[R] Getting "Error in ect, plot.new has not been called yet" despite grouping plot call

Bill Dunlap w||||@mwdun|@p @end|ng |rom gm@||@com
Thu Oct 6 16:43:56 CEST 2022 

Here is how you could have made an example that helpers could easily run.
It also includes the fix.

f <- function(print.it = FALSE) {
   pdf(file.pdf <- tempfile(fileext=".pdf"))
   series <- as.xts(setNames(sin(seq(0,10,by=.1)),
seq(as.Date("2022-10-06"),by="weeks",len=101)))
   p <- plot(series)
   if (print.it) {
       print(p)
   }
   sm_series_2 <- smooth(series / 2)
   lines(sm_series_2, col="red")
   abline(h=0.1, col="blue")
   dev.off()
   file.pdf
}
> f()
Error in plot.xy(xy.coords(x, y), type = type, ...) :
  plot.new has not been called yet
> f(TRUE)
[1]
"C:\\Users\\willi\\AppData\\Local\\Temp\\Rtmp0wX7rO\\file34843df652c.pdf"

If you remove the pdf() and dev.off() I think you will see that the added
lines do not show up.  I think plot.xts fiddles with the coordinate system
before and after it plots so that add-ons must be done in a special way.

-Bill

On Thu, Oct 6, 2022 at 12:42 AM Deramus, Thomas Patrick <
tderamus using partners.org> wrote:

> Hi Rolf.
>
> I followed your suggestion (though it's probably not as trimmed as it
> could be), but the problem unfortunately persists.
>
> Does this make it any clearer or still too many moving parts to make sense
> of?
>
> rm(list = ls(all.names = TRUE)) #will clear all objects includes hidden
> objects.
>
> #Loads the packages
> library(plyr)
> library(dplyr)
> library(ggplot2)
> library(Kendall)
> library(lubridate)
> library(xts)
> library(TTR)
> library(trend)
> library(forecast)
> library(openxlsx)
>
> #Uses the learningCurve Package from Github:
> #https://github.com/AFIT-R/learningCurve
> library(learningCurve)
>
> #Only load this if using VS Studio because it changes the plot function
> #
> https://stackoverflow.com/questions/52284345/how-to-show-r-graph-from-visual-studio-code
> library(httpgd)
> library(languageserver)
>
> #Loads the Excel files to Dataframes and cleans the data
> Game_Metrics_Word_Task <-
> read.xlsx("GamePack_Analytics_ALL_TIME_Short.xlsx", "Boggle")
> Game_Metrics_Word_Task <- Game_Metrics_Word_Task %>% filter(grepl('1440',
> StudyId))
> Game_Metrics_Word_Task$DeviceTime <-
> ymd_hms(Game_Metrics_Word_Task$DeviceTime,  tz = "America/New_York")
> Game_Metrics_Word_Task <-
> Game_Metrics_Word_Task[!duplicated(Game_Metrics_Word_Task[1:2,])]
>
> #Splits the dataframe into a tibble containing each participant
> Participant_Word_Task <-
> split(arrange(Game_Metrics_Word_Task,StudyId,DeviceTime),
> arrange(Game_Metrics_Word_Task,StudyId,DeviceTime,StudyId,DeviceTime)$StudyId)
>
> #Generates a blank output dataframe
> WordFrame <- data.frame(Participant = c(0), Task = c(0), MannKendall_Tau =
> c(0), MannKendall_P = c(0), Sen_Slope_Value = c(0), Sen_Slope_Pval = c(0),
> Pettitts_CIV = c(0), Pettitts_Pval = c(0), ARIMA_Model = c(0),
> Time_to_Petit = c(0), Number_of_Trials_to_Pettitt = c(0),
> Playtime_to_Petit_seconds = c(0), Time_Start_to_end_days = c(0),
> Number_of_Total_Trials = c(0), Total_Playtime_seconds = c(0),
> Learning_rate_days = c(0), Learning_rate_seconds = c(0), Learned_Task =
> c(0))
>
> #The number of subjects in the xlsx file
> #Reduced to 2 for ease of use
> for (i in 1:2){
>   #This timeseries only includes the trials where the participant
> completed the task
>   success_series <- xts(filter(Participant_Word_Task[[i]], GameEndReason
> == "TIMER_UP")$NumberOfSuccesfulWords , order.by=as.POSIXct(filter(Participant_Word_Task[[i]],
> GameEndReason == "TIMER_UP")$DeviceTime))
>   #This timeseries includes ALL the trials for the sake of plotting
>   original_series <-
> xts(Participant_Word_Task[[i]]$NumberOfSuccesfulWords, order.by
> =as.POSIXct(Participant_Word_Task[[i]]$DeviceTime))
>
>   #This is a decomposing process that xts seems to need for plotting.
