)
    ##       Small diameter  Nonstocked              Total
    ## 1: 19,322.9 ( 99.12) -- (    --)  42,653.6 ( 60.56)
    ## 2:       -- (    --) -- (    --)  47,917.2 ( 67.78)
    ## 3: 16,308.7 ( 71.46) -- (    --)  71,039.9 ( 43.05)
    ## 4: 13,265.0 (141.72) -- (    --)  39,520.3 ( 68.80)
    ## 5: 36,510.1 ( 74.46) -- (    --) 407,596.6 ( 16.05)
    ## 6: 24,905.9 ( 78.03) -- (    --)  24,905.9 ( 78.03)

    ## Raw data (list object) for estimate
    raw4 <- area4$raw      # extract raw data list object from output
    names(raw4)

output

    ##  [1] "unit_totest"   "unit_rowest"   "unit_colest"   "unit_grpest"
    ##  [5] "domdat"        "module"        "esttype"       "MAmethod"
    ##  [9] "predselectlst" "rowvar"        "colvar"        "areaunits"

    head(raw4$unit_totest) # estimates by estimation unit (i.e., ESTN_UNIT)

output

    ##   ONEUNIT      nhat    nhat.var NBRPLT NBRPLT.gt0 ACRES_GIS AREAUSED      est
    ## 1       1 0.5936603 0.003129767     56         37   1112412  1112412 660395.1
    ##      est.var   est.se     est.cv      pse CI99left CI99right CI95left CI95right
    ## 1 3872964796 62233.15 0.09423624 9.423624 500093.1    820697 538420.4  782369.8
    ##   CI68left CI68right
    ## 1 598506.8  722283.3

    head(raw4$totest)      # estimates for population (i.e., WY)

output

    ## NULL

    head(raw4$unit_rowest) # estimates by row, by estimation unit (i.e., ESTN_UNIT)

output

    ##   ONEUNIT                      Forest type       nhat     nhat.var NBRPLT
    ## 1       1                      Douglas-fir 0.03834336 0.0005392280     56
    ## 2       1                 Engelmann spruce 0.04307505 0.0008523855     56
    ## 3       1 Engelmann spruce / subalpine fir 0.06386110 0.0007557639     56
    ## 4       1                    Subalpine fir 0.03552668 0.0005973938     56
    ## 5       1                   Lodgepole pine 0.36640782 0.0034566717     56
    ## 6       1                            Aspen 0.02238906 0.0003052203     56
    ##   NBRPLT.gt0 FORTYPCD ACRES_GIS AREAUSED       est    est.var   est.se
    ## 1          2      201   1112412  1112412  42653.63  667273775 25831.64
    ## 2          4      265   1112412  1112412  47917.21 1054793996 32477.59
    ## 3          5      266   1112412  1112412  71039.88  935228490 30581.51
    ## 4          3      268   1112412  1112412  39520.32  739251639 27189.18
    ## 5         23      281   1112412  1112412 407596.59 4277497216 65402.58
    ## 6          1      901   1112412  1112412  24905.87  377698351 19434.46
    ##      est.cv      pse CI99left CI99right  CI95left CI95right   CI68left
    ## 1 0.6056142 60.56142      0.0 109191.53      0.00  93282.72  16965.145
    ## 2 0.6777855 67.77855      0.0 131573.95      0.00 111572.13  15619.617
    ## 3 0.4304836 43.04836      0.0 149812.62  11101.23 130978.53  40627.860
    ## 4 0.6879799 68.79799      0.0 109555.01      0.00  92810.14  12481.820
    ## 5 0.1604591 16.04591 239130.7 576062.46 279409.89 535783.28 342556.478
    ## 6 0.7803167 78.03167      0.0  74965.72      0.00  62996.71   5579.111
    ##   CI68right
    ## 1  68342.11
    ## 2  80214.81
    ## 3 101451.90
    ## 4  66558.81
    ## 5 472636.70
    ## 6  44232.62

    head(raw4$rowest)      # estimates by row for population (i.e., WY)

output

    ## NULL

    head(raw4$unit_colest) # estimates by column, by estimation unit (i.e., ESTN_UNIT)

output

    ##   ONEUNIT Stand-size class       nhat     nhat.var NBRPLT NBRPLT.gt0 STDSZCD
    ## 1       1   Large diameter 0.24052605 0.0025935705     56         18       1
    ## 2       1  Medium diameter 0.22991178 0.0019845421     56         14       2
    ## 3       1   Small diameter 0.09916524 0.0013761149     56          6       3
    ## 4       1       Nonstocked 0.02405726 0.0002336838     56          1       5
    ##   ACRES_GIS AREAUSED       est    est.var   est.se    est.cv      pse  CI99left
    ## 1   1112412  1112412 267564.15 3209443017 56651.95 0.2117322 21.17322 121638.40
    ## 2   1112412  1112412 255756.70 2455793975 49555.97 0.1937621 19.37621 128108.99
    ## 3   1112412  1112412 110312.64 1702888801 41266.07 0.3740829 37.40829   4018.28
    ## 4   1112412  1112412  26761.59  289174599 17005.13 0.6354306 63.54306      0.00
    ##   CI99right  CI95left CI95right   CI68left CI68right
    ## 1 413489.89 156528.37 378599.92 211226.172 323902.12
    ## 2 383404.42 158628.79 352884.62 206475.381 305038.03
    ## 3 216607.00  29432.62 191192.66  69275.269 151350.01
    ## 4  70563.91      0.00  60091.04   9850.701  43672.48

