updated processing of ESAM_Multi

DESCRIPTION

@@ -1,6 +1,6 @@
 Type: Package
 Package: PWFSLSmoke
-Version: 1.2.111
+Version: 1.2.112
 Title: Utilities for Working with Air Quality Monitoring Data
 Authors@R: c(
     person("Jonathan", "Callahan", email="[email protected]", role=c("aut","cre")), 

NEWS.md

@@ -1,3 +1,7 @@
+# PWFSLSmoke 1.2.112
+
+* Updated support for parsing AIRSIS "ESAM Multi" format.
+
 # PWFSLSmoke 1.2.111
 
 CRAN manual review suggestions:

R/airsis_ESAM_MULTIQualityControl.R

@@ -38,7 +38,7 @@ airsis_ESAM_MULTIQualityControl <- function(
   valid_Flow = c(1.999, 2.001),     # anything other than 2 is bad
   valid_AT = c(-Inf, 150),
   valid_RHi = c(-Inf, 55),
-  valid_Conc = c(-Inf, 5000),
+  valid_Conc = c(-Inf, 5),
   flagAndKeep = FALSE
 ) {
 
@@ -48,7 +48,7 @@ airsis_ESAM_MULTIQualityControl <- function(
 
   # > names(tbl)
   # [1] "MasterTable_ID"          "Alias"                 "Latitude"                 "Longitude"
-  # [5] "Conc.ug.m3."             "Flow.l.m."             "AT.C."                    "BP.PA."
+  # [5] "Conc.mg.m3."             "Flow.l.m."             "AT.C."                    "BP.PA."
   # [9] "RHx..."                  "RHi..."                "WS.M.S."                  "WD.Deg."
   # [13] "BV.V."                  "Alarm"                 "Oceaneering.Unit.Voltage" "TimeStamp"
   # [17] "PDate"                  "monitorName"           "monitorType"              "monitorSubtype"
@@ -182,7 +182,7 @@ airsis_ESAM_MULTIQualityControl <- function(
   goodFlow <- !is.na(tbl$Flow.l.m.) & tbl$Flow.l.m. >= valid_Flow[1] & tbl$Flow.l.m. <= valid_Flow[2]
   goodAT <- !is.na(tbl$AT.C.) & tbl$AT.C. >= valid_AT[1] & tbl$AT.C. <= valid_AT[2]
   goodRHi <- !is.na(tbl$RHi...) & tbl$RHi... >= valid_RHi[1] & tbl$RHi... <= valid_RHi[2]
-  goodConcHr <- !is.na(tbl$Conc.ug.m3.) & tbl$Conc.ug.m3. >= valid_Conc[1] & tbl$Conc.ug.m3. <= valid_Conc[2]
+  goodConcHr <- !is.na(tbl$Conc.mg.m3.) & tbl$Conc.mg.m3. >= valid_Conc[1] & tbl$Conc.mg.m3. <= valid_Conc[2]
   gooddatetime <- !is.na(tbl$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))
@@ -296,7 +296,7 @@ if ( FALSE ) {
   valid_Flow = c(1.999, 2.001)     # anything other than 2 is bad
   valid_AT = c(-Inf, 150)
   valid_RHi = c(-Inf, 55)
-  valid_Conc = c(-Inf, 5000)
+  valid_Conc = c(-Inf, 5)
   flagAndKeep = FALSE
 
 }

R/airsis_createDataDataframe.R

@@ -73,11 +73,7 @@ airsis_createDataDataframe <- function(
   if ( monitorType == 'EBAM' ) {
     pm25Var <- 'ConcHr'
   } else if ( monitorType == 'ESAM' ) {
-    if ( monitorSubtype == 'MULTI' ) {
-      pm25Var <- 'Conc.ug.m3.'
-    } else {
-      pm25Var <- 'Conc.mg.m3.'
-    }
+    pm25Var <- 'Conc.mg.m3.'
   } else if ( monitorType == 'BAM1020' ) {
     pm25Var <- 'Conc..\u00B5g.m3.'
   } else {
@@ -96,11 +92,7 @@ airsis_createDataDataframe <- function(
   }
 
   if ( monitorType == 'ESAM' ) {
-    if ( monitorSubtype == 'MULTI') {
-      melted$value <- melted$value * 1
-    } else {
-      melted$value <- melted$value * 1000
-    }
+    melted$value <- melted$value * 1000
   }
 
   # Use median if multiple values are found

R/airsis_createMonitorObject.R

@@ -188,8 +188,8 @@ if ( FALSE ) {
 
   # 2020 "ESAM Multi" format -- usfs.2072-5
 
-  startdate = MazamaCoreUtils::parseDatetime("2020-06-14", timezone = "UTC")
-  enddate = MazamaCoreUtils::parseDatetime("2020-06-20", timezone = "UTC")
+  startdate = MazamaCoreUtils::parseDatetime("2020-07-01", timezone = "UTC")
+  enddate = MazamaCoreUtils::parseDatetime("2020-07-07", timezone = "UTC")
   provider = "usfs"
   unitID = 1072
   clusterDiameter = 1000

