Package 'FIESTAutils'

Title: Utility Functions for Forest Inventory Estimation and Analysis
Description: A set of tools for data wrangling, spatial data analysis, statistical modeling (including direct, model-assisted, photo-based, and small area tools), and USDA Forest Service data base tools. These tools are aimed to help Foresters, Analysts, and Scientists extract and perform analyses on USDA Forest Service data.
Authors: Tracey Frescino [aut], Chris Toney [aut], Grayson White [aut, cre], Joshua Yamamoto [aut]
Maintainer: Grayson White <[email protected]>
License: GPL-3
Version: 1.2.3.9000
Built: 2024-11-13 18:21:01 UTC
Source: https://github.com/usdaforestservice/fiestautils

Help Index

Updates reference tables

Description

Updates reference tables

Usage

.update_refs(write = FALSE)

Arguments

write

Logical. Should the internal reference tables be overwritten?

Value

No return value. Called for side effects.

Author(s)

Josh Yamamoto

Database options.

Description

Returns a list of user-supplied parameters and parameter values for database access.

Usage

database_options(
  dbname = NULL,
  host = NULL,
  port = NULL,
  user = NULL,
  password = NULL,
  ...
)

Arguments

dbname

String. Name of database.
host

String. Name of database host.
port

String. Database port.
user

String. User name for database access.
password

String. Password for database access.
...

For extendibility.

Details

If no parameters, an empty list is returned.

Value

A list of user-supplied parameters and parameter values for saving data.

Author(s)

Tracey S. Frescino

Examples

savedata_options(outfolder = "path", overwrite_dsn = FALSE)

Spatial - Exports a data frame object.

Description

Exports a data frame object to a specified output.

Usage

datExportData(
  dfobj,
  create_dsn = FALSE,
  index.unique = NULL,
  index = NULL,
  lowernames = FALSE,
  savedata_opts = savedata_options(),
  dbconn = NULL,
  dbconnopen = FALSE
)

Arguments

dfobj

Data.frame class R object. Data frame object to export.
create_dsn

Boolean.
index.unique

String. Name of variable(s) in dfobj to make unique index.
index

String. Name of variable(s) in dfobj to make (non-unique) index.
lowernames

Logical. If TRUE, convert column names to lowercase before writing to output. dbconnopen Logical. If TRUE, keep database connection open.
savedata_opts

List. See help(savedata_options()) for a list of options.
dbconn

Open database connection.
dbconnopen

Logical. If TRUE, keep database connection open.

Details

Wrapper for sf::st_write function.

Value

An sf spatial object is written to the out_dsn.

Note

If out_fmt='shp':
The ESRI shapefile driver truncates variable names to 10 characters or less. Variable names are changed before export using an internal function (trunc10shp). Name changes are output to the outfolder, 'outshpnm'_newnames.csv.

If sf object has more than 1 record, it cannot be exported to a shapefile.

Author(s)

Tracey S. Frescino

Database - Test a PostgreSQL database.

Description

Checks a PostgreSQL database.

Usage

DBtestPostgreSQL(
  dbname = NULL,
  host = NULL,
  port = NULL,
  user = NULL,
  password = NULL,
  dbconnopen = FALSE,
  showlist = TRUE,
  ...
)

Arguments

dbname

String. Name of the database on the host.
host

String. Host name.
port

String. Port number.
user

String. User name.
password

String. Password.
dbconnopen

Logical. If TRUE, the database connection is returned and not closed.
showlist

Logical. If TRUE, prints list of tables in database.
...

Additional authentication arguments passed to DBI::dbConnect

Value

An S4 object that inherits from DBIConnection via the DBI package if dbconnopen = TRUE, or NULL otherwise. For more information, see 'help(DBI::dbConnect)'.

Author(s)

Tracey S. Frescino

Database - Checks access to a SQLite database.

Description

Checks a SQLite database.

Usage

DBtestSQLite(
  SQLitefn = NULL,
  gpkg = FALSE,
  dbconnopen = FALSE,
  outfolder = NULL,
  showlist = TRUE,
  returnpath = TRUE,
  createnew = TRUE,
  stopifnull = FALSE,
  overwrite = TRUE
)

Arguments

SQLitefn

String. Name of SQLite database (*.sqlite).
gpkg

Logical. If TRUE, Sqlite geopackage database.
dbconnopen

Logical. If TRUE, the dbconn connection is not closed.
outfolder

String. Optional. Name of output folder. If NULL, export to working directory.
showlist

Logical. If TRUE, shows list of tables in database.
returnpath

Logical. If TRUE, returns full path to SQLite file name. If FALSE, returns SQLitefn.
createnew

If TRUE, creates new SQLite database.
stopifnull

Logical. If TRUE, stops if SQLite database doesn't exist.
overwrite

Logical. If TRUE, overwrites data.

Value

Character string containing the path to the SQLite database of interest.

Author(s)

Tracey S. Frescino

List of population tables.

Description

Returns a list of user-supplied parameters and parameter values for data evaluation (FIA or custom) extraction to be supplied to *DB functions.