    head(raw4$colest)      # estimates by column for population (i.e., WY)

output

    ## NULL

    head(raw4$unit_grpest) # estimates by row and column, by estimation unit (i.e., ESTN_UNIT)

output

    ##   ONEUNIT                                           grpvar        nhat
    ## 1       1                       Douglas-fir#Large diameter 0.020973074
    ## 2       1                       Douglas-fir#Small diameter 0.017370285
    ## 3       1                  Engelmann spruce#Large diameter 0.033164010
    ## 4       1                 Engelmann spruce#Medium diameter 0.009911038
    ## 5       1  Engelmann spruce / subalpine fir#Large diameter 0.036216716
    ## 6       1 Engelmann spruce / subalpine fir#Medium diameter 0.012983698
    ##       nhat.var NBRPLT NBRPLT.gt0                      Forest type
    ## 1 2.745298e-04     56          1                      Douglas-fir
    ## 2 2.964436e-04     56          1                      Douglas-fir
    ## 3 6.048455e-04     56          3                 Engelmann spruce
    ## 4 3.013453e-04     56          1                 Engelmann spruce
    ## 5 6.243626e-04     56          3 Engelmann spruce / subalpine fir
    ## 6 7.410764e-05     56          1 Engelmann spruce / subalpine fir
    ##   Stand-size class STDSZCD FORTYPCD ACRES_GIS AREAUSED      est   est.var
    ## 1   Large diameter       1      201   1112412  1112412 23330.71 339719955
    ## 2   Small diameter       3      201   1112412  1112412 19322.92 366837446
    ## 3   Large diameter       1      265   1112412  1112412 36892.05 748472910
    ## 4  Medium diameter       2      265   1112412  1112412 11025.16 372903083
    ## 5   Large diameter       1      266   1112412  1112412 40287.92 772624533
    ## 6  Medium diameter       2      266   1112412  1112412 14443.23  91705337
    ##     est.se    est.cv       pse CI99left CI99right CI95left CI95right   CI68left
    ## 1 18431.49 0.7900101  79.00101        0  70807.09        0  59455.77  5001.3621
    ## 2 19153.00 0.9912064  99.12064        0  68657.78        0  56862.11   276.0668
    ## 3 27358.23 0.7415752  74.15752        0 107362.19        0  90513.21  9685.4439
    ## 4 19310.70 1.7515118 175.15118        0  60766.22        0  48873.43     0.0000
    ## 5 27796.12 0.6899369  68.99369        0 111885.99        0  94767.33 12645.8475
    ## 6  9576.29 0.6630299  66.30299        0  39110.12        0  33212.41  4920.0086
    ##   CI68right
    ## 1  41660.05
    ## 2  38369.77
    ## 3  64098.66
    ## 4  30228.84
    ## 5  67930.00
    ## 6  23966.44

    head(raw4$grpest)      # estimates by row and column for population (i.e., WY)

output

    ## NULL

    ## Titles (list object) for estimate
    titlelst4 <- area4$titlelst
    names(titlelst4)

output

    ##  [1] "title.estpse"  "title.unitvar" "title.ref"     "outfn.estpse"
    ##  [5] "outfn.rawdat"  "outfn.param"   "title.rowvar"  "title.row"
    ##  [9] "title.colvar"  "title.col"     "title.unitsn"

    titlelst4

output

    ## $title.estpse
    ## [1] "Area, in acres (percent sampling error), by forest type and stand-size class on forest land"
    ##
    ## $title.unitvar
    ## [1] "ONEUNIT"
    ##
    ## $title.ref
    ## [1] ", 2011-2013"
    ##
    ## $outfn.estpse
    ## [1] "WY_area_FORTYPNM_STDSZNM_forestland"
    ##
    ## $outfn.rawdat
    ## [1] "WY_area_FORTYPNM_STDSZNM_forestland_rawdata"
    ##
    ## $outfn.param
    ## [1] "WY_area_FORTYPNM_STDSZNM_forestland_parameters"
    ##
    ## $title.rowvar
    ## [1] "Forest type"
    ##
    ## $title.row
    ## [1] "Area, in acres (percent sampling error), by forest type on forest land; , 2011-2013"
    ##
    ## $title.colvar
    ## [1] "Stand-size class"
    ##
    ## $title.col
    ## [1] "Area, in acres (percent sampling error), by stand-size class on forest land; , 2011-2013"
    ##
    ## $title.unitsn
    ## [1] "acres"

    ## List output files in outfolder
    list.files(outfolder, pattern = "WY_area")

output

    ## [1] "WY_area_FORTYPNM_STDSZNM_forestland.csv"
    ## [2] "WY_area_FORTYPNM_STDSZNM_forestland_modMA_mase_greg.csv"

    list.files(paste0(outfolder, "/rawdata"), pattern = "WY_area")