>   #nweeks is needed for xts to plot the x-axis
>   success_decomp <- ts(success_series, frequency = nweeks(success_series))
>   original_decomp <- ts(original_series, frequency =
> nweeks(success_series))
>
>   #Values which will be included in the plots
>   WordFrame[i,1] <- unique(Participant_Word_Task[[i]]$StudyId)
>   WordFrame[i,5] <- sens.slope(success_decomp)$estimates
>   WordFrame[i,6] <- sens.slope(success_decomp)$p.value
>   WordFrame[i,7] <- pettitt.test(success_decomp)$estimate
>   WordFrame[i,8] <- pettitt.test(success_decomp)$p.value
>
>   #The simple moving average that will be overlayed with the plotted data
>   simplemovingaverage <- SMA(original_series, n = nweeks(original_series))
>
>   #If the three tests are statistically significant, add a green
> horizontal like to value WordFrame[i,7]
>   #Which would be where the slope changes in the series
>   #Fluid variables have been removed from all pdf() and paste() functions
> for ease-of-use
>   if (WordFrame[i,4] <= 0.05 & WordFrame[i,6] <= 0.05 & WordFrame[i,8] <=
> 0.05){
>      {
>       pdf(file = "Word_Task_Acquisition.pdf")
>       plout <- plot(original_series)
>       lines(simplemovingaverage)
>       abline(v = index(original_series[WordFrame[i,7]]),lty=2,
> col='green', lwd=3)
>       title(paste("Word Task Acquisition for Subject"))
>       dev.off()
>      }
>   #If the three tests are NOT statistically significant, generate a plot
> with NO horizontal line at WordFrame[i,7]
>   } else {
>     {
>       pdf(file = "Word_Task_Acquisition.pdf")
>       plout <- plot(original_series)
>       lines(simplemovingaverage)
>       title(paste("Word Task Acquisition for Subject"))
>       dev.off()
>     }
>   }
> }
>
> ________________________________
> From: Rolf Turner <r.turner using auckland.ac.nz>
> Sent: Wednesday, October 5, 2022 6:06 AM
> To: Deramus, Thomas Patrick <tderamus using partners.org>
> Cc: r-help using r-project.org <r-help using r-project.org>
> Subject: Re: [R] Getting "Error in ect, plot.new has not been called yet"
> despite grouping plot call
>
>         External Email - Use Caution
>
> What you doing or trying to do is far too complex for my poor feeble
> and senile brain to come anywhere near comprehending.  The code that
> you present exceeds my complexity tolerance by many orders of magnitude.
>
> I have a suggestion, but.  Strip your code down to the *essentials*.
> Construct a simple sequence of plotting commands, with *simple* names
> for the pdf files involved.  You should require only two or three such
> files and two or three index levels associated with each of your
> nested loops.
>
> Run the stripped down code and the source of the problem will almost
> surely become clear.
>
> cheers,
>
> Rolf Turner
>
> On Tue, 4 Oct 2022 23:35:09 +0000
> "Deramus, Thomas Patrick" <tderamus using partners.org> wrote:
>
> > Sorry to cross-post on Stackoverflow and here but I'm having some
> > difficulty.
