diff --git a/DESCRIPTION b/DESCRIPTION index 6d231e2..e7ccacd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: SQOUnified Type: Package Title: Tools for calculating SQO scores based on three Lines of Evidence (Benthic, Tox, Chem) -Version: 0.5.0 +Version: 0.5.1 Date: 2024-05-13 Description: Calculates Site Assessments based on the three lines of evidence as outlined in the CASQO Manual Benthic, Toxicity, and Chemistry diff --git a/R/RBI.R b/R/RBI.R index ecc47d5..0bcf78b 100644 --- a/R/RBI.R +++ b/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) )