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More Elfgen edits #141

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More Elfgen edits
SELoomis Jul 29, 2020
8cfb557
Elfgen edits - typos
SELoomis Jul 29, 2020
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29 changes: 11 additions & 18 deletions HARP-2020/Elfgen/Elfgen_Intake_Facility_Algorithm.R
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Original file line number Diff line number Diff line change
Expand Up @@ -86,22 +86,16 @@ elf <- elfgen("watershed.df" = watershed.df,

#### Solving for confidence interval lines

xdat <- c(elf$plot$data$x_var)
ydat <- c(elf$plot$data$y_var)
data <- as.data.frame(elf$plot$data)
uq <- elf$plot$plot_env$upper.quant

upper.lm <- lm(y_var ~ log(x_var), data = uq)

predict <- as.data.frame(predict(upper.lm, newdata = data.frame(x_var = mean_intake), interval = 'confidence'))

species_richness<-elf$stats$m*log(mean_intake)+elf$stats$b

# Comparing predict to actual values
#fit<-as.numeric(predict$fit)
#species_richness<-elf$stats$m*log(mean_intake)+elf$stats$b
#percent_error<-((fit-species_richness)/species_richness)*100
predict.df <- as.data.frame(predict(upper.lm, newdata = data.frame(x_var = mean_intake), interval = 'confidence'))

# this section is not necessarily needed - use as a check for percent error
# fit<-as.numeric(predict.df$fit)
# species_richness<-elf$stats$m*log(mean_intake)+elf$stats$b
# percent_error<-((fit-species_richness)/species_richness)*100

xmin <- min(uq$x_var)
xmax <- max(uq$x_var)
Expand All @@ -119,10 +113,10 @@ m <- elf$stats$m
b <- elf$stats$b
int <- m*log(mean_intake) + b # solving for mean_intake y-value

m1 <- (ymax1-ymin1)/(log(xmax)-log(xmin)) # line 1
m1 <- (ymax1-ymin1)/(log(xmax)-log(xmin)) # slope and intercept of confidence interval line 1
b1 <- ymax1-(m1*log(xmax))

m2 <- (ymax2-ymin2)/(log(xmax)-log(xmin)) # line 2
m2 <- (ymax2-ymin2)/(log(xmax)-log(xmin)) # slope and intercept of confidence interval line 2
b2 <- ymax2 - (m2*log(xmax))


Expand All @@ -143,15 +137,14 @@ elf$plot +
elf$stats$m <- m1
elf$stats$b <- b1

percent_richness_change_bound1 <- richness_change(elf$stats, "pctchg" = flow_reduction_pct, "xval" = mean_intake)
abs_richness_change_bound1 <- richness_change(elf$stats, "pctchg" = flow_reduction_pct)
pct_richness_change_1 <- richness_change(elf$stats, "pctchg" = flow_reduction_pct, "xval" = mean_intake)
abs_richness_change_1 <- richness_change(elf$stats, "pctchg" = flow_reduction_pct)

elf$stats$m <- m2
elf$stats$b <- b2

percent_richness_change_bound2 <- richness_change(elf$stats, "pctchg" = flow_reduction_pct, "xval" = mean_intake)
abs_richness_change_bound2 <- richness_change(elf$stats, "pctchg" = flow_reduction_pct)

pct_richness_change_2 <- richness_change(elf$stats, "pctchg" = flow_reduction_pct, "xval" = mean_intake)
abs_richness_change_2 <- richness_change(elf$stats, "pctchg" = flow_reduction_pct)


#### Saving
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