output

    ##  [1] "WY_area_FORTYPNM_STDSZNM_forestland_rawdata_colest.csv"
    ##  [2] "WY_area_FORTYPNM_STDSZNM_forestland_rawdata_domdat.csv"
    ##  [3] "WY_area_FORTYPNM_STDSZNM_forestland_rawdata_grpest.csv"
    ##  [4] "WY_area_FORTYPNM_STDSZNM_forestland_rawdata_modMA_mase_greg_domdat.csv"
    ##  [5] "WY_area_FORTYPNM_STDSZNM_forestland_rawdata_modMA_mase_greg_unit_colest.csv"
    ##  [6] "WY_area_FORTYPNM_STDSZNM_forestland_rawdata_modMA_mase_greg_unit_grpest.csv"
    ##  [7] "WY_area_FORTYPNM_STDSZNM_forestland_rawdata_modMA_mase_greg_unit_rowest.csv"
    ##  [8] "WY_area_FORTYPNM_STDSZNM_forestland_rawdata_modMA_mase_greg_unit_totest.csv"
    ##  [9] "WY_area_FORTYPNM_STDSZNM_forestland_rawdata_rowest.csv"
    ## [10] "WY_area_FORTYPNM_STDSZNM_forestland_rawdata_totest.csv"
    ## [11] "WY_area_FORTYPNM_STDSZNM_forestland_rawdata_unit_colest.csv"
    ## [12] "WY_area_FORTYPNM_STDSZNM_forestland_rawdata_unit_grpest.csv"
    ## [13] "WY_area_FORTYPNM_STDSZNM_forestland_rawdata_unit_rowest.csv"
    ## [14] "WY_area_FORTYPNM_STDSZNM_forestland_rawdata_unit_totest.csv"

### `modMAtree`

We will set our estimate variable and filter now. We set `estvar` to `"VOLCFNET"` for net cubic foot volume, and filter with `estvar.filter` set to `"STATUSCD == 1"` so we only consider live trees in our estimation.

    estvar <- "VOLCFNET"
    live_trees <- "STATUSCD == 1"

#### Example 6: Net cubic-foot volume of live trees, Wyoming, 2011-2013

View Example

We now will generate estimates by estimation unit (i.e., ESTN_UNIT) and sum to population (i.e., WY) with `modMAtree`.

    ## Return raw data and titles
    ## Total net cubic-foot volume of live trees (at least 5 inches diameter), Wyoming, 2011-2013
    tree1 <- modMAtree(
        MApopdat = MApopdat,         # pop - population calculations
        MAmethod = "greg",           # est - model-assisted method
        landarea = "FOREST",         # est - forest land filter
        estvar = estvar,             # est - net cubic-foot volume
        estvar.filter = live_trees,  # est - live trees only
        returntitle = TRUE           # out - return title information
        )

    names(tree1)

output

    ## [1] "est"      "titlelst" "raw"      "statecd"  "invyr"

    tree1$raw$unit_totest

output

    ##   ONEUNIT     nhat nhat.var NBRPLT NBRPLT.gt0 ACRES_GIS AREAUSED        est
    ## 1       1 1165.825  30923.7     56         34   1112412  1112412 1296877648
    ##        est.var    est.se    est.cv      pse  CI99left  CI99right  CI95left
    ## 1 3.826688e+16 195619213 0.1508386 15.08386 792995947 1800759350 913471036
    ##    CI95right   CI68left  CI68right
    ## 1 1680284261 1102342580 1491412717

#### Example 7: Net cubic-foot volume of live trees, Wyoming, 2011-2013, using the Elastic Net for variable selection

View Example

Here, we fit the same model as the above example, but rather than using `"greg"` are our model-assisted method, we can use `"gregEN"` where the EN stands for “elastic net”. The elastic net performs variable selection for us, grabbing predictors it finds to be most useful in the model.

    ## Return raw data and titles
    ## Total net cubic-foot volume of live trees (at least 5 inches diameter), Wyoming, 2011-2013
    tree2 <- modMAtree(
        MApopdat = MApopdat,         # pop - population calculations
        MAmethod = "gregEN",         # est - model-assisted method
        landarea = "FOREST",         # est - forest land filter
        estvar = estvar,             # est - net cubic-foot volume
        estvar.filter = live_trees,  # est - live trees only
        returntitle = TRUE           # out - return title information
        )

We can again see that the structure of the list is very similar to that in the above example:

    str(tree2, max.level = 2)

output

    ## List of 5
    ##  $ est     :Classes 'data.table' and 'data.frame':   1 obs. of  3 variables:
    ##   ..$ ONEUNIT               : num 1
    ##   ..$ Estimate              : num 1.31e+09
    ##   ..$ Percent Sampling Error: num 14.9
    ##   ..- attr(*, ".internal.selfref")=<externalptr>
    ##   ..- attr(*, "sorted")= chr "ONEUNIT"
    ##  $ titlelst:List of 10
    ##   ..$ title.estpse : chr "Net volume of live trees (at least 5 in dia), in cubic feet, and percent sampling error on forest land live"
    ##   ..$ title.yvar   : chr "Net volume, in cubic feet"
    ##   ..$ title.estvar : chr "Net volume of live trees (at least 5 in dia)"
    ##   ..$ title.unitvar: chr "ONEUNIT"
    ##   ..$ title.ref    : chr "Wyoming, 2011-2013"
    ##   ..$ outfn.estpse : chr "tree_VOLCFNET_live_forestland"
    ##   ..$ outfn.rawdat : chr "tree_VOLCFNET_live_forestland_rawdata"
    ##   ..$ outfn.param  : chr "tree_VOLCFNET_live_forestland_parameters"
    ##   ..$ title.tot    : chr "Net volume of live trees (at least 5 in dia), in cubic feet, on forest land live; Wyoming, 2011-2013"
    ##   ..$ title.unitsn : chr "cubic feet"
    ##  $ raw     :List of 13
    ##   ..$ unit_totest  :'data.frame':    1 obs. of  18 variables:
    ##   ..$ domdat       :'data.frame':    66 obs. of  19 variables:
    ##   ..$ plotweights  :List of 1
    ##   ..$ estvar       : chr "VOLCFNET"
    ##   ..$ estvar.filter: chr "STATUSCD == 1"
    ##   ..$ module       : chr "MA"
    ##   ..$ esttype      : chr "TREE"
    ##   ..$ MAmethod     : chr "gregEN"
    ##   ..$ predselectlst:List of 1
    ##   ..$ rowvar       : chr "TOTAL"
    ##   ..$ colvar       : chr "NONE"
    ##   ..$ areaunits    : chr "acres"
    ##   ..$ estunits     : num 1
    ##  $ statecd : int 56
    ##  $ invyr   : int [1:3] 2011 2012 2013

