modified the RBI Category Threshold Table for the display purposes in…

… the RMarkdown

R/RBI.R

@@ -373,13 +373,15 @@ RBI <- function(BenthicData, logfile = file.path(getwd(), 'logs', format(Sys.tim
  dplyr::summarise(NIT = sum(badness))
 
  writelog(
- "\n#### RBI Step 8 - Filter to Capitella capitata Cmplx and Oligochaeta and group by Stratum, StationID, Sampledate, Replicate - group and get the sum of 'badness'",
+ "\n#### RBI Step 8 - Filter to Capitella capitata Cmplx and Oligochaeta and group by Stratum, StationID, Sampledate, Replicate - group and get the sum of 'badness' (This would be the negative indicator taxa section on page 70)\n ",
  logfile = logfile,
  code = '
  rbi8 <- rbi_data %>%
  dplyr::filter(Taxon %in% c( "Capitella capitata Cmplx","Oligochaeta")) %>%
  dplyr::mutate(badness=-0.1) %>%
  dplyr::group_by(Stratum, StationID, Replicate, SampleDate) %>%
+
+ # NIT = Negative Indicator Taxa
  dplyr::summarise(NIT = sum(badness))
  ',
  data = rbi8 %>% head(25),
@@ -427,8 +429,8 @@ RBI <- function(BenthicData, logfile = file.path(getwd(), 'logs', format(Sys.tim
 
  ### RBI Category Thresholds for Southern California Marine Bays
  RBI_category_thresholds <- data.frame(
- ref_low = c(0.27, 0.16, 0.08, 0.08),
- ref_high = c(0.27, 0.27, 0.16, 0.08),
+ ref_low = c(0.27, 0.16, 0.08, 0.09),
+ ref_high = c(0.27, 0.27, 0.16, 0.09),
  category = as.factor(c("Reference","Low Disturbance","Moderate Disturbance","High Disturbance")),
  category_score = c(1, 2, 3, 4)
  )
@@ -439,8 +441,8 @@ RBI <- function(BenthicData, logfile = file.path(getwd(), 'logs', format(Sys.tim
  code = '
  ### RBI Category Thresholds for Southern California Marine Bays
  RBI_category_thresholds <- data.frame(
- ref_low = c(0.27, 0.16, 0.08, 0.08),
- ref_high = c(0.27, 0.27, 0.16, 0.08),
+ ref_low = c(0.27, 0.16, 0.08, 0.09),
+ ref_high = c(0.27, 0.27, 0.16, 0.09),
  category = as.factor(c("Reference","Low Disturbance","Moderate Disturbance","High Disturbance")),
  category_score = c(1, 2, 3, 4)
  )