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: tdera...@partners.org<mailto:tdera...@partners.org>,
tpdera...@gmail.com<mailto:tpdera...@gmail.com>
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