However now the `raw` list has an item call `predselectlst`. We can look at this item now:

    tree2$raw$predselectlst

output

    ## $totest
    ##    ONEUNIT TOTAL       dem       slp  asp_cos   asp_sin    fornf2
    ## 1:       1     1 0.6497733 -63.48846 32.55884 -536.5366 -1369.907

Notably, we can see that [INSERT CORRECT PREDS] `dem`, `slp`, `asp_cos`, and `asp_sin` were removed from the model.

#### Example 8: Net cubic-foot volume of live trees by forest type, Wyoming, 2011-2013

View Example

This example adds rows to the output for net cubic-foot volume of live trees (at least 5 inches diameter) by forest type, Wyoming, 2011-2013. We also choose to return titles with `returntitle = TRUE`.

    tree3 <- modMAtree(
        MApopdat = MApopdat,         # pop - population calculations
        MAmethod = "greg",           # est - model-assisted method
        landarea = "FOREST",         # est - forest land filter
        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
        )

Again, we investigate the output of the returned list:

    ## Look at output list
    names(tree3)

output

    ## [1] "est"      "titlelst" "raw"      "statecd"  "invyr"

    ## Estimate and percent sampling error of estimate
    tree3$est

output

    ##   Forest type     Estimate Percent Sampling Error
    ## 1         201   15329084.7                  63.95
    ## 2         265  191806950.6                  70.43
    ## 3         266  135152582.5                  66.37
    ## 4         268   49388166.9                  73.19
    ## 5         281  905200863.5                  19.75
    ## 6         901           --                     --
    ## 7         999           --                     --
    ## 8       Total 1296877648.2                  15.08

    ## Raw data (list object) for estimate
    raw3 <- tree3$raw      # extract raw data list object from output
    names(raw3)

output

    ##  [1] "unit_totest"   "unit_rowest"   "domdat"        "plotweights"
    ##  [5] "estvar"        "estvar.filter" "module"        "esttype"
    ##  [9] "MAmethod"      "predselectlst" "rowvar"        "colvar"
    ## [13] "areaunits"     "estunits"

    head(raw3$unit_totest)   # estimates by estimation unit (i.e., ESTN_UNIT)

output

    ##   ONEUNIT     nhat nhat.var NBRPLT NBRPLT.gt0 ACRES_GIS AREAUSED        est
    ## 1       1 1165.825  30923.7     56         34   1112412  1112412 1296877648
    ##        est.var    est.se    est.cv      pse  CI99left  CI99right  CI95left
    ## 1 3.826688e+16 195619213 0.1508386 15.08386 792995947 1800759350 913471036
    ##    CI95right   CI68left  CI68right
    ## 1 1680284261 1102342580 1491412717

    head(raw3$totest)        # estimates for population (i.e., WY)

output

    ## NULL

    head(raw3$unit_rowest)   # estimates by row, by estimation unit (i.e., ESTN_UNIT)

output

    ##   ONEUNIT Forest type      nhat    nhat.var NBRPLT NBRPLT.gt0 ACRES_GIS
    ## 1       1         201  13.78004    77.64629     56          2   1112412
    ## 2       1         265 172.42433 14746.63678     56          4   1112412
    ## 3       1         266 121.49504  6501.78676     56          5   1112412
    ## 4       1         268  44.39736  1055.90466     56          2   1112412
    ## 5       1         281 813.72781 25826.51205     56         23   1112412
    ## 6       1         901   0.00000     0.00000     56          0   1112412
    ##   AREAUSED       est      est.var    est.se    est.cv      pse  CI99left
    ## 1  1112412  15329085 9.608428e+13   9802259 0.6394549 63.94549         0
    ## 2  1112412 191806951 1.824839e+16 135086607 0.7042842 70.42842         0
    ## 3  1112412 135152582 8.045709e+15  89697877 0.6636786 66.36786         0
    ## 4  1112412  49388167 1.306641e+15  36147491 0.7319059 73.19059         0
    ## 5  1112412 905200864 3.195931e+16 178771664 0.1974939 19.74939 444715574
    ## 6  1112412         0 0.000000e+00         0       NaN      NaN         0
    ##    CI99right  CI95left  CI95right  CI68left  CI68right
    ## 1   40578030         0   34541159   5581151   25077018
    ## 2  539766992         0  456571836  57469009  326144892
    ## 3  366199002         0  310957191  45951822  224353343
    ## 4  142497933         0  120235947  13441010   85335324
    ## 5 1365686153 554814841 1255586886 727419973 1082981754
    ## 6          0         0          0         0          0

    head(raw3$rowest)        # estimates by row for population (i.e., WY)

output

    ## NULL

    ## Titles (list object) for estimate
    titlelst3 <- tree3$titlelst
    names(titlelst3)

output

    ##  [1] "title.estpse"  "title.yvar"    "title.estvar"  "title.unitvar"
    ##  [5] "title.ref"     "outfn.estpse"  "outfn.rawdat"  "outfn.param"
    ##  [9] "title.rowvar"  "title.row"     "title.unitsn"

