[R] Getting "Error in ect, plot.new has not been called yet" despite grouping plot call
Deramus, Thomas Patrick
tder@mu@ @end|ng |rom p@rtner@@org
Wed Oct 5 15:32:00 CEST 2022
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]
>
> “If knowledge can create problems, it is not through ignorance that
> we can solve them.”
>
> —Issac Asimov
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