[R] Getting "Error in ect, plot.new has not been called yet" despite grouping plot call
Joshua Ulrich
jo@h@m@u|r|ch @end|ng |rom gm@||@com
Thu Oct 6 03:16:18 CEST 2022
Hi,
My hunch is that you need to add print(plout) before you call dev.off().
See https://stackoverflow.com/a/39853861
Try that and let me know if that works. If not, I'll take a closer look
later.
Best,
Josh
On Wed, Oct 5, 2022, 1:40 AM Deramus, Thomas Patrick <tderamus using partners.org>
wrote:
> Sorry to cross-post on Stackoverflow and here but I'm having some
> difficulty.
>
> https://stackoverflow.com/questions/73942794/still-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://www.debian.org/"
> SUPPORT_URL="https://www.debian.org/support"
> BUG_REPORT_URL="https://bugs.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>
>
>
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> “If knowledge can create problems, it is not through ignorance that we can
> solve them.”
>
> —Issac Asimov
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