    titlelst3

output

    ## $title.estpse
    ## [1] "Net volume of live trees (at least 5 in dia), in cubic feet, and percent sampling error on forest land by forest type live"
    ##
    ## $title.yvar
    ## [1] "Net volume, in cubic feet"
    ##
    ## $title.estvar
    ## [1] "Net volume of live trees (at least 5 in dia)"
    ##
    ## $title.unitvar
    ## [1] "ONEUNIT"
    ##
    ## $title.ref
    ## [1] "Wyoming, 2011-2013"
    ##
    ## $outfn.estpse
    ## [1] "tree_VOLCFNET_live_FORTYPCD_forestland"
    ##
    ## $outfn.rawdat
    ## [1] "tree_VOLCFNET_live_FORTYPCD_forestland_rawdata"
    ##
    ## $outfn.param
    ## [1] "tree_VOLCFNET_live_FORTYPCD_forestland_parameters"
    ##
    ## $title.rowvar
    ## [1] "Forest type"
    ##
    ## $title.row
    ## [1] "Net volume of live trees (at least 5 in dia), in cubic feet, on forest land by forest type live; Wyoming, 2011-2013"
    ##
    ## $title.unitsn
    ## [1] "cubic feet"

We can also create a simple barplot from the output:

    ## Create barplot
    datBarplot(
          raw3$unit_rowest,
          xvar = titlelst3$title.rowvar,
          yvar = "est"
          )

plot

And a fancier barplot:

    ## Create fancier barplot
    datBarplot(
          raw3$unit_rowest,
          xvar = titlelst3$title.rowvar,
          yvar = "est",
          errbars = TRUE,
          sevar = "est.se",
          main = FIESTAutils::wraptitle(titlelst3$title.row, 75),
          ylabel = titlelst3$title.yvar,
          divideby = "million"
          )

plot

#### Example 9: Net cubic-foot volume of live trees by forest type and stand-size class, Wyoming, 2011-2013

View Example

This examples adds rows and columns to the output, including FIA names, for net cubic-foot volume of live trees (at least 5 inches diameter) by forest type and stand-size class, Wyoming, 2011-2013. We also use the `*_options` functions to return output with estimates (est) and percent standard error (pse) in same cell - est(pse) with `allin1 = TRUE` and save data to an outfolder with `savedata = TRUE` and `outfolder = outfolder`.

    tree4 <- modMAtree(
        MApopdat = MApopdat,         # pop - population calculations
        MAmethod = "greg",           # est - model-assisted method
        landarea = "FOREST",         # est - forest land filter
        estvar = "VOLCFNET",               # est - net cubic-foot volume
        estvar.filter = "STATUSCD  == 1",   # est - live trees only
        rowvar = "FORTYPCD",         # est - row domain
        colvar = "STDSZCD",          # est - column domain
        returntitle = TRUE,          # out - return title information
        savedata = TRUE,             # out - save data to outfolder
        table_opts = table_options(
          row.FIAname = TRUE,          # est - row domain names
          col.FIAname = TRUE,          # est - column domain names
          allin1 = TRUE                # out - return output with est(pse)
        ),
        savedata_opts = savedata_options(
          outfolder = outfolder,       # out - outfolder for saving data
          outfn.pre = "WY"             # out - prefix for output files
          )
        )

Again, we investigate the output of the returned list:

    ## Look at output list from modGBarea()
    names(tree4)

output

    ## [1] "est"      "pse"      "titlelst" "raw"      "statecd"  "invyr"

    ## Estimate and percent sampling error of estimate
    tree4$est

output

    ##                         Forest type         Large diameter
    ## 1:                      Douglas-fir  11,866,612.7 ( 79.00)
    ## 2:                 Engelmann spruce 149,865,021.5 ( 78.94)
    ## 3: Engelmann spruce / subalpine fir 113,586,516.8 ( 78.74)
    ## 4:                    Subalpine fir  49,388,166.9 ( 73.19)
    ## 5:                   Lodgepole pine 456,907,508.9 ( 34.84)
    ## 6:                            Aspen            -- (    --)
    ## 7:                       Nonstocked            -- (    --)
    ## 8:                            Total 781,613,826.8 ( 23.93)
    ##           Medium diameter        Small diameter  Nonstocked
    ## 1:            -- (    --)  3,462,472.0 ( 99.12) -- (    --)
    ## 2:  41,941,929.1 (175.15)           -- (    --) -- (    --)
    ## 3:  16,395,905.1 ( 66.30)  5,170,160.5 ( 71.46) -- (    --)
    ## 4:            -- (    --)           -- (    --) -- (    --)
    ## 5: 442,719,166.9 ( 21.99)  5,574,187.7 ( 77.89) -- (    --)
    ## 6:            -- (    --)           -- (    --) -- (    --)
    ## 7:            -- (    --)           -- (    --) -- (    --)
    ## 8: 501,057,001.1 ( 23.52) 14,206,820.3 ( 43.06) -- (    --)
    ##                       Total
    ## 1:    15,329,084.7 ( 63.95)
    ## 2:   191,806,950.6 ( 70.43)
    ## 3:   135,152,582.5 ( 66.37)
    ## 4:    49,388,166.9 ( 73.19)
    ## 5:   905,200,863.5 ( 19.75)
    ## 6:              -- (    --)
    ## 7:              -- (    --)
    ## 8: 1,296,877,648.2 ( 15.08)

