In mcsiple/mmrefpoints: Project Marine Mammal Populations and Calculate Reference Points

This report was generated using the marine mammal bycatch impacts exploration tool. The output reflects parameters that the user has entered for their marine mammal population of interest. These values are entered in the Advanced and PBR & PBR calculator tabs.

Life history parameters used

# The `params` object is available in the document.
options(knitr.table.format = "html") 
library(magrittr)

lhdf <- as.data.frame(params$lh.params)

lhdf <- lhdf %>%
  dplyr::select(S0,S1plus,AgeMat,lambdaMax,z) %>%
  dplyr::rename("$S_0$" = S0,
         "$S_{1+}$" = S1plus,
         "Age at maturity" = AgeMat,
         "$\\lambda_{max}$" = lambdaMax)

knitr::kable(format="html", # make table showing all the parameters
             lhdf) %>% 
            kableExtra::kable_styling()

Performance measures

These are the median outcomes for each of the bycatch and depletion levels.

# The `params` object is available in the document.
pm <-  params$performance 

knitr::kable(format="html",pm) %>%
  kableExtra::kable_styling(full_width = F,position="center")

Estimated reference points

The following table is based on values that the user has entered in the PBR tab of the app.

If $N_{MIN}$ and $N_{BEST}$ are the same, the user has not specified a survey CV of abundance. If several values are missing, the user may have run some projections without entering anything in the PBR tab.

Note: For this table to give the correct values, the user has to specify a current population size and an annual bycatch rate in the Advanced tab. Otherwise, the numbers below will not be based on a real population size.

# The `params` object is available in the document.
PBR <- params$pbr %>%
  dplyr::mutate(Parameter = dplyr::recode(Parameter, 
                            Nbest = "$N_{BEST}$",
                            Nmin = "$N_{MIN}$",
                            Rmax = "$R_{MAX}$",
                            Fr = "$F_R$"))
PBR %>% 
  dplyr::mutate_if(is.numeric, list(~as.character(., signif(., 2)))) %>%
  knitr::kable(format="html") %>%
  kableExtra::kable_styling(full_width = F,position="center")

mcsiple/mmrefpoints documentation built on June 17, 2022, 8:41 p.m.