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Miller, Shawn

2018-Dec-13 19:42 UTC

[R] [External] RE: help

Yes I confirmed all the dates I need are in the test.xlsx table. The
final.2.xlsx table does not have the dates  for July, August, September.

-----Original Message-----
From: David L Carlson [mailto:dcarlson at tamu.edu] 
Sent: Thursday, December 13, 2018 2:33 PM
To: Miller, Shawn <shawnmille at pa.gov>
Cc: R-help at r-project.org
Subject: RE: [External] RE: help

Use Reply-All to keep the thread on the list.

If the most recent WQN SIS Data Download table is 14June2018_WQN_Data_Download,
does it contain any data for the months July, August, September, October,
November, December? After extracting the data you create the file
"Anti-deg_requests/test.xlsx". Have you confirmed that all of the
dates you need are present in that file?

----------------------------------------
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77843-4352

-----Original Message-----
From: Miller, Shawn <shawnmille at pa.gov>
Sent: Thursday, December 13, 2018 1:15 PM
To: David L Carlson <dcarlson at tamu.edu>
Subject: RE: [External] RE: help

setwd("c:/users/shawnmille/Desktop/Anti-deg_requests/")

library(plyr)
library(reshape2)
library(RODBC)
library(dplyr)



## MAKE SURE YOU ARE USING THE 32-bit VERSION OF R (See Tools>Global
Options>General in RStudio to set this) ## READING DATA FROM EXISTING
DATABASES (EXAMPLE: ACCESS 2010) chan <- odbcConnectAccess("WQN
Datadumps.mdb")

# Show list of tables in database
sqlTables(chan,tableType='TABLE')
# Fetch the most recent WQN SIS Data Download table, this takes a couple minutes
allwqn <-
sqlFetch(chan,'14June2018_WQN_Data_Download',stringsAsFactors=FALSE)
names(allwqn)
## subset to the desired fields and values, choose your WQN by modifying command

wqn.specific <- subset(allwqn,MONITORING_POINT_ALIAS_ID
=='WQN0735',select=c('DATE_COLLECTED','MONITORING_POINT_ALIAS_ID','QUALITY_ASSURANCE_TYPE_DESC',
                                                                                
'TEST_CODE','TEST_SHORT_DESC','READING_INDICATOR_CODE','FINAL_AMOUNT','ABBREVIATION'))

###VIEW ENTIRE DATASET, this coding can be used to view any created datasets in
excel#####
library(xlsx)
write.xlsx(wqn.specific,"c:/users/shawnmille/Desktop/Anti-deg_requests/test.xlsx")

###VIEW ENTIRE DATASET#####

# FOR ACTIVE WQN STATION GET TODAY'S DATE and date of 5 years ago + 4 months
or put in last date in command# today <- Sys.Date()
TODAY.5<-today-1949
## Select data where DATA_COLLECTED >= TODAY.5## wqn.specific$DATE_COLLECTED
<- as.Date(wqn.specific$DATE_COLLECTED ,"%m/%d/%y") wqn.last5yrs
<- subset(wqn.specific,DATE_COLLECTED >= TODAY.5,
select=c('DATE_COLLECTED','MONITORING_POINT_ALIAS_ID','QUALITY_ASSURANCE_TYPE_DESC','TEST_CODE','TEST_SHORT_DESC','READING_INDICATOR_CODE','FINAL_AMOUNT','ABBREVIATION'))


#OR FOR INACTIVE WQN STATION ENTER THE LAST DATE OF RECORD BELOW AND GET PAST 5
YEARS OF DATA IN SUBSET# lastdate <- as.Date("11/01/2010", format =
"%m/%d/%Y") firstdate <- lastdate-1949 wqn.specific$DATE_COLLECTED
<- as.Date(wqn.specific$DATE_COLLECTED ,"%m/%d/%y") wqn.last5yrs
<- subset(wqn.specific,DATE_COLLECTED >= firstdate & DATE_COLLECTED
<= lastdate,
select=c('DATE_COLLECTED','MONITORING_POINT_ALIAS_ID','QUALITY_ASSURANCE_TYPE_DESC','TEST_CODE','TEST_SHORT_DESC','READING_INDICATOR_CODE','FINAL_AMOUNT','ABBREVIATION'))

#### Delete Blanks and QA column #####
wqn.removeblanks
<-subset(wqn.last5yrs,QUALITY_ASSURANCE_TYPE_DESC=="Duplicate"|is.na(QUALITY_ASSURANCE_TYPE_DESC),select=c('DATE_COLLECTED','MONITORING_POINT_ALIAS_ID',
                                                                                
'TEST_CODE','TEST_SHORT_DESC','READING_INDICATOR_CODE','FINAL_AMOUNT','ABBREVIATION'))
#### Delete Null Results####
wqn.removenull <-
subset(wqn.removeblanks,FINAL_AMOUNT!="NA",select=c('DATE_COLLECTED','MONITORING_POINT_ALIAS_ID','TEST_CODE','TEST_SHORT_DESC','READING_INDICATOR_CODE','FINAL_AMOUNT','ABBREVIATION'))