Usage

eval_options(
  Cur = FALSE,
  Endyr = NULL,
  Endyr.filter = NULL,
  All = FALSE,
  Type = "VOL",
  evalid = NULL,
  invyrs = NULL,
  measyrs = NULL,
  varCur = "INVYR",
  evalType = NULL,
  ...
)

Arguments

Cur

Logical. If eval='FIA': extract plots with most current evaluation. If eval='custom': extract the most current sampled plots in the database.
Endyr

Integer (YYYY). If eval='FIA', defines end year for extracting one or more FIA evaluation. If eval='custom', defines end year for extracting the most current sampled plots until.
Endyr.filter

Filter. If endyr != NULL, a filter to identify when to use measEndyr, such as areas or plots identified as being disturbed in a particular year. In this example, plots sampled after the disturbance will be excluded.
All

Logical. If eval='FIA': includes all evaluations in database (annual inventory only). If eval='custom': includes all years in database (annual inventory only).
Type

String vector. Evaluation types ('ALL','CURR','VOL','P2VEG', DWM','INV','CHNG','GRM','REGEN'). If eval='FIA', Type is equivalent to plots for FIA Evaluations where 'ALL' includes nonsampled plots; 'CURR' and 'VOL' include plots used for area or tree estimates, respectively; Type = 'GRM' includes plots used for growth, removals, mortality; and Type = 'CHNG' includes plots used for change estimates (See FIA database manual for regioin availability and/or differences (https://www.fia.fs.usda.gov/library/database-documentation/index.php) If eval='custom', the associated tables are extracted for each Type. Multiple Types are accepted.
evalid

Integer. Only eval='FIA': extract data for a specific evaluation period. See notes for more information about FIA Evaluations.
invyrs

Integer vector. eval='custom': defines specific inventory years of data (e.g., 2010:2015). See FIA manual for definition of INVYR.
measyrs

Integer vector. eval='custom': defines specific measurement years of data (e.g., 2010:2015).
varCur

String. Name of variable to use for most current plot ('MEASYEAR', 'INVYR').
evalType

Deprecated. Use Type instead.
...

For extendibility.

Details

If no parameters, an empty list is returned.

Value

A list of user-supplied parameters and parameter values for strata.

Author(s)

Tracey S. Frescino

Examples

eval_options(invyrs = 2015:2018)

Reference tables - gdal data types.

Description

Table with gdal data type names.

Format

A vector of 12 data type values.

Source

gdal values.

Reference table - List of RMRS plots that have fallen out of inventory because they were not found or they were in the wrong place.

Description

Table with variable codes (VALUE) and descriptions (MEANING).

Format

A dataframe

Source

FIA query. SELECT bp.STATECD, bp.COUNTYCD, bp.PLOT_FIADB NEW_PLOT, bp.START_DATE NEW_START_DATE, bp_old.COUNTYCD OLD_COUNTYCD, bp_old.PLOT_FIADB OLD_PLOT, bp_old.END_DATE OLD_END_DATE, p.CN FROM fs_nims_rmrs.NIMS_BASE_PLOT bp JOIN fs_nims_rmrs.NIMS_BASE_PLOT bp_old on (bp.PREV_NBP_CN=bp_old.CN) JOIN fs_nims_rmrs.NIMS_PLOT_RMRS_VW p on(p.NBP_CN=bp_old.CN) WHERE p.KINDCD = 1 ORDER BY bp.STATECD, bp.COUNTYCD, bp_old.PLOT_FIADB"

Multest output options.

Description

Returns a list of user-supplied parameters and parameter values for outputting multest with custom aesthetics.

Usage

multest_options(
  multest_estimators = "all",
  multest_fmt = "csv",
  multest_outfolder = NULL,
  multest_dsn = NULL,
  multest_layer = NULL,
  multest.append = FALSE,
  multest.AOIonly = FALSE,
  ...
)

Arguments

multest_estimators

String vector. If multest = TRUE, vector of estimators to include in multest output ('JU.GREG','JU.EBLUP','JFH','hbsaeU','hbsaeA'). See ref_estimators for descriptions. Use multest_estimators = 'all' to output all estimators.
multest_fmt

String. Format for multest output tables ('csv', 'sqlite', 'gpkg').
multest_outfolder

String. Outfolder for multest. If NULL, same as outfolder.
multest_dsn

String. Name of database if multest_fmt = c('sqlite', 'gpkg').
multest_layer

String. Name of database layer if multest_fmt = c('sqlite', 'gpkg').
multest.append

Logical. If TRUE, appends multest dataframe to output.
multest.AOIonly

Logical. If TRUE, appends multest dataframe (AOI=1) to output.
...

For extendibility.

Details

If no parameters, an empty list is returned.

Value

A list of user-supplied parameters and parameter values for outputting multest.

Author(s)

Grayson W. White

Examples

multest_options(multest.append = TRUE)

Population data filters.

Description

Returns a list of user-supplied parameters and parameter values for population data filters.

Usage

popFilters(
  evalid = NULL,
  states = NULL,
  evalCur = FALSE,
  evalEndyr = NULL,
  measCur = FALSE,
  measEndyr = NULL,
  invyrs = NULL,
  measyrs = NULL,
  intensity = NULL,
  ACI = FALSE,
  AOIonly = FALSE,
  pfilter = NULL,
  ...
)

Arguments

evalid

Numeric. FIA Evaluation identifier for subsetting plots for population.
states

String or numeric vector. Name (e.g., 'Arizona','New Mexico') or code (e.g., 4, 35) of state(s) for evalid. If all states in one or more FIA Research Station is desired, set states=NULL and use RS argument to define RS.
evalCur

Logical. If TRUE, the most current FIA Evaluation is extracted for state(s).
evalEndyr

Number. The end year of the FIA Evaluation of interest. Selects only sampled plots and conditions for the evaluation period. If more than one state, create a named list object with evalEndyr labeled for each state (e.g., list(Utah=2014, Colorado=2013).
measCur

Logical. If TRUE, the most current sampled plots available for state(s).
measEndyr

Number. The most current sampled plots measured before or during end given..
invyrs

Integer vector. Inventory year(s) (e.g., c(2000, 2001, 2002)).
measyrs

Integer vector. Measurement year(s) (e.g., c(2000, 2001, 2002)).
intensity

Integer code. Code(s) indicating intensity to use for population.
ACI

Logical. If TRUE, including All Condition Inventory (ACI) plots.
AOIonly

Logical. If TRUE, and there is an AOI (1/0) attribute in the population data, only AOI=1 are used for estimation.
pfilter

String. Logical filter for plot or pltassgn.
...