    ## Raw data (list object) for estimate
    raw4 <- tree4$raw      # extract raw data list object from output
    names(raw4)

output

    ##  [1] "unit_totest"   "unit_rowest"   "unit_colest"   "unit_grpest"
    ##  [5] "domdat"        "plotweights"   "estvar"        "estvar.filter"
    ##  [9] "module"        "esttype"       "MAmethod"      "predselectlst"
    ## [13] "rowvar"        "colvar"        "areaunits"     "estunits"

    head(raw4$unit_totest)   # estimates by estimation unit (i.e., ESTN_UNIT)

output

    ##   ONEUNIT     nhat nhat.var NBRPLT NBRPLT.gt0 ACRES_GIS AREAUSED        est
    ## 1       1 1165.825  30923.7     56         34   1112412  1112412 1296877648
    ##        est.var    est.se    est.cv      pse  CI99left  CI99right  CI95left
    ## 1 3.826688e+16 195619213 0.1508386 15.08386 792995947 1800759350 913471036
    ##    CI95right   CI68left  CI68right
    ## 1 1680284261 1102342580 1491412717

    head(raw4$totest)        # estimates for population (i.e., WY)

output

    ## NULL

    head(raw4$unit_rowest)   # estimates by row, by estimation unit (i.e., ESTN_UNIT)

output

    ##   ONEUNIT                      Forest type      nhat    nhat.var NBRPLT
    ## 1       1                      Douglas-fir  13.78004    77.64629     56
    ## 2       1                 Engelmann spruce 172.42433 14746.63678     56
    ## 3       1 Engelmann spruce / subalpine fir 121.49504  6501.78676     56
    ## 4       1                    Subalpine fir  44.39736  1055.90466     56
    ## 5       1                   Lodgepole pine 813.72781 25826.51205     56
    ## 6       1                            Aspen   0.00000     0.00000     56
    ##   NBRPLT.gt0 FORTYPCD ACRES_GIS AREAUSED       est      est.var    est.se
    ## 1          2      201   1112412  1112412  15329085 9.608428e+13   9802259
    ## 2          4      265   1112412  1112412 191806951 1.824839e+16 135086607
    ## 3          5      266   1112412  1112412 135152582 8.045709e+15  89697877
    ## 4          2      268   1112412  1112412  49388167 1.306641e+15  36147491
    ## 5         23      281   1112412  1112412 905200864 3.195931e+16 178771664
    ## 6          0      901   1112412  1112412         0 0.000000e+00         0
    ##      est.cv      pse  CI99left  CI99right  CI95left  CI95right  CI68left
    ## 1 0.6394549 63.94549         0   40578030         0   34541159   5581151
    ## 2 0.7042842 70.42842         0  539766992         0  456571836  57469009
    ## 3 0.6636786 66.36786         0  366199002         0  310957191  45951822
    ## 4 0.7319059 73.19059         0  142497933         0  120235947  13441010
    ## 5 0.1974939 19.74939 444715574 1365686153 554814841 1255586886 727419973
    ## 6       NaN      NaN         0          0         0          0         0
    ##    CI68right
    ## 1   25077018
    ## 2  326144892
    ## 3  224353343
    ## 4   85335324
    ## 5 1082981754
    ## 6          0

    head(raw4$rowest)        # estimates by row for population (i.e., WY)

output

    ## NULL

    head(raw4$unit_colest)   # estimates by column, by estimation unit (i.e., ESTN_UNIT)

output

    ##   ONEUNIT Stand-size class      nhat    nhat.var NBRPLT NBRPLT.gt0 STDSZCD
    ## 1       1   Large diameter 702.62958 28262.84167     56         18       1
    ## 2       1  Medium diameter 450.42380 11221.16423     56         14       2
    ## 3       1   Small diameter  12.77118    30.23649     56          4       3
    ## 4       1       Nonstocked   0.00000     0.00000     56          0       5
    ##   ACRES_GIS AREAUSED       est      est.var    est.se    est.cv      pse
    ## 1   1112412  1112412 781613827 3.497417e+16 187013826 0.2392663 23.92663
    ## 2   1112412  1112412 501057001 1.388576e+16 117837837 0.2351785 23.51785
    ## 3   1112412  1112412  14206820 3.741649e+13   6116902 0.4305609 43.05609
    ## 4   1112412  1112412         0 0.000000e+00         0       NaN      NaN
    ##    CI99left  CI99right  CI95left  CI95right  CI68left CI68right
    ## 1 299898133 1263329520 415073463 1148154191 595636453 967591201
    ## 2 197526847  804587155 270099085  732014918 383872235 618241767
    ## 3         0   29962915   2217913   26195727   8123819  20289821
    ## 4         0          0         0          0         0         0

    head(raw4$colest)        # estimates by column for population (i.e., WY)

output

    ## NULL

    head(raw4$unit_grpest)   # estimates by row and column, by estimation unit (i.e., ESTN_UNIT)

