## ----setup, message = FALSE---------------------------------------------------
library(BerkeleyForestsAnalytics)
library(dplyr)
library(tidyr)

## -----------------------------------------------------------------------------
# Note that the example data used in this vignette is included with the package
# which is why we do not have to read in the data

head(vign_trees_1)

## ----error = TRUE-------------------------------------------------------------
try({
tree_bio <- BiomassNSVB(data = vign_trees_1)
})

## -----------------------------------------------------------------------------
vign_trees_1 %>%
  filter(exp_factor == 0)

vign_trees_1 %>%
  filter(site == "post_60", plot == "112")

## ----error = TRUE, warning = FALSE--------------------------------------------
try({
tree_bio <- BiomassNSVB(data = vign_trees_2)
})

## -----------------------------------------------------------------------------
vign_trees_2 %>%
  filter(species == "15555" | species == "202222")

## -----------------------------------------------------------------------------
tree_bio <- BiomassNSVB(data = vign_trees_3)
head(tree_bio)

## -----------------------------------------------------------------------------
vign_trees_3 %>% 
  filter(status == 0, decay_class == 0 | is.na(decay_class))

## -----------------------------------------------------------------------------
tree_bio <- BiomassNSVB(data = vign_trees_4)
head(tree_bio)

## -----------------------------------------------------------------------------
vign_trees_4 %>% 
  filter(exp_factor > 0, is.na(dbh))

## -----------------------------------------------------------------------------
tree_bio <- BiomassNSVB(data = vign_trees_5)
head(tree_bio)

## ----error = TRUE-------------------------------------------------------------
try({
for_comp <- ForestComp(data = vign_trees_5,
                       relative = "ba",
                       units = "metric")
})

## -----------------------------------------------------------------------------
for_comp <- ForestComp(data = vign_trees_5,
                       relative = "BA",
                       units = "metric")

head(for_comp, n = 16)

## -----------------------------------------------------------------------------
for_comp %>%
  filter(site == "post_60", plot == "113")

## ----error = TRUE-------------------------------------------------------------
try({
for_str <- ForestStr(data = vign_trees_5)
head(for_str)
})

## -----------------------------------------------------------------------------
for_str %>%
  filter(site == "post_60", plot == "113")

## -----------------------------------------------------------------------------
head(vign_fuels_1)

## -----------------------------------------------------------------------------
vign_trees_6 <- vign_trees_5 %>%
  separate(site, c("time", "site")) %>% # separate into time and site columns 
  select(time, site, plot, exp_factor, species, dbh) # organize columns as desired 

head(vign_trees_6)

## ----error = TRUE-------------------------------------------------------------
try({
FWD <- FineFuels(tree_data = vign_trees_5,
                 fuel_data = vign_fuels_1,
                 sp_codes = "fia")
})

## -----------------------------------------------------------------------------
vign_fuels_1 %>%
  filter(time == "post", site == "400", plot == "9")

vign_fuels_1 %>%
  filter(time == "pre", site == "400", plot == "9")

## ----error = TRUE-------------------------------------------------------------
try({
FWD <- FineFuels(tree_data = vign_trees_6,
                 fuel_data = vign_fuels_2,
                 sp_codes = "fia")
})

## -----------------------------------------------------------------------------
vign_fuels_2 %>%
  mutate(count_100h_check = abs(round(count_100h))) %>%
  filter(count_100h != count_100h_check)

## ----error = TRUE, warning = FALSE--------------------------------------------
try({
FWD <- FineFuels(tree_data = vign_trees_6,
                 fuel_data = vign_fuels_3,
                 sp_codes = "fia")
})

## -----------------------------------------------------------------------------
FWD <- FineFuels(tree_data = vign_trees_6,
                 fuel_data = vign_fuels_4,
                 sp_codes = "fia")

head(FWD)

## -----------------------------------------------------------------------------
vign_fuels_4 %>%
  filter(is.na(count_10h))

## ----error = TRUE-------------------------------------------------------------
try({
CWD <- CoarseFuels(tree_data = vign_trees_6,
                   fuel_data = vign_fuels_4,
                   summed = "yes",
                   sp_codes = "fia")
})

## -----------------------------------------------------------------------------
vign_fuels_4 %>%
  filter(is.na(length_1000h))

## -----------------------------------------------------------------------------
CWD <- CoarseFuels(tree_data = vign_trees_6,
                   fuel_data = vign_fuels_5,
                   summed = "yes",
                   sp_codes = "fia")

head(CWD)

## -----------------------------------------------------------------------------
LD <- LitterDuff(tree_data = vign_trees_6,
                 fuel_data = vign_fuels_5,
                 sp_codes = "fia")

head(LD)

## -----------------------------------------------------------------------------
head(tree_bio$dataframe)

## -----------------------------------------------------------------------------
tree_bio_2 <- tree_bio$dataframe %>%
  separate(site, c("time", "site")) %>% # separate into time and site columns 
  mutate(trt_type = "fire") %>% # create a trt_type column 
  select(time, trt_type, site, plot, everything()) # organize columns as desired 

head(tree_bio_2)

## -----------------------------------------------------------------------------
# keep the defaults for wt_data (= "not_needed")
tree_bio_sum <- CompilePlots(data = tree_bio_2,
                             design = "FFS")

## -----------------------------------------------------------------------------
tree_bio_sum$site # pull out site-level summary 
tree_bio_sum$trt_type # pull out treatment-level summary 

## -----------------------------------------------------------------------------
head(FWD)

## -----------------------------------------------------------------------------
FWD_2 <- FWD %>%
  mutate(trt_type = "fire") %>% # create a trt_type column 
  select(time, trt_type, site, plot, everything()) # organize columns as desired 

head(FWD_2)

## -----------------------------------------------------------------------------
# keep the defaults for cwd_data (= "none), wt_data (= "not_needed"), and units (= "metric")
FWD_sum <- CompileSurfaceFuels(fwd_data = FWD_2,
                               design = "FFS")

## -----------------------------------------------------------------------------
FWD_sum$site # pull out site-level summary
FWD_sum$trt_type # pull out treatment-level summary