### Remove non-relevant parameters ####

wqn.removeparm <- subset(wqn.removenull,TEST_CODE!=
"571"&TEST_CODE!="572"&
                           TEST_CODE!="573"&
TEST_CODE!="543"& TEST_CODE!="561"&
TEST_CODE!="546"
                         & TEST_CODE!="595"&
TEST_CODE!="596"& TEST_CODE!="597"&
TEST_CODE!="598"
                         & TEST_CODE!="599"&
TEST_CODE!="600"& TEST_CODE!="71946"&
TEST_CODE!="71940"
                         & TEST_CODE!="587"&
TEST_CODE!="593"& TEST_CODE!="71939"&
TEST_CODE!="71937"
                         & TEST_CODE!="574"&
TEST_CODE!="549"& TEST_CODE!="99014"&
TEST_CODE!="547"
                         & TEST_CODE!="298"&
TEST_CODE!="551"& TEST_CODE!="71930"&
TEST_CODE!="70508"
                         & TEST_CODE!="564"&
TEST_CODE!="709"& TEST_CODE!="111"&
TEST_CODE!="592"
                         & TEST_CODE!="MMTECMF"&
TEST_CODE!="588"& TEST_CODE!="589"&
TEST_CODE!="590"
                         & TEST_CODE!="594"&
TEST_CODE!="71936"& TEST_CODE!="71945"&
TEST_CODE!="F00061"
                         & TEST_CODE!="71947"&
TEST_CODE!="555",
                        
select=c('DATE_COLLECTED','MONITORING_POINT_ALIAS_ID','TEST_CODE','TEST_SHORT_DESC','READING_INDICATOR_CODE','FINAL_AMOUNT','ABBREVIATION'))

###  Combine test codes that are measuring the same analyte, format testcode to
include first 5 digits###


wqn.removeparm$TEST_CODE<-substr(wqn.removeparm$TEST_CODE,1,5)


######Creates a table (wqn.det) with list of max detection limits for each
parameter,FOR EACH TEST_CODE BRING ALL  < TO THAT VALUE############

n.det <- subset(wqn.removeparm,READING_INDICATOR_CODE=='<')
wqn.det<- aggregate(n.det$FINAL_AMOUNT ,
by=list(n.det$MONITORING_POINT_ALIAS_ID,n.det$TEST_CODE),FUN=max)
colnames(wqn.det) <-
c("MONITORING_POINT_ALIAS_ID","TEST_CODE","DET_LIMIT")

wqn.mer<-merge(wqn.removeparm,wqn.det,
by=c("MONITORING_POINT_ALIAS_ID","TEST_CODE"),all=TRUE)
wqn.mer$Amount<-
ifelse(is.na(wqn.mer$'READING_INDICATOR_CODE'),wqn.mer$FINAL_AMOUNT*1,wqn.mer$DET_LIMIT*1)


######DIVIDE '<' BY HALF #####
wqn.mer$Result <-
ifelse(is.na(wqn.mer$'READING_INDICATOR_CODE'),wqn.mer$Amount*1,wqn.mer$Amount/2)

###### AVERAGE AND GROUP BY TO REMOVE DUPLICATES ########

wqn.agg<-aggregate(wqn.mer$Result,
by=list(MONITORING_POINT_ALIAS_ID=wqn.mer$'MONITORING_POINT_ALIAS_ID',DATE_COLLECTED=wqn.mer$'DATE_COLLECTED',TEST_CODE=wqn.mer$'TEST_CODE'),data=wqn.mer,
FUN="mean",na.rm=TRUE)
colnames(wqn.agg) <-
c("MONITORING_POINT_ALIAS_ID","DATE_COLLECTED","TEST_CODE","Result")

###### Calculate Median and 95% CI, alpha/2 for tailed2 (pH)..similar to
ci.median function in asbio package, using alpha for funtion
"tailed1"(other parameters)###


tailed2<-function(x){
  n <- nrow(as.matrix(x))
  L <- qbinom(.025,n,0.5)
  U <- n-L+1
  order.x <-sort(x)
  lower <- (order.x[L])
  upper <-order.x[n - 
                    L + 1]
  median <- median(x)
  coverage <- 1-(2*pbinom(qbinom(.025,n,.5)-1,n,0.5))
  y<-list(c(lower, median, upper,n,coverage))

  
  
  
  
  
}
tailed1<-function(x){
  n <- nrow(as.matrix(x))
  L <- qbinom(.05,n,0.5)
  U <- n-L+1
  order.x <-sort(x)
  lower <- (order.x[L])
  upper <-order.x[n - 
                    L+1]
  median <- median(x)
  coverage <- 1-(2*pbinom(qbinom(.05,n,.5)-1,n,0.5))
  y<-list(c(lower, median, upper,n,coverage))
  
  
  
  
} 


###Create two data sets, one with all the parameters except pH and one with just
pH##### wqn.ph <-
subset(wqn.agg,TEST_CODE=='00403'|TEST_CODE=="F0040",select=c("MONITORING_POINT_ALIAS_ID","DATE_COLLECTED","TEST_CODE","Result"))
wqn.noph <-subset(wqn.agg,TEST_CODE!='00403'&
TEST_CODE!="F0040",select=c("MONITORING_POINT_ALIAS_ID","DATE_COLLECTED","TEST_CODE","Result"))
                   