output

    ##   ONEUNIT                                           grpvar      nhat
    ## 1       1                       Douglas-fir#Large diameter  10.66746
    ## 2       1                       Douglas-fir#Small diameter   3.11258
    ## 3       1                  Engelmann spruce#Large diameter 134.72075
    ## 4       1                 Engelmann spruce#Medium diameter  37.70358
    ## 5       1  Engelmann spruce / subalpine fir#Large diameter 102.10828
    ## 6       1 Engelmann spruce / subalpine fir#Medium diameter  14.73905
    ##       nhat.var NBRPLT NBRPLT.gt0                      Forest type
    ## 1    71.021071     56          1                      Douglas-fir
    ## 2     9.518513     56          1                      Douglas-fir
    ## 3 11310.014570     56          3                 Engelmann spruce
    ## 4  4361.052579     56          1                 Engelmann spruce
    ## 5  6464.613685     56          3 Engelmann spruce / subalpine fir
    ## 6    95.500443     56          1 Engelmann spruce / subalpine fir
    ##   Stand-size class STDSZCD FORTYPCD ACRES_GIS AREAUSED       est      est.var
    ## 1   Large diameter       1      201   1112412  1112412  11866613 8.788582e+13
    ## 2   Small diameter       3      201   1112412  1112412   3462472 1.177879e+13
    ## 3   Large diameter       1      265   1112412  1112412 149865022 1.399570e+16
    ## 4  Medium diameter       2      265   1112412  1112412  41941929 5.396634e+15
    ## 5   Large diameter       1      266   1112412  1112412 113586517 7.999709e+15
    ## 6  Medium diameter       2      266   1112412  1112412  16395905 1.181781e+14
    ##      est.se    est.cv       pse CI99left CI99right CI95left CI95right
    ## 1   9374744 0.7900101  79.00101        0  36014353        0  30240773
    ## 2   3432024 0.9912064  99.12064        0  12302781        0  10189116
    ## 3 118303443 0.7894000  78.94000        0 454594497        0 381735510
    ## 4  73461783 1.7515118 175.15118        0 231166942        0 185924378
    ## 5  89441092 0.7874270  78.74270        0 343971502        0 288887835
    ## 6  10870975 0.6630299  66.30299        0  44397681        0  37702625
    ##      CI68left CI68right
    ## 1  2543824.72  21189401
    ## 2    49468.39   6875476
    ## 3 32217229.75 267512813
    ## 4        0.00 114996578
    ## 5 24641118.08 202531916
    ## 6  5585178.40  27206632

    head(raw4$grpest)        # estimates by row and column for population (i.e., WY)

output

    ## NULL

    ## Titles (list object) for estimate
    titlelst4 <- tree4$titlelst
    names(titlelst4)

output

    ##  [1] "title.estpse"  "title.yvar"    "title.estvar"  "title.unitvar"
    ##  [5] "title.ref"     "outfn.estpse"  "outfn.rawdat"  "outfn.param"
    ##  [9] "title.rowvar"  "title.row"     "title.colvar"  "title.col"
    ## [13] "title.unitsn"

    titlelst4

output

    ## $title.estpse
    ## [1] "Net volume of live trees (at least 5 in dia), in cubic feet (percent sampling error), by forest type and stand-size class on forest land live"
    ##
    ## $title.yvar
    ## [1] "Net volume, in cubic feet"
    ##
    ## $title.estvar
    ## [1] "Net volume of live trees (at least 5 in dia)"
    ##
    ## $title.unitvar
    ## [1] "ONEUNIT"
    ##
    ## $title.ref
    ## [1] "Wyoming, 2011-2013"
    ##
    ## $outfn.estpse
    ## [1] "WY_tree_VOLCFNET_live_FORTYPNM_STDSZNM_forestland"
    ##
    ## $outfn.rawdat
    ## [1] "WY_tree_VOLCFNET_live_FORTYPNM_STDSZNM_forestland_rawdata"
    ##
    ## $outfn.param
    ## [1] "WY_tree_VOLCFNET_live_FORTYPNM_STDSZNM_forestland_parameters"
    ##
    ## $title.rowvar
    ## [1] "Forest type"
    ##
    ## $title.row
    ## [1] "Net volume of live trees (at least 5 in dia), in cubic feet (percent sampling error), by forest type on forest land live; Wyoming, 2011-2013"
    ##
    ## $title.colvar
    ## [1] "Stand-size class"
    ##
    ## $title.col
    ## [1] "Net volume of live trees (at least 5 in dia), in cubic feet (percent sampling error), by stand-size class on forest land live; Wyoming, 2011-2013"
    ##
    ## $title.unitsn
    ## [1] "cubic feet"

    ## List output files in outfolder
    list.files(outfolder, pattern = "WY_tree")

output

    ## [1] "WY_tree_VOLCFNET_live_FORTYPNM_STDSZNM_forestland.csv"
    ## [2] "WY_tree_VOLCFNET_live_FORTYPNM_STDSZNM_forestland_modMA_mase_greg.csv"

    list.files(paste0(outfolder, "/rawdata"), pattern = "WY_tree")