For extendibility.

Details

If no parameters, an empty list is returned.

Value

A list of user-supplied parameters and parameter values for population data filters.

Author(s)

Grayson W. White

List of population table unique IDs.

Description

Returns a list of user-supplied parameters and parameter values for data table unique IDs to be supplied to *pop functions.

Usage

popTableIDs(
  cond = "PLT_CN",
  plt = "CN",
  tree = "PLT_CN",
  seed = "PLT_CN",
  seedling = "PLT_CN",
  vsubpspp = "PLT_CN",
  p2veg_subplot_spp = "PLT_CN",
  vsubpstr = "PLT_CN",
  p2veg_subp_structure = "PLT_CN",
  invsubp = "PLT_CN",
  invasive_subplot_spp = "PLT_CN",
  subplot = "PLT_CN",
  subp_cond = "PLT_CN",
  dwm = "PLT_CN",
  cond_dwm_calc = "PLT_CN",
  sccm = "PLT_CN",
  subp_cond_chng_mtrx = "PLT_CN",
  grm = "PLT_CN",
  tree_grm_component = "PLT_CN",
  begin = "PLT_CN",
  tree_grm_begin = "PLT_CN",
  midpt = "PLT_CN",
  tree_grm_midpt = "PLT_CN",
  plot = "CN",
  pltu = "CN",
  plotu = "CN",
  condu = "PLT_CN",
  ...
)

Arguments

cond

String. Unique identifier of plot in cond.
plt

String. Unique identifier of plot in plt.
tree

String. Unique identifier of plot in tree and seed.
seed

String.
seedling

String.
vsubpspp

String.
p2veg_subplot_spp

String.
vsubpstr

String.
p2veg_subp_structure

String.
invsubp

String.
invasive_subplot_spp

String.
subplot

String.
subp_cond

String.
dwm

String.
cond_dwm_calc

String.
sccm

String.
subp_cond_chng_mtrx

String.
grm

String.
tree_grm_component

String.
begin

String.
tree_grm_begin

String.
midpt

String.
tree_grm_midpt

String.
plot

String.
pltu

String.
plotu

String.
condu

String.
...

For extendibility.

Details

If no parameters, an empty list is returned.

Value

A list of user-supplied parameters and parameter values for strata.

Author(s)

Grayson W. White

List of population tables.

Description

Returns a list of user-supplied parameters and parameter values for data tables to be supplied to *pop functions.

Usage

popTables(
  cond = "COND",
  plt = "PLOT",
  tree = "TREE",
  seed = "SEEDLING",
  seedling = "SEEDLING",
  vsubpspp = "P2VEG_SUBPLOT_SPP",
  p2veg_subplot_spp = "P2VEG_SUBPLOT_SPP",
  vsubpstr = "P2VEG_SUBP_STRUCTURE",
  p2veg_subp_structure = "P2VEG_SUBP_STRUCTURE",
  invsubp = "INVASIVE_SUBPLOT_SPP",
  invasive_subplot_spp = "INVASIVE_SUBPLOT_SPP",
  subplot = "SUBPLOT",
  subp_cond = "SUBP_COND",
  dwm = "COND_DWM_CALC",
  cond_dwm_calc = "COND_DWM_CALC",
  sccm = "SUBP_COND_CHNG_MTRX",
  subp_cond_chng_mtrx = "SUBP_COND_CHNG_MTRX",
  grm = "TREE_GRM_COMPONENT",
  tree_grm_component = "TREE_GRM_COMPONENT",
  begin = "TREE_GRM_BEGIN",
  tree_grm_begin = "TREE_GRM_BEGIN",
  midpt = "TREE_GRM_MIDPT",
  tree_grm_midpt = "TREE_GRM_MIDPT",
  plot = "plot",
  pltu = "pltu",
  plotu = "plotu",
  condu = "condu",
  ...
)

Arguments

cond

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Condition-level data with one record for each condition, including or excluding nonsampled conditions. Plot variables and strata/estimation unit variable(s) may be included if plt and pltassgn=NULL. See details for necessary variables to include.
plt

DF/DT, Optional. R object, sf R object, comma-delimited file(*.csv), layer or spatial layer in dsn, or shapefile(*.shp). Plot-level data with one record for each plot, including or excluding nonsampled conditions. If nonsampled plots are included, PLOT_STATUS_CD variable must be in table or a filter defined in plt.nonsamp.filter.
tree

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Tree-level data with one record for each tree. Tree data are aggregated to condition-level. See details for necessary variables to include.
seed

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Seedling data with one record for each seedling count.
seedling

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Seedling data with one record for each seedling count.
vsubpspp

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Vegetation species-level data with one record for each species (P2VEG_SUBPLOT_SPP).
p2veg_subplot_spp

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Vegetation species-level data with one record for each species (P2VEG_SUBPLOT_SPP).
vsubpstr

