Warn (once) if dead trees are detected in the census data

[maurolepore]

@gonzalezeb and @teixeirak,

• Should we warn if calclating the biomass for dead trees?

Some dead trees in SCBI have non-missing dbh values. Am I right in thinking that some other ForestGEO plots do not record dbh of dead trees?

library(tidyverse)

fgeo.biomass::scbi_tree1 %>% 
  filter(status != "A") %>%
  select(matches("status"), dbh) %>% 
  as_tibble()
#> # A tibble: 10,228 x 3
#>    DFstatus status   dbh
#>    <chr>    <chr>  <dbl>
#>  1 dead     D       42.6
#>  2 dead     D       37  
#>  3 dead     D      318  
#>  4 dead     D      179. 
#>  5 dead     D      203. 
#>  6 dead     D      137. 
#>  7 dead     D       55  
#>  8 dead     D      164. 
#>  9 dead     D      242. 
#> 10 dead     D      238. 
#> # ... with 10,218 more rows

fgeo.biomass::scbi_tree1 %>% 
  mutate(missing_dbh = if_else(is.na(dbh), TRUE, FALSE)) %>% 
  select(matches("status"), missing_dbh) %>%
  arrange(status, DFstatus) %>% 
  unique()
#> # A tibble: 7 x 3
#>   DFstatus  status missing_dbh
#>   <chr>     <chr>  <lgl>      
#> 1 alive     A      FALSE      
#> 2 alive     A      TRUE       
#> 3 lost_stem A      FALSE      
#> 4 dead      D      FALSE      
#> 5 dead      D      TRUE       
#> 6 missing   M      TRUE       
#> 7 prior     P      TRUE

Created on 2019-03-14 by the reprex package (v0.2.1)

[teixeirak]

Let's display a warning (for the entire run, not per tree!): "Live tree allometries applied to calculate biomass on dead trees."

Really, I don't think we should need to warn about dead trees at the step of calculating biomass, but it may be good to give this reminder, and also to highlight that biomass will be overestimated on trees that have undergone a fair amount of decomposition.

We'll mainly care about live/dead later--- for example, a function that sums individual biomass values to get whole-ecosystem biomass will definitely need to have users specify whether dead trees should be included.