fix: updated EBAM valid_RHi from 45 -> 50

MazamaScience · Jul 7, 2021 · 397df1c · 397df1c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Type: Package
 Package: PWFSLSmoke
-Version: 1.2.113
+Version: 1.2.114
 Title: Utilities for Working with Air Quality Monitoring Data
 Authors@R: c(
     person("Jonathan", "Callahan", email="[email protected]", role=c("aut","cre")), 

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# PWFSLSmoke 1.2.114
+
+* Updated AIRSIS EBAM QC RHi threshold from 45% to 50%.
+
 # PWFSLSmoke 1.2.113
 
 * Updated `docker/` files to use R 3.6.3.

diff --git a/R/airsis_BAM1020QualityControl.R b/R/airsis_BAM1020QualityControl.R
@@ -93,7 +93,7 @@ airsis_BAM1020QualityControl <- function(
   badRowCount <- sum(badRows)
   if ( badRowCount > 0 ) {
     logger.trace(paste(verb,"%s rows with invalid location information"), badRowCount)
-    badLocations <- paste('(',tbl$Longitude[badRows],',',tbl$Latitude[badRows],')',sep='')
+    badLocations <- paste('(',tbl$Longitude[badRows],',',tbl$Latitude[badRows],')',sep = '')
     logger.trace("Bad locations: %s", unique(badLocations))
     if ( flagAndKeep ) {
       # apply flags
@@ -112,18 +112,18 @@ airsis_BAM1020QualityControl <- function(
   if (nrow(tbl) < 1 && !flagAndKeep) {
     err_msg <- paste0("No valid PM2.5 data for ", monitorName)
     logger.warn(err_msg) # This is more of a warning than some error in the data.
-    stop(err_msg, call.=FALSE)
+    stop(err_msg, call. = FALSE)
   }
 
   # ----- Time ----------------------------------------------------------------
 
   # Add a POSIXct datetime
-  tbl$datetime <- lubridate::floor_date(lubridate::mdy_hms(tbl$TimeStamp), unit="hour") - lubridate::dhours(1)
+  tbl$datetime <- lubridate::floor_date(lubridate::mdy_hms(tbl$TimeStamp), unit = "hour") - lubridate::dhours(1)
   if ( flagAndKeep ) {
     # TODO: Unable to get datetime moved from tbl to tblFlagged without timezone and/or display getting messed up.
     # For now just duplicating the calculation, then assigning row values to NA after the fact for rows that were
     # removed from tbl prior to calculating datetime above. Clean up later if possible.
-    tblFlagged$datetime <- lubridate::floor_date(lubridate::mdy_hms(tblFlagged$TimeStamp), unit="hour") - lubridate::dhours(1)
+    tblFlagged$datetime <- lubridate::floor_date(lubridate::mdy_hms(tblFlagged$TimeStamp), unit = "hour") - lubridate::dhours(1)
     tblFlagged$datetime[ which(!(tblFlagged$rowID %in% tbl$rowID)) ] <- NA
   }
 
@@ -165,15 +165,15 @@ airsis_BAM1020QualityControl <- function(
   gooddatetime <- !is.na(tbl$datetime) & tbl$datetime < lubridate::now(tzone = "UTC") # saw a future date once
 
   logger.trace("Flow has %s missing or out of range values", sum(!goodFlow))
-  if (sum(!goodFlow) > 0) logger.trace("Bad Flow values:  %s", paste0(sort(unique(tbl$Qtot..m3.[!goodFlow]),na.last=TRUE), collapse=", "))
+  if (sum(!goodFlow) > 0) logger.trace("Bad Flow values:  %s", paste0(sort(unique(tbl$Qtot..m3.[!goodFlow]),na.last = TRUE), collapse = ", "))
   logger.trace("AT has %s missing or out of range values", sum(!goodAT))
-  if (sum(!goodAT) > 0) logger.trace("Bad AT values:  %s", paste0(sort(unique(tbl$Ambient.Temp..C.[!goodAT]),na.last=TRUE), collapse=", "))
+  if (sum(!goodAT) > 0) logger.trace("Bad AT values:  %s", paste0(sort(unique(tbl$Ambient.Temp..C.[!goodAT]),na.last = TRUE), collapse = ", "))
   logger.trace("RHi has %s missing or out of range values", sum(!goodRHi))
-  if (sum(!goodRHi) > 0) logger.trace("Bad RHi values:  %s", paste0(sort(unique(tbl$RH....[!goodRHi]),na.last=TRUE), collapse=", "))
+  if (sum(!goodRHi) > 0) logger.trace("Bad RHi values:  %s", paste0(sort(unique(tbl$RH....[!goodRHi]),na.last = TRUE), collapse = ", "))
   logger.trace("Conc has %s missing or out of range values", sum(!goodConcHr))
-  if (sum(!goodConcHr) > 0) logger.trace("Bad Conc values:  %s", paste0(sort(unique(tbl$'Conc..\u00B5g.m3.'[!goodConcHr]),na.last=TRUE), collapse=", "))
+  if (sum(!goodConcHr) > 0) logger.trace("Bad Conc values:  %s", paste0(sort(unique(tbl$'Conc..\u00B5g.m3.'[!goodConcHr]),na.last = TRUE), collapse = ", "))
   logger.trace("datetime has %s missing or out of range values", sum(!gooddatetime))
-  if (sum(!gooddatetime) > 0) logger.trace("Bad datetime values:  %s", paste0(sort(unique(tbl$datetime[!gooddatetime]),na.last=TRUE), collapse=", "))
+  if (sum(!gooddatetime) > 0) logger.trace("Bad datetime values:  %s", paste0(sort(unique(tbl$datetime[!gooddatetime]),na.last = TRUE), collapse = ", "))
 