###Run tailed1 function on all data except for pH###                   
                   
stats<-aggregate(wqn.noph$Result,
by=list(wqn.noph$MONITORING_POINT_ALIAS_ID,wqn.noph$TEST_CODE), FUN=tailed1)
colnames(stats) <-
c("MONITORING_POINT_ALIAS_ID","TEST_CODE","x")

stats$lower <-unlist(lapply(stats$x, '[[', 1))
stats$median<-unlist(lapply(stats$x, '[[', 2)) stats$upper
<-unlist(lapply(stats$x, '[[', 3)) stats$n
<-unlist(lapply(stats$x, '[[', 4))
stats1 <-
stats[order(stats$"MONITORING_POINT_ALIAS_ID",stats$"TEST_CODE"),]

###Run tailed2 function on pH (lab and field) data####
ph.stats<-aggregate(wqn.ph$Result,
by=list(wqn.ph$MONITORING_POINT_ALIAS_ID,wqn.ph$TEST_CODE), FUN=tailed2)
colnames(ph.stats) <-
c("MONITORING_POINT_ALIAS_ID","TEST_CODE","x")

ph.stats$lower <-unlist(lapply(ph.stats$x, '[[', 1))
ph.stats$median<-unlist(lapply(ph.stats$x, '[[', 2)) ph.stats$upper
<-unlist(lapply(ph.stats$x, '[[', 3)) ph.stats$n
<-unlist(lapply(ph.stats$x, '[[', 4))
ph.stats1 <-
ph.stats[order(ph.stats$"MONITORING_POINT_ALIAS_ID",ph.stats$"TEST_CODE"),]

###Combine datasets vertically###
stats2 <- rbind(stats1,ph.stats1)


####PeriodofRecordTable####

library(dplyr)

my.dt<-(format(as.Date(wqn.removeparm$"DATE_COLLECTED"),"%m/%d/%Y"))

my.dt1<-aggregate(my.dt,
by=list(wqn.removeparm$MONITORING_POINT_ALIAS_ID,wqn.removeparm$TEST_CODE),
FUN=first)
colnames(my.dt1) <-
c("MONITORING_POINT_ALIAS_ID","TEST_CODE","FirstDate")

my.dtlast<-aggregate(my.dt,
by=list(wqn.removeparm$MONITORING_POINT_ALIAS_ID,wqn.removeparm$TEST_CODE),
FUN=last)
colnames(my.dtlast) <-
c("MONITORING_POINT_ALIAS_ID","TEST_CODE","LastDate")



####Merging Tables Dates and Stats#################### all.dt <-
merge(my.dt1,my.dtlast,by=c("MONITORING_POINT_ALIAS_ID","TEST_CODE"))

dt.stats<-merge(all.dt,stats2,by=c("MONITORING_POINT_ALIAS_ID","TEST_CODE"))


####Calculate Period Of record in Table, Old coding 2 lines:
dt.stats$pdofrecord<-(mdy(dt.stats$"LastDate"))-(mdy(dt.stats$"FirstDate"))
###dt.stats$pd<-round(dt.stats$pdofrecord/31563000, digits=1), lubridate is
glitchy test new code on this step more######


dt.stats$pd <- round((as.Date(dt.stats$LastDate,format =
"%m/%d/%Y")-as.Date(dt.stats$FirstDate,format =
"%m/%d/%Y"))/365,digits=1)



####Retrieve Test Descriptions and Merge######
t1 <-
subset(dt.stats,select=c('MONITORING_POINT_ALIAS_ID','TEST_CODE','FirstDate','LastDate','pd','lower','median','upper','n'))
t2<-subset(wqn.removeparm,select=c('TEST_CODE','TEST_SHORT_DESC','ABBREVIATION'))
t3 <- unique( t2 )

t4<-merge(t1,t3, by='TEST_CODE',all.t3=TRUE)
######ReorderColumns,sort, rename columns#######
t5 <- t4[ ,c(2,1,10,3,4,5,9,6,7,8,11)]
t6 <-
t5[order(t5$"MONITORING_POINT_ALIAS_ID",t5$"TEST_SHORT_DESC"),]
names(t6)

####This does not need to be run. It produces an error. You still get the
correct results.
library(plyr)
library(dplyr)
library(reshape2)
final.tab<-rename(t6, c("FirstDate"="FIRST_DATE",
"LastDate"="LAST_DATE","pd"="PERIOD_OF_RECORD(yrs)","n"="SAMPLE_SIZE","lower"
            
="L_95_CI","median"="MEDIAN_","upper"="U_95_CI","ABBREVIATION"="UNITS"))