> >
> https://secure-web.cisco.com/1_juqv4RvefQFJofsnOQcQA3Ixge89s4uC26pjoPBaYOSxSLGisKtgUTZkanxeHNRqNmjl30B8wYKfsppHje4T8Su77i7t8UbMKzs3GBKEyQva4yTjPH76Q9-l6tT24bB4qNMPQeFAxrkG5lpozNpGrDIAjfKCMvgS-5Qjs-QmvhWZfo84_3SK9rHhJjJvO9CqXb0MewWwI-dEmkZemjxnliGe_D9nooo7Ebjuw0dpBuMnrdaTzQxDdivsbkujPnrGurdjLARh93RW5IWPszNwaoziRD7P-30McF1PrAP8_yjWrhxQ_S3AgG6k40EoQJU/https%3A%2F%2Fstackoverflow.com%2Fquestions%2F73942794%2Fstill-getting-error-in-ect-plot-new-has-not-been-called-yet-despite-grouping
> >
> > Trying to make a nested loop that produces PDFs off different graphs,
> > one for ACF/PACF diagnostics and another for the actual data, based
> > on some time-series analyses I'm doing.
> >
> > Unfortunately, I keep getting the dreaded: Error plot.new has not
> > been called yet
> >
> > The code is meant to write a PDF containing the ACF and PACF graphs,
> > then do some analyses on the timeseries, and then make a separate PDF
> > containing a plot describing the timeseries based on the p-values of
> > each test for each individual.
> >
> > library(plyr)
> > library(dplyr)
> > library(ggplot2)
> > library(Kendall)
> > library(lubridate)
> > library(xts)
> > library(TTR)
> > library(trend)
> > library(forecast)
> > library(openxlsx)
> >
> > Game_Metrics_Word_Task <-
> > read.xlsx("GamePack_Analytics_ALL_TIME_Short.xlsx", "Boggle")
> > Game_Metrics_Word_Task <- Game_Metrics_Word_Task %>%
> > filter(grepl('1440', StudyId)) Game_Metrics_Word_Task$DeviceTime <-
> > ymd_hms(Game_Metrics_Word_Task$DeviceTime,  tz = "America/New_York")
> > Game_Metrics_Word_Task <-
> > Game_Metrics_Word_Task[!duplicated(Game_Metrics_Word_Task[1:2,])]
> >
> > Participant_Word_Task <-
> > split(arrange(Game_Metrics_Word_Task,StudyId,DeviceTime),
> >
> arrange(Game_Metrics_Word_Task,StudyId,DeviceTime,StudyId,DeviceTime)$StudyId)
> >
> > WordFrame <- data.frame(Participant = c(0), Task = c(0),
> > MannKendall_Tau = c(0), MannKendall_P = c(0), Sen_Slope_Value = c(0),
> > Sen_Slope_Pval = c(0), Pettitts_CIV = c(0), Pettitts_Pval = c(0),
> > ARIMA_Model = c(0), Time_to_Petit = c(0), Number_of_Trials_to_Pettitt
> > = c(0), Playtime_to_Petit_seconds = c(0), Time_Start_to_end_days =
> > c(0), Number_of_Total_Trials = c(0), Total_Playtime_seconds = c(0),
> > Learning_rate_days = c(0), Learning_rate_seconds = c(0), Learned_Task
> > = c(0))
> >
> > for (i in 1:length(Participant_Word_Task)){
> >     success_series <- xts(filter(Participant_Word_Task[[i]],
> > GameEndReason == "TIMER_UP")$NumberOfSuccesfulWords ,
> > order.by=as.POSIXct(filter(Participant_Word_Task[[i]], GameEndReason
> > == "TIMER_UP")$DeviceTime)) original_series <-
> > xts(Participant_Word_Task[[i]]$NumberOfSuccesfulWords,
> > order.by=as.POSIXct(Participant_Word_Task[[i]]$DeviceTime))
> > success_decomp <- ts(success_series, frequency =
> > nweeks(success_series)) original_decomp <- ts(original_series,
> > frequency = nweeks(success_series))
> >
> >
>  pdf(paste("Word_Task_Autocorrelation_plots_for_subject_",unique(Participant_Word_Task[[i]]$StudyId),".pdf"
> > ,collapse = NULL, sep = "")) par(mfrow=c(1,2))
> >     Autocorrelationplot <- acf(success_decomp, main=paste(""))
> >     PartialAutocorrelationplot <- pacf(success_decomp, main=paste(""))
