[R] [External] RE: help
David L Carlson
dc@rl@on @ending from t@mu@edu
Thu Dec 13 20:32:38 CET 2018
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 using pa.gov>
Sent: Thursday, December 13, 2018 1:15 PM
To: David L Carlson <dcarlson using 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 using tamu.edu]
Sent: Thursday, December 13, 2018 2:12 PM
To: Miller, Shawn <shawnmille using pa.gov>; R-help using 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 using 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 using r-project.org> On Behalf Of Miller, Shawn
Sent: Thursday, December 13, 2018 11:29 AM
To: R-help using 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&data=02%7C01%7Cshawnmille%40pa.gov%7Cdfe052e5375647a1c32f08d6612eec13%7C418e284101284dd59b6c47fc5a9a1bde%7C1%7C1%7C636803251493279248&sdata=ScL5NIrFc1A4g9wKVAYxhZ6Hrwnb7qvgjijh2WHEENY%3D&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&data=02%7C01%7Cshawnmille%40pa.gov%7Cdfe052e5375647a1c32f08d6612eec13%7C418e284101284dd59b6c47fc5a9a1bde%7C1%7C1%7C636803251493279248&sdata=H6VzxlE9wQCOszIoDOZXOoI5%2BZmsu2qVfP1Y%2BEU50SU%3D&reserved=0>
[[alternative HTML version deleted]]
______________________________________________
R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-help&data=02%7C01%7Cshawnmille%40pa.gov%7Cdfe052e5375647a1c32f08d6612eec13%7C418e284101284dd59b6c47fc5a9a1bde%7C1%7C1%7C636803251493279248&sdata=WM4AQs45%2FgKgmoxl4bS%2B5sTSaWYhCt0YhmkVSlwqgeY%3D&reserved=0
PLEASE do read the posting guide https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.R-project.org%2Fposting-guide.html&data=02%7C01%7Cshawnmille%40pa.gov%7Cdfe052e5375647a1c32f08d6612eec13%7C418e284101284dd59b6c47fc5a9a1bde%7C1%7C1%7C636803251493279248&sdata=BSVgu1ome5ob4rGe%2Bck3hcInxJn6tF0N%2F1CBJezIKG4%3D&reserved=0
and provide commented, minimal, self-contained, reproducible code.
More information about the R-help
mailing list