R/airsis_identifyMonitorType.R

@@ -42,9 +42,8 @@ airsis_identifyMonitorType <- function(df) {
 
   # ----- Different header styles ----------------------------------------------
 
-  # USFS_esamMulti, provider = "usfs", unitID=1072-5 (starting in June, 2020)
-                   ###"MasterTable_ID,Alias,Latitude,Longitude,Conc(mg/m3),Flow(l/m),AT(C),BP(PA),RHx(%),RHi(%),WS(M/S),WD(Deg),BV(V),Alarm,Oceaneering Unit Voltage,TimeStamp,PDate"
-  esamMulti_header <- "MasterTable_ID,Alias,Latitude,Longitude,Conc(ug/m3),Flow(l/m),AT(C),BP(PA),RHx(%),RHi(%),WS(M/S),WD(Deg),BV(V),Alarm,Oceaneering Unit Voltage,TimeStamp,PDate"
+  # USFS_esamMulti, provider = "usfs", unitID=1072-5 (starting in July 08, 2020; was mistakenly in units of ug/m3 before that)
+  esamMulti_header <- "MasterTable_ID,Alias,Latitude,Longitude,Conc(mg/m3),Flow(l/m),AT(C),BP(PA),RHx(%),RHi(%),WS(M/S),WD(Deg),BV(V),Alarm,Oceaneering Unit Voltage,TimeStamp,PDate"
   esamMulti_rawNames <- unlist(stringr::str_split(esamMulti_header, ','))
   esamMulti_names <- make.names(esamMulti_rawNames)
   # "64424513,USFS 1072,,,2,2.0,33.3,86107,1,13,2.6,175,14,,,6/14/2020 12:05:13 AM,6/14/2020 12:05:00 AM"

docker/Dockerfile

@@ -18,6 +18,5 @@ RUN install2.r --error -r "https://cran.rstudio.com" \
 
 # Install latest updates from GitHub
 RUN installGithub.r \
-    mazamascience/MazamaCoreUtils \
     mazamascience/PWFSLSmoke
 

docker/Makefile

@@ -3,5 +3,7 @@
 
 # PRODUCTION version -----------------------------------------------------------
 production_build:
-	docker build --no-cache -t mazamascience/pwfslsmoke:1.2.108 -t mazamascience/pwfslsmoke:latest .
+	docker build --no-cache -t mazamascience/pwfslsmoke:1.2.112 -t mazamascience/pwfslsmoke:latest .
 
+production_publish:
+	docker login && docker push mazamascience/pwfslsmoke:1.2.112

docker/README.md

@@ -13,7 +13,7 @@ You should then be able to see something like the following:
 ```
 $ docker images
 REPOSITORY                          TAG                     IMAGE ID            CREATED             SIZE
-mazamascience/pwfslsmoke            1.2.108                 1824e396e3f3        34 seconds ago      2.61GB
+mazamascience/pwfslsmoke            1.2.112                 1824e396e3f3        34 seconds ago      2.61GB
 mazamascience/pwfslsmoke            latest                  1824e396e3f3        34 seconds ago      2.61GB
 ...
 ```
@@ -27,7 +27,8 @@ the docker image in `/home/mazama/data/Spatial`.
 ## Test the Docker Image ##
 
 Having built the docker image we can now test it. The following output was 
-obtained on April 03, 2019:
+obtained on July 08, 2020 -- Fourth of July Fireworks!!!:
+
 
 ```
 docker run -ti mazamascience/pwfslsmoke R --vanilla
@@ -40,30 +41,27 @@ ids <- names(maxValues)
 df <- wa$meta[ids,c('siteName','countyName')]
 df$max_pm25 <- maxValues
 print(df)
-                               siteName countyName max_pm25
-840530390006_01     Mobile-White Salmon  Klickitat     63.2
-TT1010003_01                  Inchelium       <NA>     51.8
-530650002_01    Wellpinit-Spokane Tribe    Stevens     51.3
-840530739992_01   Maple Falls-Azure Way    Whatcom     49.7
-530070011_01         Wenatchee-Fifth St     Chelan     49.4
-530610020_01          Darrington-Fir St  Snohomish     49.0
+                          siteName   countyName max_pm25
+530330080_01   Seattle-Beacon Hill         King    943.0
+530272002_01  Aberdeen-Division St Grays Harbor    203.7
+530611007_01    Marysville-7th Ave    Snohomish    134.0
+530650005_01     Colville-E 1st St      Stevens    123.0
+530110024_01 Vancouver-NE 84th Ave        Clark    115.0
+530350007_01  Bremerton-Spruce Ave       Kitsap    113.0
 ```
 
 
 ## Publish the Docker Image ##
 
 ```
-docker login
-...
-docker push mazamascience/pwfslsmoke:1.2.108
+make production_publish
 ```
 
-
 ## Download the Docker Image ##
 
-A recent image can also be obtained from DockerHub with:
+This image can also be pulled from DockerHub with:
 
 ```
-docker pull mazamascience/pwfslsmoke:1.2.108
+docker pull mazamascience/pwfslsmoke:1.2.112
 ```