####BRING VALUES UP TO DETECTION LIMITS merge with wqn.det######
less<-function(x){
  sprintf("< %3.2f", x)
} 

wqn.final
<-merge(t6,wqn.det,by=c("MONITORING_POINT_ALIAS_ID","TEST_CODE"),all=TRUE)
wqn.final$DET_LIMIT[is.na(wqn.final$DET_LIMIT)] <- 0 wqn.final$LOW_95_CL
<- ifelse(wqn.final$lower <
wqn.final$DET_LIM,less(wqn.final$DET_LIM*1),wqn.final$lower*1)
wqn.final$MEDIAN <- ifelse(wqn.final$median <
wqn.final$DET_LIM,less(wqn.final$DET_LIM*1),wqn.final$median*1)
wqn.final$UPP_95_CL <- ifelse(wqn.final$upper <
wqn.final$DET_LIM,less(wqn.final$DET_LIM*1),wqn.final$upper*1)

####ONLY REPORT MINIMUM FOR ALKALINITY, PH, DO, TEMP, SPECIFIC cONDUCTANCE######

wqn.final$LOWER_95_CL <-
ifelse(wqn.final$TEST_CODE=="00403"|wqn.final$TEST_CODE=="00410"|wqn.final$TEST_CODE=="F0040"|
                                   
wqn.final$TEST_CODE=="F0030"|wqn.final$TEST_CODE=="F0043",wqn.final$LOW_95_CL,"NA")

wqn.final$UPPER_95_CL <-
ifelse(wqn.final$TEST_CODE=="00410"|wqn.final$TEST_CODE=="F0043"|
                                 
wqn.final$TEST_CODE=="F0030","NA",wqn.final$UPP_95_CL)


names(wqn.final)                                  
final.1<-subset(wqn.final,
select=c('MONITORING_POINT_ALIAS_ID','TEST_CODE','TEST_SHORT_DESC','FirstDate',
                                    'LastDate',
'pd',"n","LOWER_95_CL",'MEDIAN',
                                   
'UPPER_95_CL','ABBREVIATION'))
final.2 <-
final.1[order(final.1$"MONITORING_POINT_ALIAS_ID",final.1$"TEST_SHORT_DESC"),]

###VIEW IN EXCEL##
library(xlsx)
write.xlsx(final.2,"c:/users/shawnmille/Desktop/Anti-deg_requests/final.2.xlsx")


-----Original Message-----
From: David L Carlson [mailto:dcarlson at tamu.edu]
Sent: Thursday, December 13, 2018 2:12 PM
To: Miller, Shawn <shawnmille at pa.gov>; R-help at r-project.org
Subject: [External] RE: help

ATTENTION: This email message is from an external sender. Do not open links or
attachments from unknown sources. To report suspicious email, forward the
message as an attachment to CWOPA_SPAM at pa.gov.

You need Santa Claus not r-help. You haven't given us a fraction of the
information we would need to help. You don't show us your code. You
don't tell us where the information is coming from except "today's
date." You don't tell us what data you want. You don't seem to know
the difference between R and R-Studio.

----------------------------------------
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77843-4352


-----Original Message-----
From: R-help <r-help-bounces at r-project.org> On Behalf Of Miller, Shawn
Sent: Thursday, December 13, 2018 11:29 AM
To: R-help at r-project.org
Subject: [R] help

Need help with R studio. Code is to pull data from todays date plus 5 years 4
months from now. I am missing the last 3 months of data. Can you please help?

Shawn Miller | Aquatic Biologist II | Assessment Section Environmental
Protection | Clean Water Rachel Carson State Office Building
400 Market Street | Harrisburg, PA 17101
Phone: 717.772.2185 | Fax: 717.772.3249
https://na01.safelinks.protection.outlook.com/?url=www.depweb.state.pa.us&amp;data=02%7C01%7Cshawnmille%40pa.gov%7Ce275c28afad54d99b5d608d66131bec5%7C418e284101284dd59b6c47fc5a9a1bde%7C1%7C0%7C636803263627811233&amp;sdata=SetioLDNtYwPWgXTfgp4XNoH2ptEpbMkVCkYBcBFJAE%3D&amp;reserved=0<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwebmail.state.pa.us%2FOWA%2Fredir.aspx%3FC%3Dt4jGxr3_mkC5mWY30vM0D8N-9RdJ8s9IgIGFizoEzsd1aNOJaDwGjjpEh4RqLFX24CIJXV9M2ic.%26URL%3Dhttp%253a%252f%252fwww.depweb.state.pa.us%252f&amp;data=02%7C01%7Cshawnmille%40pa.gov%7Ce275c28afad54d99b5d608d66131bec5%7C418e284101284dd59b6c47fc5a9a1bde%7C1%7C0%7C636803263627811233&amp;sdata=8mPY9gVwTHUVb6EhpRueVUcHQIyTyd7QYYctDdbwBsM%3D&amp;reserved=0>


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and provide commented, minimal, self-contained, reproducible code.

David L Carlson

2018-Dec-13 20:43 UTC

head link

[R] [External] RE: help

OK. Follow the chain of subsets to figure out where the dates go missing.