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Vegetation species-structure data with one record for each species (P2VEG_SUBP_STRUCTURE).
p2veg_subp_structure

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Vegetation species-structure data with one record for each species (P2VEG_SUBP_STRUCTURE).
invsubp

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Invasive species data with one record for each species (INVASIVE_SUBPLOT_SPP).
invasive_subplot_spp

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Invasive species data with one record for each species (INVASIVE_SUBPLOT_SPP).
subplot

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Subplot-level data with one record for each species (SUBPLOT).
subp_cond

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Subplot condition-level data with one record for each species (SUBP_COND).
dwm

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Calculated down woody material (COND_DWM_CALC).
cond_dwm_calc

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Calculated down woody material (COND_DWM_CALC).
sccm

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Subplot-level data (SUBP_COND_CHNG_MTRX).
subp_cond_chng_mtrx

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Subplot-level data (SUBP_COND_CHNG_MTRX).
grm

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Tree-level growth, removal, and mortality data (TREE_GRM_COMPONENT).
tree_grm_component

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Tree-level growth, removal, and mortality data (TREE_GRM_COMPONENT).
begin

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Tree-level growth, removal, and mortality data (TREE_GRM_BEGIN).
tree_grm_begin

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Tree-level growth, removal, and mortality data (TREE_GRM_BEGIN).
midpt

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Tree-level growth, removal, and mortality data (TREE_GRM_MIDPT).
tree_grm_midpt

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Tree-level growth, removal, and mortality data (TREE_GRM_MIDPT).
plot

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Plot data unioned with remeasured plot data.
pltu

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Plot data unioned with remeasured plot data.
plotu

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Plot data unioned with remeasured plot data.
condu

DF/DT, R object, comma-delimited file(*.csv), or layer in dsn. Cond data unioned with remeasured cond data.
...

For extendibility.

Details

If no parameters, an empty list is returned.

Value

A list of user-supplied parameters and parameter values for strata.

Author(s)

Grayson W. White

Class "Rcpp_CmbTable"

Description

C++ program to combine raster files.

Extends

Class "C++Object", directly.

All reference classes extend and inherit methods from "envRefClass".

Author(s)

Chris Toney

Class "Rcpp_RunningStats"

Description

C++ program to calculate mean and variance on a data stream.

Extends

Class "C++Object", directly.

All reference classes extend and inherit methods from "envRefClass".

Author(s)

Chris Toney

Reference tables - Code definitions.

Description

Table with variable codes (VALUE) and descriptions (MEANING).

Format

A dataframe with 7 columns, VARIABLE, VALUE, MEANING, COLORHEX, GROUP, GROUPNM, GROUPHEX.

Source

FIA look-up tables.

References

O'Connell, B.M.; LaPoint, E.B.; Turner, J.A.; Ridley, T.; Boyer, D.; Wilson, A.M.; Waddell, K.L.; Christensen, G.; Conkling, B.L. 2012. The Forest Inventory and Analysis Database: Database Description and Users Manual Version 5.1.2 for Phase 2. U.S. Department of Agriculture. (http://fia.fs.fed.us/library/database-documentation/current/ver5-2012/FIADB_user manual_5-1-2_p2_07_2012.pdf)

Reference tables - Code definitions (Archive).

Description

Table with variable codes (VALUE) and descriptions (MEANING).

Format

A dataframe with 7 columns, VARIABLE, VALUE, MEANING, COLORHEX, GROUP, GROUPNM, GROUPHEX.

Source

FIA look-up tables.

References

O'Connell, B.M.; LaPoint, E.B.; Turner, J.A.; Ridley, T.; Boyer, D.; Wilson, A.M.; Waddell, K.L.; Christensen, G.; Conkling, B.L. 2012. The Forest Inventory and Analysis Database: Database Description and Users Manual Version 5.1.2 for Phase 2. U.S. Department of Agriculture. (http://fia.fs.fed.us/library/database-documentation/current/ver5-2012/FIADB_user manual_5-1-2_p2_07_2012.pdf)

Reference table - Metadata for cond default variables output from DBgetPlots()

Description

Data frame with variable names and descriptions

Format

A data frame with 61 rows and 3 columns VARIABLE - Variable in cond data frame DESCRIPTION - Description of variable in cond data frame TABLE - Table in database where variable originates or if derived

Source

FIA look-up table

References

O'Connell, B.M.; LaPoint, E.B.; Turner, J.A.; Ridley, T.; Boyer, D.; Wilson, A.M.; Waddell, K.L.; Christensen, G.; Conkling, B.L. 2012. The Forest Inventory and Analysis Database: Database Description and Users Manual Version 5.1.2 for Phase 2. U.S. Department of Agriculture. (http://fia.fs.fed.us/library/database-documentation/current/ver5-2012/FIADB_user manual_5-1-2_p2_07_2012.pdf)

Reference table - for conversion factors.

Description

Table with conversion factors from English to metric units.

Format

A dataframe with 6 columns: TYPE, ENGLISH, ENGLISH_ABBR, METRIC, METRIC_ABBR, CONVERSION.

Source

Conversion table.

Reference table - diameter 2-inch class codes (DIA).

Description

Table with min (MIN), max (MAX), and 2-inch class diameter codes (MEANING).

Format

A dataframe with 3 columns, MIN, MAX, and MEANING.

Source

Imported from comma-delimited file.

