VM0010-starter.R

## ----setup------------------------------------------------------------------------------------------------------------------
#| warning: false
#| message: false
#| error: false
#| include: false
#| echo: false

install.packages("easypackages")
easypackages::packages(
  "animation",
  "BIOMASS",
  "dataMaid",
  "dplyr",
  "extrafont",
  "htmltools",
  "janitor",
  "kableExtra",
  "knitr",
  "readxl",
  "tinytex")
knitr::opts_chunk$set(echo = TRUE, message = FALSE, warning = FALSE,
  error = TRUE, comment = NA, tidy.opts = list(width.cutoff = 60)) 
options(htmltools.dir.version = FALSE, htmltools.preserve.raw = FALSE)
sf::sf_use_s2(use_s2 = FALSE)


## div.column {
##     display: inline-block;
##     vertical-align: top;
##     width: 50%;
## }
## 
## #TOC::before {
##   content: "";
##   display: block;
##   height:200px;
##   width: 200px;
##   background-size: contain;
##   background-position: 50% 50%;
##   padding-top: 80px !important;
##   background-repeat: no-repeat;
## }

## ----dummy-import-----------------------------------------------------------------------------------------------------------
#| warning: false
#| message: false
#| error: false
#| echo: true

set.seed(333)
dataset_raw <- read_excel("./R/assets/dataset_raw.xlsx")
write.csv(dataset_raw, "./R/assets/dataset_tidy.csv", row.names = FALSE)
dataset_tidy <- read.csv("./R/assets/dataset_tidy.csv")
dataset_tidy |> kbl() |> kable_styling()


## ----dummy-audit------------------------------------------------------------------------------------------------------------
#| warning: false
#| message: false
#| error: false
#| eval: false
#| echo: true

# str(dataset_tidy)
# dplyr::count(dataset_tidy, Species..j.)
# 
# saveHTML(dataMaid::makeDataReport(
#   dataset_tidy,
#   output = "html",
#   codebook = TRUE,
#   onlyProblematic = TRUE,
#   visuals = setVisuals(all = "basicVisual"),
#   replace = TRUE
#   )
# ) # output "dataMaid_dataset_tidy.html" shown in Appendix A.1


## ----dummy-audit-quiet------------------------------------------------------------------------------------------------------
#| warning: false
#| message: false
#| error: false
#| eval: true
#| echo: false

str(dataset_tidy)
dplyr::count(dataset_tidy, Species..j.)


## ----dummy-audit-tidy-------------------------------------------------------------------------------------------------------
#| warning: false
#| message: false
#| error: false
#| eval: true
#| echo: true

data.table::setnames(dataset_tidy, old = "Stratum...i.", new = "stratum_i", skip_absent = TRUE)
data.table::setnames(dataset_tidy, old = "Species..j.", new = "species_j", skip_absent = TRUE)
data.table::setnames(dataset_tidy, old = "Plot..sp.", new = "plot_sp", skip_absent = TRUE)
data.table::setnames(dataset_tidy, old = "Tree..l.", new = "tree_l", skip_absent = TRUE)
data.table::setnames(dataset_tidy, old = "Volume..V_.l.j.I.sp..", new = "volume", skip_absent = TRUE)
dataset_tidy$species_j[dataset_tidy$species_j == "sp4"] <- "Sp4"
dataset_tidy$species_j  = as.factor(dataset_tidy$species_j)
dataset_tidy$stratum_i  = as.factor(dataset_tidy$stratum_i)


## ----dummy-audit-save-------------------------------------------------------------------------------------------------------
#| warning: false
#| message: false
#| error: false
#| eval: true
#| echo: true

dataset_tidy$bcef_r     = 0.7
dataset_tidy$cf         = 0.5
dataset_tidy$d          = 0.5
dataset_tidy$a_sp       = 0.1
dataset_tidy$a_sp_m2    = dataset_tidy$a_sp * 10000

dataset_tidy = dataset_tidy %>%
  group_by(stratum_i) %>%
  mutate(a_I_m2 = sum(a_sp_m2), a_I_ha = sum(a_sp)) 

write.csv(dataset_tidy, "./R/assets/dataset_tidy.csv", row.names = FALSE)
dataset_tidy |> kbl() |> kable_styling()


## ----eq1--------------------------------------------------------------------------------------------------------------------
#| warning: false
#| message: false
#| error: false
#| eval: true
#| echo: true

dataset_tidy = dataset_tidy |>
  group_by(species_j, stratum_i, plot_sp) |>
  mutate(vji_sp_m3 = sum(volume))

# compute new variable 'vji_sp_m3'
data.table::setDT(dataset_tidy)[, .(
  vji_sp_m3 = sum(volume)
  ),
  by = .(stratum_i, plot_sp, species_j)
] |> kbl() |> kable_styling()


## ----eq2--------------------------------------------------------------------------------------------------------------------
#| warning: false
#| message: false
#| error: false
#| eval: true
#| echo: true

dataset_tidy = dataset_tidy |>
  group_by(stratum_i, species_j) |>
  mutate(vji_ha_m3 = mean(vji_sp_m3) * 10)

data.table::setDT(dataset_tidy)[, .(
  vji_sp_m3,
  vji_ha_m3
  ),
  by = .(stratum_i, species_j)
] |> kbl() |> kable_styling()


## ----eq3--------------------------------------------------------------------------------------------------------------------
#| warning: false
#| message: false
#| error: false
#| eval: true
#| echo: true


dataset_tidy <- dataset_tidy %>%
  mutate(chb_ha_tC = vji_ha_m3 * bcef_r * cf)

data.table::setDT(dataset_tidy)[, .(
  vji_sp_m3,
  vji_ha_m3,
  chb_ha_tC
  ),
  by = .(stratum_i, species_j)
] |> kbl() |> kable_styling()


## ----eq4--------------------------------------------------------------------------------------------------------------------
#| warning: false
#| message: false
#| error: false
#| eval: true
#| echo: true

dataset_tidy <- dataset_tidy %>%
  mutate(cex_ha_tC = vji_ha_m3 * d * cf)

data.table::setDT(dataset_tidy)[, .(
  vji_sp_m3,
  vji_ha_m3,
  chb_ha_tC,
  cex_ha_tC
  ),
  by = .(stratum_i, species_j)
] |> kbl() |> kable_styling()


## ----eq6--------------------------------------------------------------------------------------------------------------------
#| warning: false
#| message: false
#| error: false
#| eval: true
#| echo: true

dataset_tidy = dataset_tidy %>%
  mutate(f_rsd = 1.74)

dataset_tidy = dataset_tidy %>%
  mutate(c_rsd = cex_ha_tC * f_rsd)

data.table::setDT(dataset_tidy)[, .(
  vji_sp_m3,
  vji_ha_m3,
  chb_ha_tC,
  c_rsd
  ),
  by = .(stratum_i, species_j)
] |> kbl() |> kable_styling()


## ---------------------------------------------------------------------------------------------------------------------------
#| eval: false
# htmltools::includeHTML("dataMaid_dataset_tidy.html")


## ---------------------------------------------------------------------------------------------------------------------------
devtools::session_info()