> >     mtext(paste("Word Task Auto and Partialauto correlations for
> > subject ",unique(Participant_Word_Task[[i]]$StudyId)), side = 3, line
> > = -3, outer = TRUE) dev.off()
> >
> >     AutomatedArimaoutputs <- auto.arima(success_decomp)
> >     p <- length(AutomatedArimaoutputs$model$phi)
> >     #AR component
> >     q <- length(AutomatedArimaoutputs$model$theta)
> >     #MA component
> >     d <- AutomatedArimaoutputs$model$Delta
> >     #order of difference
> >     WordFrame[i,1] <- unique(Participant_Word_Task[[i]]$StudyId)
> >     WordFrame[i,2] <- "Word"
> >     WordFrame[i,3] <- MannKendall(success_decomp)$tau[1]
> >     WordFrame[i,4] <- MannKendall(success_decomp)$sl[1]
> >     WordFrame[i,5] <- sens.slope(success_decomp)$estimates
> >     WordFrame[i,6] <- sens.slope(success_decomp)$p.value
> >     WordFrame[i,7] <- pettitt.test(success_decomp)$estimate
> >     WordFrame[i,8] <- pettitt.test(success_decomp)$p.value
> >     WordFrame[i,9] <- paste("ARIMA(",p,",",q,",",d,")", collapse =
> > NULL, sep = "") WordFrame[i,10] <-
> > difftime(time(success_series[WordFrame[i,7]]),time(original_series[1]))
> > WordFrame[i,11] <- tail(which(grepl(success_series[WordFrame[i,7]],
> > original_series)), n=1) WordFrame[i,12] <-
> >
> sum(Participant_Word_Task[[i]]$TotalDuration[1:WordFrame[i,11]])-sum(Participant_Word_Task[[i]]$TotalTimePaused[1:WordFrame[i,11]])
> > WordFrame[i,13] <-
> >
> difftime(time(original_series[length(original_series)]),time(original_series[1]))
> > WordFrame[i,14] <- length(original_series) WordFrame[i,15] <-
> >
> sum(Participant_Word_Task[[i]]$TotalDuration[1:length(original_series)])-sum(Participant_Word_Task[[i]]$TotalTimePaused[1:length(original_series)])
> >
> >
> >     simplemovingaverage <- SMA(original_series, n =
> > nweeks(original_series))
> >
> >     if (WordFrame[i,4] <= 0.05 & WordFrame[i,6] <= 0.05 &
> > WordFrame[i,8] <= 0.05){ {
> >
>  pdf(paste(WordFrame[i,1],"_Word_Task_Acquisition.pdf",collapse
> > = NULL, sep = "")) plout <-
> > plot(original_series,type='l',col='blue',xlab="Date of
> > Play",ylab="Number of Successful Words")
> > lines(simplemovingaverage,type='l',col='red') title(paste("Word Task
> > Acquisition for Subject", WordFrame[i,1])) abline(v =
> > index(original_series[WordFrame[i,7]]),lty=2, col='green', lwd=3)
> > dev.off() } WordFrame[i,18] <- T
> >               WordFrame[i,16] <- (1-(WordFrame[i,10]/WordFrame[i,13]))
> >               WordFrame[i,17] <- (1-(WordFrame[i,12]/WordFrame[i,15]))
> >     } else {
> >               {
> >
>  pdf(paste(WordFrame[i,1],"_Word_Task_Acquisition.pdf",collapse
> > = NULL, sep = "")) plout <-
> > plot(original_series,type='l',col='blue',xlab="Date of
> > Play",ylab="Number of Successful Words")
> > lines(simplemovingaverage,type='l',col='red') title(paste("Word Task
> > Acquisition for Subject", WordFrame[i,1])) dev.off() }
> >               WordFrame[i,18] <- F
> >               WordFrame[i,16] <- 0
> >               WordFrame[i,17] <- 0
> >     }
> > }
> >
> > It will work just fine if I run the lines individually (e.g. set i =
> > 1, 2, ect), and if I comment out abline and title (lines seems to
> > work fine). But it will throw the error everytime I try to run the
> > loop without these commented.