References

O'Connell, B.M.; LaPoint, E.B.; Turner, J.A.; Ridley, T.; Boyer, D.; Wilson, A.M.; Waddell, K.L.; Christensen, G.; Conkling, B.L. 2012. The Forest Inventory and Analysis Database: Database Description and Users Manual Version 5.1.2 for Phase 2. U.S. Department of Agriculture. (http://fia.fs.fed.us/library/database-documentation/current/ver5-2012/FIADB_user manual_5-1-2_p2_07_2012.pdf)

Reference table - for generating tables.

Description

Table with row/column domain (VARNM) and their pretty names for table output (TABLENM).

Format

A dataframe with 2 columns, VARNM and TABLENM.

Source

FIA look-up table.

Reference table - FIESTA estimators.

Description

Table with list of estimators currently in FIESTA.

Format

A dataframe with 7 columns: ESTIMATOR, SHORTNAME, PACKAGE, OUTNAME, ESTIMATOR_TYPE, ESTIMATOR_DATA, DESCRIPTION, CITATION

Source

Comma-delimited file.

Reference table - for generating estimates

Description

Data frame with variable names and descriptions

Format

A data frame to use a reference for estimation variables and filters.

Reference table - for generating tables.

Description

Table with row/column domain (VARNM) and their pretty names for table output (TABLENM).

Format

A dataframe with 3 columns, EVAL_TYP_CD, EVAL_TYP, DESCRIPTION.

Source

FIA look-up table.

Reference table - Metadata for plt default variables output from DBgetPlots()

Description

Data frame with variable names and descriptions.

Format

A data frame with 43 rows and 3 columns VARIABLE - Variable in plt data frame DESCRIPTION - Description of variable in plt data frame TABLE - Table in database where variable originates or if derived

Source

FIA look-up table

References

O'Connell, B.M.; LaPoint, E.B.; Turner, J.A.; Ridley, T.; Boyer, D.; Wilson, A.M.; Waddell, K.L.; Christensen, G.; Conkling, B.L. 2012. The Forest Inventory and Analysis Database: Database Description and Users Manual Version 5.1.2 for Phase 2. U.S. Department of Agriculture. (http://fia.fs.fed.us/library/database-documentation/current/ver5-2012/FIADB_user manual_5-1-2_p2_07_2012.pdf)

Reference table - popType codes.

Description

Table with population type (popType) and associated evaluation code (EVAL_TYP_CD).

Format

A dataframe with 2 columns, VARNM and TITLE.

Source

Comma-delimited file.

Reference table - Metadata for shp_* default variables output from DBgetPlots()

Description

Data frame with variable names and descriptions

Format

A dataframe with 63 rows and 4 columns VARIABLE - Variable in plt data frame DESCRIPTION - Description of variable in plt data frame TABLE - Table in database where variable originates or if derived SHPEXPORT - Name of variable for exported shapefile (<= 10 characters)

Source

FIA look-up table

References

O'Connell, B.M.; LaPoint, E.B.; Turner, J.A.; Ridley, T.; Boyer, D.; Wilson, A.M.; Waddell, K.L.; Christensen, G.; Conkling, B.L. 2012. The Forest Inventory and Analysis Database: Database Description and Users Manual Version 5.1.2 for Phase 2. U.S. Department of Agriculture. (http://fia.fs.fed.us/library/database-documentation/current/ver5-2012/FIADB_user manual_5-1-2_p2_07_2012.pdf)

Reference table - Code definitions.

Description

Table with species information downloaded from datamart FIADB_REFERENCES, subset from REF_SPECIES TABLE.

Format

A dataframe with 14 columns: SPCD, COMMON_NAME, GENUS, SPECIES, SPECIES_SYMBOL, E_SPGRCD, W_SPGRPCD, C_SPGRPCD, P_SPGRPCD, MAJOR_SPGRPCD, JENKINS_TOTAL_B1, JENKINS_TOTAL_B2, DRYWT_TO_GREENWT_CONERSION, SCIENTIFIC_NAME (GENUS + SPECIES).

Source

Imported from comma-delimited file.

References

O'Connell, B.M.; LaPoint, E.B.; Turner, J.A.; Ridley, T.; Boyer, D.; Wilson, A.M.; Waddell, K.L.; Christensen, G.; Conkling, B.L. 2012. The Forest Inventory and Analysis Database: Database Description and Users Manual Version 5.1.2 for Phase 2. U.S. Department of Agriculture. (http://fia.fs.fed.us/library/database-documentation/current/ver5-2012/FIADB_user manual_5-1-2_p2_07_2012.pdf)

Reference table - state codes (STATECD).

Description

Table with state codes (VALUE), name (MEANING), abbreviation (ABBR), and UNIT.

Format

A dataframe with 4 columns, VALUE, MEANING, ABBR, UNIT.

Source

Imported from comma-delimited file.

References

O'Connell, B.M.; LaPoint, E.B.; Turner, J.A.; Ridley, T.; Boyer, D.; Wilson, A.M.; Waddell, K.L.; Christensen, G.; Conkling, B.L. 2012. The Forest Inventory and Analysis Database: Database Description and Users Manual Version 5.1.2 for Phase 2. U.S. Department of Agriculture. (http://fia.fs.fed.us/library/database-documentation/current/ver5-2012/FIADB_user manual_5-1-2_p2_07_2012.pdf)

Reference table - Variable titles.

Description

Table with variable name (VARNM) and associated title (TITLE).

Format

A dataframe with 2 columns, VARNM and TITLE.

Source

Comma-delimited file.

