Multiplier variability not incorporated into bootdht

[LHMarshall]

Minimum reproducible example: multiplier uncertainty exclusion

Altered the sikadeer data set to perform a bootstrap with 30%CVs in creation and decay rate and similar analysis where the multiplier CVs were set to 0. The reported stratum-specific confidence intervals are virtually identical after 1000 bootstrap replicates. Evidence to me that multiplier uncertainty is not propogated in bootdht.

library(Distance)
data(sikadeer)
cu <- convert_units("centimeter", "kilometer", "square kilometer")
easy <- ds(sikadeer, key="hn", truncation="10%", convert_units = cu)
mult.se <- list(creation = data.frame(rate=25, SE=25*0.3),
             decay    = data.frame(rate=163, SE=163*0.3))
mult.nose <- list(creation = data.frame(rate=25, SE=0),
                     decay    = data.frame(rate=163, SE=0))
deer.ests <- dht2(easy, flatfile=sikadeer, strat_formula=~Region.Label,
                  convert_units=cu, multipliers=mult.se, 
                  stratification="geographical")
print(deer.ests, report="density")

boot.with.se <- bootdht(easy, flatfile = sikadeer, resample_transects = TRUE,
                  convert_units=cu, summary_fun=bootdht_Dhat_summarize,
                  multipliers = mult.se, 
                  cores=10, nboot=1000)
boot.no.se <- bootdht(easy, flatfile = sikadeer, resample_transects = TRUE,
                        convert_units=cu, summary_fun=bootdht_Dhat_summarize,
                        multipliers = mult.nose, 
                        cores=10, nboot=1000)

plain.estimates <- attr(deer.ests, which = "density")
analy.cis <- plain.estimates[, c("Region.Label", "LCI", "UCI")]

library(dplyr)
boot.se <- boot.with.se %>%
  group_by(Label) %>%
  summarize(LowerBound = quantile(Dhat, probs = 0.025), 
            UpperBound = quantile(Dhat, probs = 0.975))

boot.without <- boot.no.se %>%
  group_by(Label) %>%
  summarize(LowerBound = quantile(Dhat, probs = 0.025), 
            UpperBound = quantile(Dhat, probs = 0.975))

knitr::kable(as.data.frame(boot.se), caption="Multipliers with 30%CV", 
             row.names = FALSE, digits=3)
knitr::kable(as.data.frame(boot.without), caption="Multipliers without uncertainty", 
             row.names = FALSE, digits=3)

Output

Table: Multipliers with 30%CV

|Label | LowerBound| UpperBound|
|:-----|----------:|----------:|
|A     |     51.246|    100.438|
|B     |     19.011|     55.353|
|C     |      2.684|      5.371|
|E     |      0.839|      7.135|
|F     |     13.201|     16.930|
|G     |      4.243|     28.815|
|H     |      1.366|      1.751|
|J     |      6.373|      8.173|
|Total |    117.509|    194.044|

Table: Multipliers without uncertainty

|Label | LowerBound| UpperBound|
|:-----|----------:|----------:|
|A     |     50.911|     98.927|
|B     |     19.176|     52.884|
|C     |      2.647|      5.381|
|E     |      0.860|      7.180|
|F     |     13.149|     16.847|
|G     |      4.189|     28.461|
|H     |      1.360|      1.743|
|J     |      6.348|      8.133|
|Total |    117.460|    186.972|

Originally posted by @erex in #155