Scanning the code I see the following subsets: wqn.last5yrs, wqn.removeblanks,
wqn.removenull, wqn.removeparm, n.det, wqn.ph, wqn.noph. Use the range function
to find out where the observations get dropped out.

range(wqn.last5yrs$DATE_COLLECTED)

David C

-----Original Message-----
From: Miller, Shawn <shawnmille at pa.gov> 
Sent: Thursday, December 13, 2018 1:42 PM
To: David L Carlson <dcarlson at tamu.edu>
Cc: R-help at r-project.org
Subject: RE: [External] RE: help

Yes I confirmed all the dates I need are in the test.xlsx table. The
final.2.xlsx table does not have the dates  for July, August, September.

-----Original Message-----
From: David L Carlson [mailto:dcarlson at tamu.edu] 
Sent: Thursday, December 13, 2018 2:33 PM
To: Miller, Shawn <shawnmille at pa.gov>
Cc: R-help at r-project.org
Subject: RE: [External] RE: help

Use Reply-All to keep the thread on the list.

If the most recent WQN SIS Data Download table is 14June2018_WQN_Data_Download,
does it contain any data for the months July, August, September, October,
November, December? After extracting the data you create the file
"Anti-deg_requests/test.xlsx". Have you confirmed that all of the
dates you need are present in that file?

----------------------------------------
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77843-4352

-----Original Message-----
From: Miller, Shawn <shawnmille at pa.gov>
Sent: Thursday, December 13, 2018 1:15 PM
To: David L Carlson <dcarlson at tamu.edu>
Subject: RE: [External] RE: help

setwd("c:/users/shawnmille/Desktop/Anti-deg_requests/")

library(plyr)
library(reshape2)
library(RODBC)
library(dplyr)



## MAKE SURE YOU ARE USING THE 32-bit VERSION OF R (See Tools>Global
Options>General in RStudio to set this) ## READING DATA FROM EXISTING
DATABASES (EXAMPLE: ACCESS 2010) chan <- odbcConnectAccess("WQN
Datadumps.mdb")

# Show list of tables in database
sqlTables(chan,tableType='TABLE')
# Fetch the most recent WQN SIS Data Download table, this takes a couple minutes
allwqn <-
sqlFetch(chan,'14June2018_WQN_Data_Download',stringsAsFactors=FALSE)
names(allwqn)
## subset to the desired fields and values, choose your WQN by modifying command

wqn.specific <- subset(allwqn,MONITORING_POINT_ALIAS_ID
=='WQN0735',select=c('DATE_COLLECTED','MONITORING_POINT_ALIAS_ID','QUALITY_ASSURANCE_TYPE_DESC',
                                                                                
'TEST_CODE','TEST_SHORT_DESC','READING_INDICATOR_CODE','FINAL_AMOUNT','ABBREVIATION'))

###VIEW ENTIRE DATASET, this coding can be used to view any created datasets in
excel#####
library(xlsx)
write.xlsx(wqn.specific,"c:/users/shawnmille/Desktop/Anti-deg_requests/test.xlsx")

###VIEW ENTIRE DATASET#####

# FOR ACTIVE WQN STATION GET TODAY'S DATE and date of 5 years ago + 4 months
or put in last date in command# today <- Sys.Date()
TODAY.5<-today-1949
## Select data where DATA_COLLECTED >= TODAY.5## wqn.specific$DATE_COLLECTED
<- as.Date(wqn.specific$DATE_COLLECTED ,"%m/%d/%y") wqn.last5yrs
<- subset(wqn.specific,DATE_COLLECTED >= TODAY.5,
select=c('DATE_COLLECTED','MONITORING_POINT_ALIAS_ID','QUALITY_ASSURANCE_TYPE_DESC','TEST_CODE','TEST_SHORT_DESC','READING_INDICATOR_CODE','FINAL_AMOUNT','ABBREVIATION'))


#OR FOR INACTIVE WQN STATION ENTER THE LAST DATE OF RECORD BELOW AND GET PAST 5
YEARS OF DATA IN SUBSET# lastdate <- as.Date("11/01/2010", format =
"%m/%d/%Y") firstdate <- lastdate-1949 wqn.specific$DATE_COLLECTED
<- as.Date(wqn.specific$DATE_COLLECTED ,"%m/%d/%y") wqn.last5yrs
<- subset(wqn.specific,DATE_COLLECTED >= firstdate & DATE_COLLECTED
<= lastdate,
select=c('DATE_COLLECTED','MONITORING_POINT_ALIAS_ID','QUALITY_ASSURANCE_TYPE_DESC','TEST_CODE','TEST_SHORT_DESC','READING_INDICATOR_CODE','FINAL_AMOUNT','ABBREVIATION'))

#### Delete Blanks and QA column #####
wqn.removeblanks
<-subset(wqn.last5yrs,QUALITY_ASSURANCE_TYPE_DESC=="Duplicate"|is.na(QUALITY_ASSURANCE_TYPE_DESC),select=c('DATE_COLLECTED','MONITORING_POINT_ALIAS_ID',
                                                                                