Reference table - Metadata for tree default variables output from DBgetPlots()

Description

Data frame with variable names and descriptions

Format

A data frame with 72 rows and 3 columns VARIABLE - Variable in tree data frame DESCRIPTION - Description of variable in tree data frame TABLE - Table in database where variable originates

Source

FIA look-up table

References

O'Connell, B.M.; LaPoint, E.B.; Turner, J.A.; Ridley, T.; Boyer, D.; Wilson, A.M.; Waddell, K.L.; Christensen, G.; Conkling, B.L. 2012. The Forest Inventory and Analysis Database: Database Description and Users Manual Version 5.1.2 for Phase 2. U.S. Department of Agriculture. (http://fia.fs.fed.us/library/database-documentation/current/ver5-2012/FIADB_user manual_5-1-2_p2_07_2012.pdf)

Reference table - for variable units.

Description

Table with units for TREE variables. The WOODLAND column was added to identify which variables include woodland species.The kg2tons column was added to identify which variables are commonly converted from kilograms to tons in estimation process.

Format

A dataframe with 4 columns: VARIABLE, UNITS, METRICUNITS, WOODLAND, kg2tons.

Source

Units table.

Data saving options.

Description

Returns a list of user-supplied parameters and parameter values for saving data.

Usage

savedata_options(
  outfolder = NULL,
  out_fmt = "csv",
  outsp_fmt = "shp",
  outobj_fmt = "rds",
  out_dsn = NULL,
  out_layer = "outdat",
  outfn.pre = NULL,
  outfn.date = FALSE,
  addtitle = TRUE,
  raw_fmt = "csv",
  raw_dsn = NULL,
  overwrite_dsn = FALSE,
  overwrite_layer = TRUE,
  append_layer = FALSE,
  add_layer = TRUE,
  layer.pre = NULL,
  outconn = NULL,
  ...
)

Arguments

outfolder

String. The outfolder to write files to. If NULL, files are written to working directory, or if gui=TRUE, a window to browse.
out_fmt

String. Format for output tables ('csv', 'sqlite', 'gpkg', 'gdb').
outsp_fmt

String. Format for output spatial ('shp', sqlite', 'gpkg', 'gdb').
outobj_fmt

String. Format for output spatial ('rda', 'rds', 'llo').
out_dsn

String. Data source name for output. If extension is not included, out_fmt is used. Use full path if outfolder=NULL.
out_layer

outlayer.
outfn.pre

String. If savedata=TRUE, prefix for output files. If rawdata=TRUE, prefix for rawdata files (if raw_fmt = 'csv') or raw_dsn (if raw_fmt != 'csv').
outfn.date

Logical. If TRUE, add current date to out_dsn.
addtitle

Logical. If TRUE and savedata=TRUE, adds title to outfile.
raw_fmt

String. Format for output rawdata tables ('sqlite', 'gpkg', 'csv', 'gdb').
raw_dsn

String. Data source name for rawdata output. If extension is not included, out_fmt is used. Use full path if outfolder=NULL.
overwrite_dsn

Logical. If TRUE, overwrites raw_dsn, if exists.
overwrite_layer

Logical. If TRUE, overwrites the output. If rawdata=TRUE, overwrites out_layer in rawdata folder (if raw_fmt = 'csv') or out_layers in raw_dsn (if raw_fmt != 'csv').
append_layer

Logical. If TRUE, and appends data to existing *.csv files (if *_fmt = 'csv') or *_dsn layers (if *_fmt != 'csv".
add_layer

Logical. If TRUE, adds layer to an existing out_dsn (if out_fmt != c('csv','shp')).
layer.pre

Layer prefix.
outconn

Open database connection to save to.
...

For extendibility.

Details

If no parameters, an empty list is returned.

Value

A list of user-supplied parameters and parameter values for saving data.

Author(s)

Grayson W. White

Examples

savedata_options(outfolder = "path", overwrite_dsn = FALSE)

Make SpatialPoints options

Description

Returns a list of user-supplied parameters and parameter values for making SpatialPoints.

Usage

spMakeSpatial_options(
  xvar = NULL,
  yvar = NULL,
  xy.crs = 4269,
  prj = NULL,
  datum = NULL,
  zone = NULL,
  zoneS = FALSE,
  aea.param = "USGS",
  ...
)

Arguments

xvar

String. Name of variable in xyplt defining x coordinate.
yvar

String. Name of variable in xyplt defining y coordinate.
xy.crs

PROJ.4 String or CRS object or Integer EPSG code defining Coordinate Reference System. (e.g., EPSG:4269-Geodetic coordinate system for North America, NAD83).
prj

String. Projection, or coordinate system of the X/Y coordinates ("longlat", "utm", "aea"). If other, include PROJ.4 string in prj4str.
datum

String. Datum of projection ("WGS84", "NAD83", "NAD27").
zone

Integer. If prj="utm", the UTM zone.
zoneS

Logical. If prj="utm", if the UTM zone is in the Southern hemisphere.
aea.param

String. If prj="aea", the associated lat/lon parameters (USGS: " +lat_1=29.5 +lat_2=45.5 +lat_0=23 +lon_0=-96 +x_0=0 +y_0=0"). If other, include PROJ.4 string in prj4str.
...

For extendibility.

Details

If no parameters, an empty list is returned.

Value

A list of user-supplied parameters and parameter values for strata.

Author(s)

Grayson W. White

Examples

spMakeSpatial_options()

Strata options.

Description

Returns a list of user-supplied parameters and parameter values for strata.