> >
> > Have tried just about everything I could find on the Stack forums to
> > run everything as a single argument and I'm just not sure what is
> > wrong with it.
> >
> > dev.list() spits out:
> >
> > pdf
> >   2
> > following the error.
> >
> > With abline and title commented out and lines run individually it's
> > NULL.
> >
> > Happens in both RStudio
> >
> > 2022.07.2+576 "Spotted Wakerobin" Release
> > (e7373ef832b49b2a9b88162cfe7eac5f22c40b34, 2022-09-06) for Ubuntu
> > Bionic Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML,
> > like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36
> >
> > And R:
> >
> > platform       x86_64-pc-linux-gnu
> > arch           x86_64
> > os             linux-gnu
> > system         x86_64, linux-gnu
> > status
> > major          4
> > minor          2.1
> > year           2022
> > month          06
> > day            23
> > svn rev        82513
> > language       R
> > version.string R version 4.2.1 (2022-06-23)
> > nickname       Funny-Looking Kid
> >
> >
> > My OS:
> > PRETTY_NAME="Debian GNU/Linux 11 (bullseye)"
> > NAME="Debian GNU/Linux"
> > VERSION_ID="11"
> > VERSION="11 (bullseye)"
> > VERSION_CODENAME=bullseye
> > ID=debian
> > HOME_URL="
> https://secure-web.cisco.com/1Ruvt90Q90ixR-GE-RDiKJgzRpfDjlNz-lZTqQQGM8Tf4GAoj5QOfE2vXMaMWxMoexuf1npQrX7uAjFuU2viz28h42RPmHQK7jGDX7BpRLkTNcERyxHVKJTxgYegXo-n9N7rqegcKsrr47xlGmTcMOJcBAqH7SpTPQlYDOGgjz1ErtetQRzUsd-eKs9l4oCVPiF6SKV40C7s_NXm0tuCswL2Jhyfv70-edCtBO_4j9-3dSi5ZdFLYaWsMScnwwxNIGYU2n0vw5NH4GJcZNsv6Scu-r6W8ndJaGL4UmX9J3PX0LrdFyjLbGtA7RqPpKFUQ/https%3A%2F%2Fwww.debian.org
> "
> > SUPPORT_URL="
> https://secure-web.cisco.com/1gveQttVrJNRSM85857IiydpLraxrrtJobMyCNkRvQ4V2f00DH67Z0hEa50LLpCVYQvIjMsQZxHAVMZvYQV_Cp2-e82TDZzPY4aSR2td2th3bwuXGxtI7CTgSUudOWgPpmnwVLT5r34EnwXEmwnMoiPVnOEC7slpF1fLGq11wSynuyttcTagMfpN6qdYfgtbu_mz0JOBUecQ-etUQYw5BDmXEKv5JZ_y5Uyt8Q89Kirhi7Hk8FMbCVcxRZpOZZmghxlPMxYaNVIOnln-R0H8J2QIzqE49cQQPKkFZ9O29zpr8odlBXqjObKn24ReYPDhH/https%3A%2F%2Fwww.debian.org%2Fsupport
> "
> > BUG_REPORT_URL="
> https://secure-web.cisco.com/1tepDnCjDgHsmvw9Eth-7nfyKi3doVSOFKVzz83wskdyf8lsrEVkG2NYw7am6ePhSFfjQXdDyceMyc21Un-vqTirSQYKdPavRdKJy85HgHMP66Xk-OgxFf-5KXiPzmFreDfuuJlYizGSUNOLcADyNVTCo47xFfRgtB83Hs8j3yYAJFrff7TqNOFWzSzTcfrycio_WSSfbQkLpUl-1xGzg-dvP16tKuwkRr62bkPeydXJC_iH1FfnWv5b1G04au3aFmRTem8t2RS40LPMS9Mh0UmMvHD_9qwX16cFMHQ8U4x9Sp9IUcAFhgnbffOyPQm1C/https%3A%2F%2Fbugs.debian.org
> "
> > No LSB modules are available.