'TEST_CODE','TEST_SHORT_DESC','READING_INDICATOR_CODE','FINAL_AMOUNT','ABBREVIATION'))
#### Delete Null Results####
wqn.removenull <-
subset(wqn.removeblanks,FINAL_AMOUNT!="NA",select=c('DATE_COLLECTED','MONITORING_POINT_ALIAS_ID','TEST_CODE','TEST_SHORT_DESC','READING_INDICATOR_CODE','FINAL_AMOUNT','ABBREVIATION'))

### Remove non-relevant parameters ####

wqn.removeparm <- subset(wqn.removenull,TEST_CODE!=
"571"&TEST_CODE!="572"&
                           TEST_CODE!="573"&
TEST_CODE!="543"& TEST_CODE!="561"&
TEST_CODE!="546"
                         & TEST_CODE!="595"&
TEST_CODE!="596"& TEST_CODE!="597"&
TEST_CODE!="598"
                         & TEST_CODE!="599"&
TEST_CODE!="600"& TEST_CODE!="71946"&
TEST_CODE!="71940"
                         & TEST_CODE!="587"&
TEST_CODE!="593"& TEST_CODE!="71939"&
TEST_CODE!="71937"
                         & TEST_CODE!="574"&
TEST_CODE!="549"& TEST_CODE!="99014"&
TEST_CODE!="547"
                         & TEST_CODE!="298"&
TEST_CODE!="551"& TEST_CODE!="71930"&
TEST_CODE!="70508"
                         & TEST_CODE!="564"&
TEST_CODE!="709"& TEST_CODE!="111"&
TEST_CODE!="592"
                         & TEST_CODE!="MMTECMF"&
TEST_CODE!="588"& TEST_CODE!="589"&
TEST_CODE!="590"
                         & TEST_CODE!="594"&
TEST_CODE!="71936"& TEST_CODE!="71945"&
TEST_CODE!="F00061"
                         & TEST_CODE!="71947"&
TEST_CODE!="555",
                        
select=c('DATE_COLLECTED','MONITORING_POINT_ALIAS_ID','TEST_CODE','TEST_SHORT_DESC','READING_INDICATOR_CODE','FINAL_AMOUNT','ABBREVIATION'))

###  Combine test codes that are measuring the same analyte, format testcode to
include first 5 digits###


wqn.removeparm$TEST_CODE<-substr(wqn.removeparm$TEST_CODE,1,5)


######Creates a table (wqn.det) with list of max detection limits for each
parameter,FOR EACH TEST_CODE BRING ALL  < TO THAT VALUE############

n.det <- subset(wqn.removeparm,READING_INDICATOR_CODE=='<')
wqn.det<- aggregate(n.det$FINAL_AMOUNT ,
by=list(n.det$MONITORING_POINT_ALIAS_ID,n.det$TEST_CODE),FUN=max)
colnames(wqn.det) <-
c("MONITORING_POINT_ALIAS_ID","TEST_CODE","DET_LIMIT")

wqn.mer<-merge(wqn.removeparm,wqn.det,
by=c("MONITORING_POINT_ALIAS_ID","TEST_CODE"),all=TRUE)
wqn.mer$Amount<-
ifelse(is.na(wqn.mer$'READING_INDICATOR_CODE'),wqn.mer$FINAL_AMOUNT*1,wqn.mer$DET_LIMIT*1)


######DIVIDE '<' BY HALF #####
wqn.mer$Result <-
ifelse(is.na(wqn.mer$'READING_INDICATOR_CODE'),wqn.mer$Amount*1,wqn.mer$Amount/2)

###### AVERAGE AND GROUP BY TO REMOVE DUPLICATES ########

wqn.agg<-aggregate(wqn.mer$Result,
by=list(MONITORING_POINT_ALIAS_ID=wqn.mer$'MONITORING_POINT_ALIAS_ID',DATE_COLLECTED=wqn.mer$'DATE_COLLECTED',TEST_CODE=wqn.mer$'TEST_CODE'),data=wqn.mer,
FUN="mean",na.rm=TRUE)
colnames(wqn.agg) <-
c("MONITORING_POINT_ALIAS_ID","DATE_COLLECTED","TEST_CODE","Result")

###### Calculate Median and 95% CI, alpha/2 for tailed2 (pH)..similar to
ci.median function in asbio package, using alpha for funtion
"tailed1"(other parameters)###


tailed2<-function(x){
  n <- nrow(as.matrix(x))
  L <- qbinom(.025,n,0.5)
  U <- n-L+1
  order.x <-sort(x)
  lower <- (order.x[L])
  upper <-order.x[n - 
                    L + 1]
  median <- median(x)
  coverage <- 1-(2*pbinom(qbinom(.025,n,.5)-1,n,0.5))
  y<-list(c(lower, median, upper,n,coverage))

  
  
  
  
  
}
tailed1<-function(x){
  n <- nrow(as.matrix(x))
  L <- qbinom(.05,n,0.5)
  U <- n-L+1
  order.x <-sort(x)
  lower <- (order.x[L])
  upper <-order.x[n - 
                    L+1]
  median <- median(x)
  coverage <- 1-(2*pbinom(qbinom(.05,n,.5)-1,n,0.5))
  y<-list(c(lower, median, upper,n,coverage))
  
  
  