Usage

strata_options(
  getwt = FALSE,
  getwtvar = "P1POINTCNT",
  strwtvar = "strwt",
  stratcombine = TRUE,
  minplotnum.strat = 2,
  pivot = FALSE,
  nonresp = FALSE,
  ...
)

Arguments

getwt

Logical. If TRUE, calculates strata weights from stratatlut getwtvar. If FALSE, strwtvar variable must be in stratalut.
getwtvar

String. If getwt=TRUE, name of variable in stratalut to calculate weights (Default = 'P1POINTCNT').
strwtvar

String. If getwt=FALSE, name of variable in stratalut with calculated weights (Default = 'strwt').
stratcombine

Logical. If TRUE, and strata=TRUE, automatically combines strata categories if less than minplotnum.strat plots in any one stratum. See notes for more info.
minplotnum.strat

Integer. Minimum number of plots for a stratum within an estimation unit.
pivot

Logical. If TRUE, pivot stratalut.
nonresp

Deprecated.
...

For extendibility.

Details

If no parameters, an empty list is returned.

Value

A list of user-supplied parameters and parameter values for strata.

Author(s)

Grayson W. White

Examples

strata_options(getwt = FALSE)

SpatialPolygonsDataFrame with FIA state, unit, county codes and names

Description

Polygon feature class with state and county boundaries defined by Census Bureau, including Federal Information Processing Standards (FIPS) codes. The FIA Survey Unit code and name attributes (UNITCD, UNITNM) were appended to dataset, with joining columns of STATECD and COUNTYCD.

Format

A SpatialPolygonsDataFrame with 3233 features and 8 attributes RS - FIA Research Station name RSCD - FIA Research Station code STATECD - FIPS state code STATENM - FIPS state name STATEAB - FIPS state abbreviation UNITCD - FIA survey unit code UNITNM - FIA survey unit name COUNTYCD - FIPS county code COUNTYNM - FIPS county name

Details

Derived from cb_2018_us_county_5m. STATEFP was converted to numeric and named STATECD COUNTYFP was converted to numeric and named COUNTYCD Lookup table for FIA Research Station (REF_RESEARCH_STATION) was downloaded from FIA DataMart on 20191105 (FIADB_1.6.1.00) and joined by STATECD. A lookup table for UNITCD was created from plot data using unique STATECD, COUNTYCD, UNITCD and joined to table.

Converted to simple feature
Transformed CRS from longlat(EPSG:4269) to Albers (EPSG:5070)
Saved to R object, with compression='xz'

Source

Downloaded from the United States Census Bureau on 2019 November 3, format Esri Shapefile (https://www.census.gov/geographies/mapping-files/time-series/geo/carto-boundary-file.html) Projection: Geographic (GCS_North_American_1983) EPSG: 4269

Table aesthetics and output options.

Description

Returns a list of user-supplied parameters and parameter values for outputting tables with custom aesthetics.

Usage

table_options(
  row.FIAname = FALSE,
  col.FIAname = FALSE,
  row.orderby = NULL,
  col.orderby = NULL,
  row.add0 = FALSE,
  col.add0 = FALSE,
  rowlut = NULL,
  collut = NULL,
  row.classify = NULL,
  col.classify = NULL,
  rawonly = FALSE,
  raw.keep0 = FALSE,
  rowgrp = FALSE,
  rowgrpnm = NULL,
  rowgrpord = NULL,
  totals = TRUE,
  allin1 = FALSE,
  metric = FALSE,
  estround = 1,
  pseround = 2,
  estnull = "--",
  psenull = "--",
  divideby = NULL,
  ...
)

Arguments

row.FIAname

Logical. If TRUE, retrieves default FIA reference names for rowvar located in ref_codes data frame. Names are only available for certain variables (Check sort(unique(ref_codes$VARIABLE)) for available names. If row.FIAname = TRUE and rowvar is in ref_codes, the rowvar name is used for the output table, and the rowvar code is used to sort.
col.FIAname

Logical. If TRUE, retrieves default FIA reference names for colvar located in ref_codes data frame. Names are only available for certain variables. Check: sort(unique(ref_codes$VARIABLE)) for available names. If col.FIAname = TRUE and rowvar is in ref_codes, the colvar name is used for the output table, and the colvar code is used to sort.
row.orderby

String. Optional. Name of variable to sort table rows. Both the rowvar and row.orderby variables must be included in the same input data.frame. if NULL, and row.FIAname=FALSE or rowvar is not in ref_codes, the rows are ordered by rowvar.
col.orderby

String. Optional. Name of variable to sort table columns. Both the colvar and col.orderby variables must be included in the same input data.frame. if NULL, and col.FIAname=FALSE or colvar is not in ref_codes, the columns are ordered by colvar.
row.add0

Logical. If TRUE, include rows with 0 values to the output table.
col.add0

Logical. If TRUE, include columns with 0 values to the output table.
rowlut

Data frame. A lookup table with variable codes and code names to include as rows of output table (See notes for more information and format).
collut

Data frame. A lookup table with variable codes and code names to include as columns of output table (See notes for more information and format).
row.classify

Data frame (if categorical) or Vector (if continuous). If clasifying categories, input a dataframe with two columns ('FROM' and 'TO'). If classifying continuous values, input a vector of class breaks for row
col.classify

Data frame (if categorical) or Vector (if continuous). If clasifying categories, input a dataframe with two columns ('FROM' and 'TO'). If classifying continuous values, input a vector of class breaks for column
rawonly

Logical. If TRUE, only rawdata are output. If dataset includes many estimation units, and only raw data tables are desired, it is more efficient to output raw data only.
raw.keep0