> > Distributor ID: Debian
> > Description: Debian GNU/Linux 11 (bullseye)
> > Release: 11
> > Codename: bullseye
> >          Icon name: computer-desktop
> >            Chassis: desktop
> >         Machine ID: 053ebf23707f49c8ad4e0684f4cf19d3
> >            Boot ID: d0e6294d3b944286bef10e76c21e6401
> >   Operating System: Debian GNU/Linux 11 (bullseye)
> >             Kernel: Linux 5.10.0-18-amd64
> >       Architecture: x86-64
> >
> >
> > Any suggestions would be greatly appreciated.
> >
> > --
> >
> > Thomas DeRamus (He/Him/His)
> >
> > Data Analyst
> >
> > Massachusetts General Hospital Brigham
> >
> > Alzheimer’s Clinical & Translational Research Unit
> >
> > 149 13th Street
> >
> > Charlestown, MA 02129
> >
> > Phone: 205-834-5066
> >
> > Email: tderamus using partners.org<mailto:tderamus using partners.org>,
> > tpderamus using gmail.com<mailto:tpderamus using gmail.com>
> >
> >
> > [
> https://secure-web.cisco.com/1AI4S4rz4bDZGM8naa-19GTAeSORO5ZmNe056Q_nhPRk4JVAzPiRKUBWitBK5TpxoKBLoLvNfoMDanGd1n5Bnf4SJFT7l7HnaLcjjH7oVk2BZdDfCLHo8a8eePvD4XrF2Fw3iuxKgIZY5dwdesP3P8pSvkmVGvyZ-HiEKRetk4uJHhRa6gSgOQ8MbCVKmi6XP1dtozTEH1RpDrFJ4EyevPO52UzaTAY6CR8USLWNbsxXJsnsjUz1G6_4P7B3ULuMu9mEPeQz_GnTrSXTrGZooK_idhoEougti7I8NYV0CS09Yahmp4Fe_vh9wu4Jkdal3/https%3A%2F%2Fci3.googleusercontent.com%2Fmail-sig%2FAIorK4we2sU30P2HyfDQF5hpEjYTt-9FTBK7cAVsP7EenrZ0nsKCf48fuYMtElj6Szn_2fpSPWr66eQ][https://ci3.googleusercontent.com/mail-sig/AIorK4yyY0DlImU0UONJrHTbPc5T3lJj8Kmu8SbDKJJ3XjcX6CgvVsvSueYKwficYFz4zXt6fZV8YIY
> <https://secure-web.cisco.com/1AI4S4rz4bDZGM8naa-19GTAeSORO5ZmNe056Q_nhPRk4JVAzPiRKUBWitBK5TpxoKBLoLvNfoMDanGd1n5Bnf4SJFT7l7HnaLcjjH7oVk2BZdDfCLHo8a8eePvD4XrF2Fw3iuxKgIZY5dwdesP3P8pSvkmVGvyZ-HiEKRetk4uJHhRa6gSgOQ8MbCVKmi6XP1dtozTEH1RpDrFJ4EyevPO52UzaTAY6CR8USLWNbsxXJsnsjUz1G6_4P7B3ULuMu9mEPeQz_GnTrSXTrGZooK_idhoEougti7I8NYV0CS09Yahmp4Fe_vh9wu4Jkdal3/https%3A%2F%2Fci3.googleusercontent.com%2Fmail-sig%2FAIorK4we2sU30P2HyfDQF5hpEjYTt-9FTBK7cAVsP7EenrZ0nsKCf48fuYMtElj6Szn_2fpSPWr66eQ%5D%5Bhttps://ci3.googleusercontent.com/mail-sig/AIorK4yyY0DlImU0UONJrHTbPc5T3lJj8Kmu8SbDKJJ3XjcX6CgvVsvSueYKwficYFz4zXt6fZV8YIY>
> ]
> >
> > “If knowledge can create problems, it is not through ignorance that
> > we can solve them.”
> >
> > —Issac Asimov
>
> The information in this e-mail is intended only for th...{{dropped:22}}

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