fix missing values are not allowed in subscripted assignments error u…

…sing %in%
pbs-assess · Nov 15, 2024 · 5495a76 · 5495a76
1 parent 7647d90
commit 5495a76
Showing 1 changed file with 15 additions and 15 deletions.
diff --git a/R/correct-ssids.R b/R/correct-ssids.R
@@ -6,30 +6,30 @@
 #
 correct_ssids <- function(dat, specimens = FALSE) {
   try(dat[dat$survey_series_id %in% c(6, 7), ]$survey_id <- NA, silent = TRUE)
-  try(dat[((dat$survey_series_id == 6 & dat$major_stat_area_code %in% c("03", "04"))), ]$survey_series_id <- 7, silent = TRUE)
-  try(dat[((dat$survey_series_id == 7 & dat$major_stat_area_code %in% c("05", "06"))), ]$survey_series_id <- 6, silent = TRUE)
-  try(dat[((dat$survey_series_og == 6 & dat$major_stat_area_code %in% c("03", "04"))), ]$survey_series_og <- 7, silent = TRUE)
-  try(dat[((dat$survey_series_og == 7 & dat$major_stat_area_code %in% c("05", "06"))), ]$survey_series_og <- 6, silent = TRUE)
+  try(dat[((dat$survey_series_id %in% 6 & dat$major_stat_area_code %in% c("03", "04"))), ]$survey_series_id <- 7, silent = TRUE)
+  try(dat[((dat$survey_series_id %in% 7 & dat$major_stat_area_code %in% c("05", "06"))), ]$survey_series_id <- 6, silent = TRUE)
+  try(dat[((dat$survey_series_og %in% 6 & dat$major_stat_area_code %in% c("03", "04"))), ]$survey_series_og <- 7, silent = TRUE)
+  try(dat[((dat$survey_series_og %in% 7 & dat$major_stat_area_code %in% c("05", "06"))), ]$survey_series_og <- 6, silent = TRUE)
 
   # SABLE doesn't work with SSIDs, use reason_desc and or grouping codes instead?
   try(dat[dat$survey_series_id %in% c(35, 41, 42, 43), ]$survey_id <- NA, silent = TRUE) # this throws a warning when others don't
   try(dat[dat$survey_series_id %in% c(35, 41, 42, 43), ]$survey_series_id <- 35, silent = TRUE)
   try(dat[dat$survey_series_og %in% c(35, 41, 42, 43), ]$survey_series_og <- 35, silent = TRUE)
-  # try(dat[ ((dat$survey_series_id %in% c(35, 41, 42, 43) & dat$reason_desc == "EXPLORATORY")), ]$survey_series_id <- 35, silent = TRUE)
-  # try(dat[ ((dat$survey_series_id %in% c(35, 41, 42, 43) & dat$reason_desc == "SABLEFISH STANDARDIZED OFFSHORE SURVEY")), ]$survey_series_id <- 42, silent = TRUE)
+  # try(dat[ ((dat$survey_series_id %in% c(35, 41, 42, 43) & dat$reason_desc %in% "EXPLORATORY")), ]$survey_series_id <- 35, silent = TRUE)
+  # try(dat[ ((dat$survey_series_id %in% c(35, 41, 42, 43) & dat$reason_desc %in% "SABLEFISH STANDARDIZED OFFSHORE SURVEY")), ]$survey_series_id <- 42, silent = TRUE)
 
   # Jig surveys are split into too many separate survey series, so we'll assume all were assigned correctly and drop everything that doesn't match
-  dat <- dat[(!(dat$survey_series_id == 82 & !(dat$minor_stat_area_code %in% c("12")))), ]
-  dat <- dat[(!(dat$survey_series_id == 83 & !(dat$minor_stat_area_code %in% c("13")))), ]
-  dat <- dat[(!(dat$survey_series_id == 84 & !(dat$minor_stat_area_code %in% c("15")))), ]
-  dat <- dat[(!(dat$survey_series_id == 85 & !(dat$minor_stat_area_code %in% c("16")))), ]
-  dat <- dat[(!(dat$survey_series_id == 86 & !(dat$minor_stat_area_code %in% c("18")))), ]
-  dat <- dat[(!(dat$survey_series_id == 87 & !(dat$minor_stat_area_code %in% c("19")))), ]
+  dat <- dat[(!(dat$survey_series_id %in% 82 & !(dat$minor_stat_area_code %in% c("12")))), ]
+  dat <- dat[(!(dat$survey_series_id %in% 83 & !(dat$minor_stat_area_code %in% c("13")))), ]
+  dat <- dat[(!(dat$survey_series_id %in% 84 & !(dat$minor_stat_area_code %in% c("15")))), ]
+  dat <- dat[(!(dat$survey_series_id %in% 85 & !(dat$minor_stat_area_code %in% c("16")))), ]
+  dat <- dat[(!(dat$survey_series_id %in% 86 & !(dat$minor_stat_area_code %in% c("18")))), ]
+  dat <- dat[(!(dat$survey_series_id %in% 87 & !(dat$minor_stat_area_code %in% c("19")))), ]
 
   # for IPHC station specific ssids, drop everything that doesn't match
-  dat <- dat[(!(dat$survey_series_id == 17 & !(dat$minor_stat_area_code %in% c("3")))), ] # 3CD
-  dat <- dat[(!(dat$survey_series_id == 18 & !(dat$minor_stat_area_code %in% c("6")))), ] # 5AB
-  dat <- dat[(!(dat$survey_series_id == 19 & !(dat$minor_stat_area_code %in% c("7")))), ] # 5CD
+  dat <- dat[(!(dat$survey_series_id %in% 17 & !(dat$minor_stat_area_code %in% c("3")))), ] # 3CD
+  dat <- dat[(!(dat$survey_series_id %in% 18 & !(dat$minor_stat_area_code %in% c("6")))), ] # 5AB
+  dat <- dat[(!(dat$survey_series_id %in% 19 & !(dat$minor_stat_area_code %in% c("7")))), ] # 5CD
 
   dat |> dplyr::distinct()
 }