Logical. If TRUE, keep 0 values in raw data tables.
rowgrp

Logical. If TRUE, appends row groups to first column of table. Only available if group category exists in ref_codes table or defined in rowgrpnm (e.g., FORTYPGRPCD, OWNGRPCD).
rowgrpnm

String. Name of variable for grouping rowvar. Variable must be included in same input table as rowvar.
rowgrpord

String. Name of variable to sort row group variable. Variable must be included in same input table as rowgrpnm.
totals

Logical. If TRUE, returns total estimate (mean * AREAUSED).
allin1

Logical. If TRUE, both estimates and percent sample error are output in one table as: estimates (percent sample error).
metric

Logical. If TRUE, output if returned in metric units.
estround

Integer. Number of decimal places for estimates.
pseround

Integer. Number of decimal places for percent sampling error.
estnull

Number or character. The number or symbol to use to indicate 'not sampled' for estimate.
psenull

Number or character. The number or symbol to use to indicate 'not sampled' for percent standard error.
divideby

String. Conversion number for output ('hundred', 'thousand', 'million').
...

For extendibility.

Details

If no parameters, an empty list is returned.

Value

A list of user-supplied parameters and parameter values for outputting tables with custom aesthetics.

Author(s)

Grayson W. White

Examples

table_options(row.FIAname = TRUE, col.FIAname = TRUE)

Title output options.

Description

Returns a list of user-supplied parameters and parameter values for outputting title with custom aesthetics.

Usage

title_options(
  title.main = NULL,
  title.ref = NULL,
  title.rowvar = NULL,
  title.colvar = NULL,
  title.unitvar = NULL,
  title.estvar = NULL,
  title.estvarn = NULL,
  title.filter = NULL,
  title.units = "acres",
  ...
)

Arguments

title.main

String. TITLE, if savedata=TRUE and/or returntitle=TRUE: the complete title used for table. If title.main=NULL, the title.* parameters are used to generate title string. Note: if title.ref is not NULL, it is added to title.main.
title.ref

String. TITLE, if savedata=TRUE and/or returntitle=TRUE: the ending text of the table title (e.g., Nevada, 2004-2005). If NULL, = "".
title.rowvar

String. TITLE, if savedata=TRUE and/or returntitle=TRUE: pretty name for the row domain variable. If NULL, = rowvar.
title.colvar

String. TITLE, if savedata=TRUE and/or returntitle=TRUE: pretty name for the column domain variable. If NULL, = colvar.
title.unitvar

String. TITLE, if savedata=TRUE and/or returntitle=TRUE: pretty name for the estimation unit variable. If NULL, = unitvar.
title.estvar

String. TITLE: if savedata=TRUE and/or returntitle=TRUE: pretty name for the estimate variable. If NULL, title.estvar = estvar.name.
title.estvarn

String. TITLE: if savedata=TRUE and/or returntitle=TRUE: pretty name for the estimate variable. If NULL, title.estvar = estvar.name.
title.filter

String. TITLE, if savedata=TRUE and/or returntitle=TRUE: pretty name for filter(s). If title.filter=NULL, a default is generated from cfilter. If title.filter="", no title.filter is used.
title.units

String.
...

For extendibility.

Details

If no parameters, an empty list is returned.

Value

A list of user-supplied parameters and parameter values for outputting titles with custom aesthetics.

Author(s)

Grayson W. White

Examples

title_options(title.main = "My fancy title", title.estvar = "Estimate title")

Unit options.

Description

Returns a list of user-supplied parameters and parameter values for unit.

Usage

unit_options(
  unitvar2 = NULL,
  areaunits = "acres",
  minplotnum.unit = 10,
  unit.action = "keep",
  npixelvar = "npixels",
  ...
)

Arguments

unitvar2

String. Name of a second level estimation unit variable in unitarea and cond or pltassgn with assignment for each plot (e.g., 'STATECD').
areaunits

String. Units of areavar in unitarea ('acres', 'hectares').
minplotnum.unit

Integer. Minimum number of plots for estimation unit.
unit.action

String. What to do if number of plots in an estimation unit is less than minplotnum.unit ('keep', 'remove' 'combine'). If unit.action='keep', estimation units with less that minplotnum.unit will be kept in output tables; if unit.action='remove', the estimation units with less that minplotnum.unit will be removed from the output tables; and if unit.action='combine', combines estimation unit to the following estimation unit, ordered in stratalut or unitzonal.
npixelvar

String. Name of variable in unitlut defining number of pixels by estimation unit.
...

For extendibility.

Details

If no parameters, an empty list is returned.

Value

A list of user-supplied parameters and parameter values for strata.

Author(s)

Grayson W. White

Examples

unit_options()

List of population tables.

Description

Returns a list of user-supplied parameters and parameter values for data xyuation (FIA or custom) extraction to be supplied to *DB functions.

Usage

xy_options(
  xy.uniqueid = "CN",
  xvar = "LON",
  yvar = "LAT",
  xy.crs = 4269,
  xyjoinid = NULL,
  ...
)

Arguments

xy.uniqueid

String. Unique identifier of xy.
xvar

String. Name of variable in xy defining x coordinate.
yvar

String. Name of variable in xy defining y coordinate.
xy.crs

PROJ.4 String or CRS object or Integer EPSG code defining Coordinate Reference System.
xyjoinid

String. Name of variable in xy to join to plot data. If NULL, xyjoinid = xy.uniqueid.
...

For extendibility.

Details

If no parameters, an empty list is returned.

Value

A list of user-supplied parameters and parameter values for strata.

Author(s)

Tracey S. Frescino

Examples

xy_options(xvar="LON", yvar="LAT")