   goodMask <- goodFlow & goodAT & goodRHi & goodConcHr & gooddatetime
   badQCCount <- sum(!goodMask)
@@ -204,7 +204,7 @@ airsis_BAM1020QualityControl <- function(
   if (nrow(tbl) < 1 && !flagAndKeep) {
     err_msg <- paste0("No valid PM2.5 data for ", monitorName)
     logger.warn(err_msg) # This is more of a warning than some error in the data.
-    stop(err_msg, call.=FALSE)
+    stop(err_msg, call. = FALSE)
   }
 
   # ----- Duplicate Hours -----------------------------------------------------
@@ -220,7 +220,7 @@ airsis_BAM1020QualityControl <- function(
 
   if ( dupHrCount > 0 ) {
     logger.trace(paste(verb,"%s duplicate time entries"), dupHrCount)
-    logger.trace("Duplicate Hours (may be >1 per timestamp):  %s", paste0(sort(unique(tbl$TimeStamp[dupHrMask])), collapse=", "))
+    logger.trace("Duplicate Hours (may be >1 per timestamp):  %s", paste0(sort(unique(tbl$TimeStamp[dupHrMask])), collapse = ", "))
     if ( flagAndKeep ) {
       # apply flags
       tblFlagged$QCFlag_duplicateHr[tbl$rowID[dupHrMask]] <- TRUE
@@ -236,7 +236,7 @@ airsis_BAM1020QualityControl <- function(
   if (nrow(tbl) < 1 && !flagAndKeep) {
     err_msg <- paste0("No valid PM2.5 data for ", monitorName)
     logger.warn(err_msg) # This is more of a warning than some error in the data.
-    stop(err_msg, call.=FALSE)
+    stop(err_msg, call. = FALSE)
   }
 
   # ----- More QC -------------------------------------------------------------

diff --git a/R/airsis_EBAMQualityControl.R b/R/airsis_EBAMQualityControl.R
@@ -37,7 +37,7 @@ airsis_EBAMQualityControl <- function(
   remove_Lat_zero = TRUE,
   valid_Flow = c(16.7*0.95,16.7*1.05),
   valid_AT = c(-Inf,45),
-  valid_RHi = c(-Inf,45),
+  valid_RHi = c(-Inf,50),
   valid_Conc = c(-Inf,5.000),
   flagAndKeep = FALSE
 ) {
@@ -176,6 +176,7 @@ airsis_EBAMQualityControl <- function(
   # Leland Tarnay QC -----------------------------------------------------------
 
   # NOTE:  Override ConcHr high value with 5.000 as per conversation with Mike Broughton
+  # NOTE:  2021-07-07 Update RHi from 45 -> 50 as per conversation with Pete Lahm
 
   ###tmp.2014_YOSE_ebam1_ftp$concQA <- with(tmp.2014_YOSE_ebam1_ftp,
   ###                              ifelse(Flow < 16.7 * .95, "FlowLow",

diff --git a/R/airsis_EBAM_MULTI2QualityControl.R b/R/airsis_EBAM_MULTI2QualityControl.R
@@ -39,7 +39,7 @@ airsis_EBAM_MULTI2QualityControl <- function(
   remove_Lat_zero = TRUE,
   valid_Flow = c(16.7*0.95,16.7*1.05),
   valid_AT = c(-Inf,45),
-  valid_RHi = c(-Inf,45),
+  valid_RHi = c(-Inf,50),
   valid_Conc = c(-Inf,5.000),
   flagAndKeep = FALSE
 ) {
@@ -178,6 +178,7 @@ airsis_EBAM_MULTI2QualityControl <- function(
   # Leland Tarnay QC -----------------------------------------------------------
 
   # NOTE:  Override ConcHr high value with 5.000 as per conversation with Mike Broughton
+  # NOTE:  2021-07-07 Update RHi from 45 -> 50 as per conversation with Pete Lahm
 