output

    ##  [1] "WY_tree_VOLCFNET_live_FORTYPNM_STDSZNM_forestland_rawdata_colest.csv"
    ##  [2] "WY_tree_VOLCFNET_live_FORTYPNM_STDSZNM_forestland_rawdata_domdat.csv"
    ##  [3] "WY_tree_VOLCFNET_live_FORTYPNM_STDSZNM_forestland_rawdata_grpest.csv"
    ##  [4] "WY_tree_VOLCFNET_live_FORTYPNM_STDSZNM_forestland_rawdata_modMA_mase_greg_domdat.csv"
    ##  [5] "WY_tree_VOLCFNET_live_FORTYPNM_STDSZNM_forestland_rawdata_modMA_mase_greg_unit_colest.csv"
    ##  [6] "WY_tree_VOLCFNET_live_FORTYPNM_STDSZNM_forestland_rawdata_modMA_mase_greg_unit_grpest.csv"
    ##  [7] "WY_tree_VOLCFNET_live_FORTYPNM_STDSZNM_forestland_rawdata_modMA_mase_greg_unit_rowest.csv"
    ##  [8] "WY_tree_VOLCFNET_live_FORTYPNM_STDSZNM_forestland_rawdata_modMA_mase_greg_unit_totest.csv"
    ##  [9] "WY_tree_VOLCFNET_live_FORTYPNM_STDSZNM_forestland_rawdata_rowest.csv"
    ## [10] "WY_tree_VOLCFNET_live_FORTYPNM_STDSZNM_forestland_rawdata_totest.csv"
    ## [11] "WY_tree_VOLCFNET_live_FORTYPNM_STDSZNM_forestland_rawdata_unit_colest.csv"
    ## [12] "WY_tree_VOLCFNET_live_FORTYPNM_STDSZNM_forestland_rawdata_unit_grpest.csv"
    ## [13] "WY_tree_VOLCFNET_live_FORTYPNM_STDSZNM_forestland_rawdata_unit_rowest.csv"
    ## [14] "WY_tree_VOLCFNET_live_FORTYPNM_STDSZNM_forestland_rawdata_unit_totest.csv"

#### Example 10: Number of live trees by species, Wyoming, 2011-2013

View Example

We can use tree domain in estimation output rows:

    ## Number of live trees (at least 1 inch diameter) by species
    tree5 <- modMAtree(
        MApopdat = MApopdat,         # pop - population calculations
        MAmethod = "greg",           # est - model-assisted method
        landarea = "FOREST",         # est - forest land filter
        estvar = "TPA_UNADJ",               # est - number of trees per acre
        estvar.filter = "STATUSCD == 1",    # est - live trees only
        rowvar = "SPCD",             # est - row domain
        returntitle = TRUE,          # out - return title information
        table_opts = table_options(
          row.FIAname = TRUE,          # est - row domain names
          allin1 = FALSE               # out - return output with est and pse
          )
        )

We can also look at the output list and estimates again:

    ## Look at output list
    names(tree5)

output

    ## [1] "est"      "titlelst" "raw"      "statecd"  "invyr"

    ## Estimate and percent sampling error of estimate
    tree5$est

output

    ##            Species    Estimate Percent Sampling Error
    ## 1    quaking aspen  11153476.9                  73.73
    ## 2      limber pine   4461866.7                  90.07
    ## 3   lodgepole pine 184898322.4                  18.59
    ## 4    subalpine fir  68658860.9                  29.14
    ## 5 Engelmann spruce  50806944.2                  29.77
    ## 6      Douglas-fir    24655901                  73.84
    ## 7            Total 344635372.3                  13.07

#### Example 11: Number of live trees (plus seedlings) by species, Wyoming, 2011-2013

View Example

We can also add seedlings.

Note: seedling data are only available for number of trees (estvar = TPA_UNADJ).

Note: must include seedling data in population data calculations.

    MApopdat_seed <- modMApop(popTabs = list(tree = WYtree,
                                             cond = WYcond,
                                             seed = WYseed),
                         pltassgn = WYpltassgn,
                         auxdat = modeldat)

    ## Number of live trees by species, including seedlings
    tree6 <- modMAtree(
        MApopdat = MApopdat_seed,         # pop - population calculations
        MAmethod = "greg",           # est - model-assisted method
        estseed = "add",             # est - add seedling data
        landarea = "FOREST",         # est - forest land filter
        estvar = "TPA_UNADJ",               # est - number of trees per acre
        estvar.filter = "STATUSCD == 1",    # est - live trees only
        rowvar = "SPCD",             # est - row domain
        returntitle = TRUE,          # out - return title information
        table_opts = table_options(
          row.FIAname = TRUE,          # est - row domain names
          allin1 = FALSE)              # out - return output with est and pse
        )

And again we can look at our outputs and compare estimates:

    ## Look at output list
    names(tree6)

output

    ## [1] "est"      "titlelst" "raw"      "statecd"  "invyr"

    ## Estimate and percent sampling error of estimate
    tree6$est

output

    ##            Species    Estimate Percent Sampling Error
    ## 1    quaking aspen 105867206.7                  60.84
    ## 2      limber pine  38477186.7                  92.27
    ## 3   lodgepole pine 251790363.6                  18.03
    ## 4    subalpine fir 396440112.5                  23.94
    ## 5 Engelmann spruce 107965157.9                  33.92
    ## 6      Douglas-fir  49218941.8                  80.24
    ## 7            Total 949758969.2                  16.07

    ## Compare estimates with and without seedlings
    head(tree5$est)

output

    ##            Species    Estimate Percent Sampling Error
    ## 1    quaking aspen  11153476.9                  73.73
    ## 2      limber pine   4461866.7                  90.07
    ## 3   lodgepole pine 184898322.4                  18.59
    ## 4    subalpine fir  68658860.9                  29.14
    ## 5 Engelmann spruce  50806944.2                  29.77
    ## 6      Douglas-fir    24655901                  73.84

    head(tree6$est)

output

    ##            Species    Estimate Percent Sampling Error
    ## 1    quaking aspen 105867206.7                  60.84
    ## 2      limber pine  38477186.7                  92.27
    ## 3   lodgepole pine 251790363.6                  18.03
    ## 4    subalpine fir 396440112.5                  23.94
    ## 5 Engelmann spruce 107965157.9                  33.92
    ## 6      Douglas-fir  49218941.8                  80.24