RSFIA_utils: RSFIA Utility functions
In bmcnellis/RSFIA: FIA Tree Mortality Analysis

Function families are:

generic_utilities FIA_processing plot_wrappers package_utilities soil_data_utilities daymet_utilities

PrepPlotEnvir(ret = "plots", clear = T)

PullTreeMeta(df, out_cols)

PullPlotMeta(CNs, df, out_cols, db_ver = 7.2)

PullLatLongs(plots)

PullPlotVars(plots, vars)

RoadCodeConvert(vec, db_ver = 7.2, na_fix = T)

WaterCodeConvert(vec, db_ver = 7.2, na_fix = T)

IterativeStatistics(df, vars, type = "adj_r2")

TrapezoidalIntegrateSoil(ref, d1, d2)

ShowDaymetMeta()

MinMaxByQuarter(x, n = 90, fun = sum)

PasteUniqueFactor(df, uniq = 1)

CollapseIdenticalVars(df)

ListMortVars()

r2_rf(rf)

CombineLandsatDaymet(df, ...)

SubsToAcres(n, r = 24, hectare = F)

KeyAgentCode(db_ver)

KeySpeciesCode(db_ver, by = "species")

MakeStateCodeKey(ver)

KeyStateCode(x, db_ver)

e1 %NA-% e2

ReplaceSPCD(x, by = "species", db_ver = 7.2)

KeyForestType(x, db_ver = 7.2)

Multiplot(..., plotlist = NULL, file, cols = 1, layout = NULL)

KeyOwnerCode(x, ret = "logical", db_ver = 7.2)

AggregateDominantAgent(in_df, cname, join_df = NULL, FUN0, join = F,
  scale = NULL)

PlotStacked(stacked_df, by = "Section", bar_fill = NULL, llab, yylab)

se(x)

PlotBarPlot(df, xx = 1, yy = 2, SE = 3, ylab)

LoopStatus(from, to, big_inc = 1000, digits = 1)

BinUncommonForestType(mort_df = NULL)

SubDominantForestType(mort_df = NULL, sub = T, n_plot_cutoff = 400)

KeyForestGroup(x, db_ver = 7.2)

AggForTypeByProv(mort_df = NULL)

TransposeUnevenMatrix(x, fill = F)

GroupLogicalMatrix(x)

CalcCategoricalMortByIQR(x, group)

ComorbidAgentTable(mort_df = NULL, only_multiple = F, only_mort = F)

AgentTypeDiffTest()

KeyDamageAgentCode(x, db_ver = 7.2)

PrepPlotEnvir: Prep function for other plot functions
PullTreeMeta: Summarizes metadata from a tree file
PullPlotMeta: Summarizes metadata from a plot file
PullLatLongs: Pulls lat/longs
PullPlotVars: Pulls a plot-level variable
RoadCodeConvert: Converts the RDDISTCD to minimum distance to road in meters
WaterCodeConvert: Converts WATERCD to categorical variable
IterativeStatistics: Brute-force correlations with given explanatory variables
TrapezoidalIntegrateSoil: Numerical soil layer integration using trapezoidal rule
ShowDaymetMeta: Displays Daymet variable info
MinMaxByQuarter: Find min/max quarterly value
PasteUniqueFactor: Pastes a unique factor variable to other columns in input df
CollapseIdenticalVars: Combines identical variables, e.g. with weather data
ListMortVars: Lists available mortality variables
r2_rf: Print r2 for RF object
CombineLandsatDaymet: Adds Landsat/Daymet data by lat/long
SubsToAcres: Converts subplot size, # subplots to acres
KeyAgentCode: Provides a keymatch function for AGENTCD
KeySpeciesCode: Provides a keymatch for SPCD
MakeStateCodeKey: Returns STATECD metadata
KeyStateCode: Keys STATECD
%NA-%: Subtraction operator that doesnt fail on NAs
ReplaceSPCD: Replaces species codes with names
KeyForestType: Keys the forest type codes
Multiplot: Multi-panel ggplot wrapper
KeyOwnerCode: Keys OWNCD
AggregateDominantAgent: Aggregation function for calculating dominant AGENTCD
PlotStacked: Wrapper for stacked bar plot
se: Standard error
PlotBarPlot: Barplot wrapper
LoopStatus: Prints loop progress
BinUncommonForestType: Bins common forest types
SubDominantForestType: Subsets/excludes dominant forest types
KeyForestGroup: Keys hardwood/softwood from forest type
AggForTypeByProv: Aggregates forest_type by dominant Cleland_province
TransposeUnevenMatrix: Transpose/mirror an uneven matrix
GroupLogicalMatrix: Group a logical matrix by row/col names
CalcCategoricalMortByIQR: Generates summary table for binned mortality using IQR
ComorbidAgentTable: Generates mort cause cross-table
AgentTypeDiffTest: Statistical test for tree vs plot AGENTCD tallies
KeyDamageAgentCode: Keys damage codes