   ###tmp.2014_YOSE_ebam1_ftp$concQA <- with(tmp.2014_YOSE_ebam1_ftp,
   ###                              ifelse(Flow < 16.7 * .95, "FlowLow",

diff --git a/R/airsis_EBAM_PLUS_MULTIQualityControl.R b/R/airsis_EBAM_PLUS_MULTIQualityControl.R
@@ -39,7 +39,7 @@ airsis_EBAM_PLUS_MULTIQualityControl <- function(
   remove_Lat_zero = TRUE,
   valid_Flow = c(16.7*0.95,16.7*1.05),
   valid_AT = c(-Inf,45),
-  valid_RHi = c(-Inf,45),
+  valid_RHi = c(-Inf,50),
   valid_Conc = c(-Inf,5.000),
   flagAndKeep = FALSE
 ) {
@@ -180,6 +180,7 @@ airsis_EBAM_PLUS_MULTIQualityControl <- function(
   # Leland Tarnay QC -----------------------------------------------------------
 
   # NOTE:  Override ConcHr high value with 5.000 as per conversation with Mike Broughton
+  # NOTE:  2021-07-07 Update RHi from 45 -> 50 as per conversation with Pete Lahm
 
   ###tmp.2014_YOSE_ebam1_ftp$concQA <- with(tmp.2014_YOSE_ebam1_ftp,
   ###                              ifelse(Flow < 16.7 * .95, "FlowLow",
@@ -297,19 +298,3 @@ airsis_EBAM_PLUS_MULTIQualityControl <- function(
 
 }
 
-# ===== DEBUGGING ==============================================================
-
-if ( FALSE ) {
-
-  # tbl <- ...
-  valid_Longitude = c(-180,180)
-  valid_Latitude = c(-90,90)
-  remove_Lon_zero = TRUE
-  remove_Lat_zero = TRUE
-  valid_Flow = c(16.7*0.95,16.7*1.05)
-  valid_AT = c(-Inf,45)
-  valid_RHi = c(-Inf,45)
-  valid_Conc = c(-Inf,5.000)
-  flagAndKeep = FALSE
-
-}
diff --git a/R/airsis_createMonitorObject.R b/R/airsis_createMonitorObject.R
@@ -42,7 +42,7 @@
 #' \item{\code{remove_Lat_zero = TRUE}}
 #' \item{\code{valid_Flow = c(16.7*0.95,16.7*1.05)}}
 #' \item{\code{valid_AT = c(-Inf,45)}}
-#' \item{\code{valid_RHi = c(-Inf,45)}}
+#' \item{\code{valid_RHi = c(-Inf,50)}}
 #' \item{\code{valid_Conc = c(-Inf,5.000)}}
 #' }
 #'

diff --git a/R/airsis_qualityControl.R b/R/airsis_qualityControl.R
@@ -26,7 +26,7 @@
 #' \item{\code{remove_Lat_zero = TRUE}}
 #' \item{\code{valid_Flow = c(16.7*0.95,16.7*1.05)}}
 #' \item{\code{valid_AT = c(-Inf,45)}}
-#' \item{\code{valid_RHi = c(-Inf,45)}}
+#' \item{\code{valid_RHi = c(-Inf,50)}}
 #' \item{\code{valid_Conc = c(-Inf,5.000)}}
 #' }
 #'

diff --git a/R/wrcc_EBAMQualityControl.R b/R/wrcc_EBAMQualityControl.R
@@ -44,7 +44,7 @@ wrcc_EBAMQualityControl <- function(
   remove_Lat_zero = TRUE,
   valid_Flow = c(16.7*0.95,16.7*1.05),
   valid_AT = c(-Inf,45),
-  valid_RHi = c(-Inf,45),
+  valid_RHi = c(-Inf,50),
   valid_Conc = c(-Inf,5000),
   flagAndKeep = FALSE
 ) {
@@ -170,6 +170,7 @@ wrcc_EBAMQualityControl <- function(
   # Leland Tarnay QC for E-BAM ------------------------------------------------
 
   # NOTE:  Override ConcHr high value with 5000 as per conversation with Mike Broughton
+  # NOTE:  2021-07-07 Update RHi from 45 -> 50 as per conversation with Pete Lahm
 
   ###tmp.2014_YOSE_ebam1_ftp$concQA <- with(tmp.2014_YOSE_ebam1_ftp,
   ###                              ifelse(Flow < 16.7 * .95, "FlowLow",

diff --git a/R/wrcc_createMonitorObject.R b/R/wrcc_createMonitorObject.R
@@ -41,7 +41,7 @@
 #' \item{\code{remove_Lat_zero = TRUE}}
 #' \item{\code{valid_Flow = c(16.7*0.95,16.7*1.05)}}
 #' \item{\code{valid_AT = c(-Inf,45)}}
-#' \item{\code{valid_RHi = c(-Inf,45)}}
+#' \item{\code{valid_RHi = c(-Inf,50)}}
 #' \item{\code{valid_Conc = c(-Inf,5000)}}
 #' }
 #'

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diff --git a/docs/articles/PWFSLSmoke.html b/docs/articles/PWFSLSmoke.html