minor updates, want tripcode in some functions

PlanktonTeam · Apr 5, 2024 · 0d5e52f · 0d5e52f
1 parent b7be108
commit 0d5e52f
Show file tree

Hide file tree

Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/R/utils.R b/R/utils.R
@@ -595,7 +595,7 @@ pr_get_Coeffs <-  function(df){
         dplyr::filter(.data$StationName == stations)
     }
 
-    m <- stats::lm(Values ~ Year_Local , data = lmdat) #+ pr_harmonic(Month, k = 1)
+    m <- stats::lm(Values ~ Year_Local + pr_harmonic(Month, k = 1), data = lmdat)
 
     lmdat <- tibble::tibble(lmdat %>%
                               dplyr::bind_cols(fv = m$fitted.values))

diff --git a/R/utils_bgc.R b/R/utils_bgc.R
@@ -26,7 +26,7 @@ pr_get_NRSChemistry <- function(){
                   DIN_umolL = sum(.data$NOx_umolL, .data$Ammonium_umolL, na.rm = TRUE),
                   Redfield = mean(.data$NOx_umolL, na.rm = TRUE)/mean(.data$Phosphate_umolL, na.rm = TRUE),
                   Redfield = ifelse(is.infinite(.data$Redfield), NA, .data$Redfield)) %>%
-    dplyr::select("Project", "SampleTime_Local", "Month_Local", "SampleDepth_m",
+    dplyr::select("Project", "SampleTime_Local", "Month_Local", "SampleDepth_m", "TripCode",
                   "StationName", "StationCode", tidyselect::all_of(var_names)) %>%
     tidyr::pivot_longer(tidyselect::all_of(var_names), values_to = "Values", names_to = 'Parameters') %>%
     pr_reorder()

diff --git a/R/utils_boo_data.R b/R/utils_boo_data.R
@@ -52,7 +52,7 @@ pr_get_FuncGroups <- function(Survey = "NRS", Type = "Z", ...){
 
   if(Type == "P"){
     df <- df %>%
-      dplyr::mutate(Parameters = ifelse(.data$Parameters %in% c("Ciliate","Foraminifera", "Radiozoa", "Silicoflagellate"), "Other", .data$Parameters),
+      dplyr::mutate(Parameters = ifelse(.data$Parameters %in% c("Centric diatom", "Pennate diatom", "Dinoflagellate", "Cyanobacteria"), .data$Parameters, "Other"),
                     Parameters = factor(.data$Parameters, levels = c("Centric diatom", "Pennate diatom", "Dinoflagellate", "Cyanobacteria",
                                                                      "Other")))
   } else if(Type == "Z"){