  
} 


###Create two data sets, one with all the parameters except pH and one with just
pH##### wqn.ph <-
subset(wqn.agg,TEST_CODE=='00403'|TEST_CODE=="F0040",select=c("MONITORING_POINT_ALIAS_ID","DATE_COLLECTED","TEST_CODE","Result"))
wqn.noph <-subset(wqn.agg,TEST_CODE!='00403'&
TEST_CODE!="F0040",select=c("MONITORING_POINT_ALIAS_ID","DATE_COLLECTED","TEST_CODE","Result"))
                   
###Run tailed1 function on all data except for pH###                   
                   
stats<-aggregate(wqn.noph$Result,
by=list(wqn.noph$MONITORING_POINT_ALIAS_ID,wqn.noph$TEST_CODE), FUN=tailed1)
colnames(stats) <-
c("MONITORING_POINT_ALIAS_ID","TEST_CODE","x")

stats$lower <-unlist(lapply(stats$x, '[[', 1))
stats$median<-unlist(lapply(stats$x, '[[', 2)) stats$upper
<-unlist(lapply(stats$x, '[[', 3)) stats$n
<-unlist(lapply(stats$x, '[[', 4))
stats1 <-
stats[order(stats$"MONITORING_POINT_ALIAS_ID",stats$"TEST_CODE"),]

###Run tailed2 function on pH (lab and field) data####
ph.stats<-aggregate(wqn.ph$Result,
by=list(wqn.ph$MONITORING_POINT_ALIAS_ID,wqn.ph$TEST_CODE), FUN=tailed2)
colnames(ph.stats) <-
c("MONITORING_POINT_ALIAS_ID","TEST_CODE","x")

ph.stats$lower <-unlist(lapply(ph.stats$x, '[[', 1))
ph.stats$median<-unlist(lapply(ph.stats$x, '[[', 2)) ph.stats$upper
<-unlist(lapply(ph.stats$x, '[[', 3)) ph.stats$n
<-unlist(lapply(ph.stats$x, '[[', 4))
ph.stats1 <-
ph.stats[order(ph.stats$"MONITORING_POINT_ALIAS_ID",ph.stats$"TEST_CODE"),]

###Combine datasets vertically###
stats2 <- rbind(stats1,ph.stats1)


####PeriodofRecordTable####

library(dplyr)

my.dt<-(format(as.Date(wqn.removeparm$"DATE_COLLECTED"),"%m/%d/%Y"))

my.dt1<-aggregate(my.dt,
by=list(wqn.removeparm$MONITORING_POINT_ALIAS_ID,wqn.removeparm$TEST_CODE),
FUN=first)
colnames(my.dt1) <-
c("MONITORING_POINT_ALIAS_ID","TEST_CODE","FirstDate")

my.dtlast<-aggregate(my.dt,
by=list(wqn.removeparm$MONITORING_POINT_ALIAS_ID,wqn.removeparm$TEST_CODE),
FUN=last)
colnames(my.dtlast) <-
c("MONITORING_POINT_ALIAS_ID","TEST_CODE","LastDate")



####Merging Tables Dates and Stats#################### all.dt <-
merge(my.dt1,my.dtlast,by=c("MONITORING_POINT_ALIAS_ID","TEST_CODE"))

dt.stats<-merge(all.dt,stats2,by=c("MONITORING_POINT_ALIAS_ID","TEST_CODE"))


####Calculate Period Of record in Table, Old coding 2 lines:
dt.stats$pdofrecord<-(mdy(dt.stats$"LastDate"))-(mdy(dt.stats$"FirstDate"))
###dt.stats$pd<-round(dt.stats$pdofrecord/31563000, digits=1), lubridate is
glitchy test new code on this step more######


dt.stats$pd <- round((as.Date(dt.stats$LastDate,format =
"%m/%d/%Y")-as.Date(dt.stats$FirstDate,format =
"%m/%d/%Y"))/365,digits=1)



####Retrieve Test Descriptions and Merge######
t1 <-
subset(dt.stats,select=c('MONITORING_POINT_ALIAS_ID','TEST_CODE','FirstDate','LastDate','pd','lower','median','upper','n'))
t2<-subset(wqn.removeparm,select=c('TEST_CODE','TEST_SHORT_DESC','ABBREVIATION'))
t3 <- unique( t2 )

t4<-merge(t1,t3, by='TEST_CODE',all.t3=TRUE)
######ReorderColumns,sort, rename columns#######
t5 <- t4[ ,c(2,1,10,3,4,5,9,6,7,8,11)]
t6 <-
t5[order(t5$"MONITORING_POINT_ALIAS_ID",t5$"TEST_SHORT_DESC"),]
names(t6)

####This does not need to be run. It produces an error. You still get the
correct results.
library(plyr)
library(dplyr)
library(reshape2)
final.tab<-rename(t6, c("FirstDate"="FIRST_DATE",
"LastDate"="LAST_DATE","pd"="PERIOD_OF_RECORD(yrs)","n"="SAMPLE_SIZE","lower"
            
="L_95_CI","median"="MEDIAN_","upper"="U_95_CI","ABBREVIATION"="UNITS"))

####BRING VALUES UP TO DETECTION LIMITS merge with wqn.det######
less<-function(x){
  sprintf("< %3.2f", x)
} 

wqn.final
<-merge(t6,wqn.det,by=c("MONITORING_POINT_ALIAS_ID","TEST_CODE"),all=TRUE)
wqn.final$DET_LIMIT[is.na(wqn.final$DET_LIMIT)] <- 0 wqn.final$LOW_95_CL
<- ifelse(wqn.final$lower <
wqn.final$DET_LIM,less(wqn.final$DET_LIM*1),wqn.final$lower*1)
wqn.final$MEDIAN <- ifelse(wqn.final$median <
wqn.final$DET_LIM,less(wqn.final$DET_LIM*1),wqn.final$median*1)
wqn.final$UPP_95_CL <- ifelse(wqn.final$upper <
wqn.final$DET_LIM,less(wqn.final$DET_LIM*1),wqn.final$upper*1)

####ONLY REPORT MINIMUM FOR ALKALINITY, PH, DO, TEMP, SPECIFIC cONDUCTANCE######

wqn.final$LOWER_95_CL <-
ifelse(wqn.final$TEST_CODE=="00403"|wqn.final$TEST_CODE=="00410"|wqn.final$TEST_CODE=="F0040"|
                                   
wqn.final$TEST_CODE=="F0030"|wqn.final$TEST_CODE=="F0043",wqn.final$LOW_95_CL,"NA")

wqn.final$UPPER_95_CL <-
ifelse(wqn.final$TEST_CODE=="00410"|wqn.final$TEST_CODE=="F0043"|
                                 
wqn.final$TEST_CODE=="F0030","NA",wqn.final$UPP_95_CL)


names(wqn.final)                                  
final.1<-subset(wqn.final,
select=c('MONITORING_POINT_ALIAS_ID','TEST_CODE','TEST_SHORT_DESC','FirstDate',
                                    'LastDate',
'pd',"n","LOWER_95_CL",'MEDIAN',
                                   
'UPPER_95_CL','ABBREVIATION'))
final.2 <-
final.1[order(final.1$"MONITORING_POINT_ALIAS_ID",final.1$"TEST_SHORT_DESC"),]

###VIEW IN EXCEL##
library(xlsx)
write.xlsx(final.2,"c:/users/shawnmille/Desktop/Anti-deg_requests/final.2.xlsx")


-----Original Message-----
From: David L Carlson [mailto:dcarlson at tamu.edu]
Sent: Thursday, December 13, 2018 2:12 PM
To: Miller, Shawn <shawnmille at pa.gov>; R-help at r-project.org
Subject: [External] RE: help

ATTENTION: This email message is from an external sender. Do not open links or
attachments from unknown sources. To report suspicious email, forward the
message as an attachment to CWOPA_SPAM at pa.gov.

You need Santa Claus not r-help. You haven't given us a fraction of the
information we would need to help. You don't show us your code. You
don't tell us where the information is coming from except "today's
date." You don't tell us what data you want. You don't seem to know
the difference between R and R-Studio.

----------------------------------------
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77843-4352


-----Original Message-----
From: R-help <r-help-bounces at r-project.org> On Behalf Of Miller, Shawn
Sent: Thursday, December 13, 2018 11:29 AM
To: R-help at r-project.org
Subject: [R] help

Need help with R studio. Code is to pull data from todays date plus 5 years 4
months from now. I am missing the last 3 months of data. Can you please help?

Shawn Miller | Aquatic Biologist II | Assessment Section Environmental
Protection | Clean Water Rachel Carson State Office Building
400 Market Street | Harrisburg, PA 17101
Phone: 717.772.2185 | Fax: 717.772.3249
https://na01.safelinks.protection.outlook.com/?url=www.depweb.state.pa.us&amp;data=02%7C01%7Cshawnmille%40pa.gov%7Ce275c28afad54d99b5d608d66131bec5%7C418e284101284dd59b6c47fc5a9a1bde%7C1%7C0%7C636803263627811233&amp;sdata=SetioLDNtYwPWgXTfgp4XNoH2ptEpbMkVCkYBcBFJAE%3D&amp;reserved=0<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwebmail.state.pa.us%2FOWA%2Fredir.aspx%3FC%3Dt4jGxr3_mkC5mWY30vM0D8N-9RdJ8s9IgIGFizoEzsd1aNOJaDwGjjpEh4RqLFX24CIJXV9M2ic.%26URL%3Dhttp%253a%252f%252fwww.depweb.state.pa.us%252f&amp;data=02%7C01%7Cshawnmille%40pa.gov%7Ce275c28afad54d99b5d608d66131bec5%7C418e284101284dd59b6c47fc5a9a1bde%7C1%7C0%7C636803263627811233&amp;sdata=8mPY9gVwTHUVb6EhpRueVUcHQIyTyd7QYYctDdbwBsM%3D&amp;reserved=0>


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R help - Dec 2018 - [External] RE: help

[R] [External] RE: help

[R] [External] RE: help