First of all, I must say I'm completely noob in R. So I apologize in advance for asking for help with such a simple task. My task is to form a graph of COVID-19 cases for a certain period using data from the CSV file. Unfortunately, at the moment I cannot contact the person from the World Health Organization who provided the data and the script for launching. But I was left with an error that I cannot fix either myself, not with the help of Google.
script.R
library(EpiEstim)
library(ggplot2)
COVID<-read.csv("dataset.csv")
res_parametric_si<-estimate_R(COVID$I,method="parametric_si",config=make_config(list(mean_si=4,std_si=3)))
plot(res_parametric_si)
dataset.csv
Date,Suspected per day,Total suspected,Discarded/pending,Confirmed per day,Total confirmed,Deaths per day,Deaths Total,Case fatality rate,Daily confirmed,Recovered per day,Recovered total,Active cases,Tested with PCR,# of PCR tests total,average tests/ 7 days,Inf HCW,Inf HCW/d,Vent HCW,Susp per day
01-Jul-20,1239,91172,45285,889,45887,12,1185,2.58%,889,505,20053,24649,11109,676684,10073,6828,63,,1239
02-Jul-20,1249,92421,45658,876,46763,27,1212,2.59%,876,505,20558,24993,13167,689851,9966,6874,46,,1249
03-Jul-20,1288,93709,46032,914,47677,15,1227,2.57%,914,597,21155,25295,11825,701676,9915.7,6937,63,,1288
04-Jul-20,926,94635,46135,823,48500,22,1249,2.58%,823,221,21376,25875,9934,711610,9957,6990,53,,926
05-Jul-20,680,95315,46272,543,49043,13,1262,2.57%,543,327,21703,26078,6696,718306,9963.7,7030,40,,680
06-Jul-20,871,96186,46579,564,49607,21,1283,2.59%,564,490,22193,26131,9343,727649,10303.9,7046,16,,871
07-Jul-20,1170,97356,46942,807,50414,23,1306,2.59%,807,926,23119,25989,13568,741217,10806,7092,46,,1170
Error
Error in process_I(incid) (script.R#4): incid must be a vector or a dataframe with either i) a column called 'I', or ii) 2 columns called 'local' and 'imported'.
For the example data the issue seems to be that it does only cover 7 data points, and the configurator assumes that there it can window over more than 7 days. What worked for me was the following code (working in the sense that it does not throw an error).
config <- make_config(incid = COVID$Daily.confirmed,
method="parametric_si",
list(mean_si=4,std_si=3, t_start = c(2,3),t_end = c(6,7)))
res_parametric_si<-estimate_R(COVID$Daily.confirmed,method="parametric_si",config=config)
plot(res_parametric_si)
I need to do exactly the graph that has been made on this page (the second one)
http://www.animatedgraphs.co.uk/line.html
Here is my actual code :
timemax<-151737 # number of frames (and observations - so no interpolation needed)
setwd("C:/Users/victo/Downloads/ffmpeg/ffmpeg/bin/")
vis<-100 # how many time points are on the screen at one time
gdata<-data.frame('Temps'= data$time,'RH_Xacc'= data$RH_Xacc)
gname<-paste("g",1:timemax,".tif", sep="") # holds the names of the picture files
right<-(((1:timemax)<=vis)*100)+(((1:timemax)>vis)*1:timemax) # rightmost time on screen
left<- right-vis+2 # leftmost time on screen
leftlab<-200*ceiling((left-1)/200) # leftmost x label
rightlab<-200*floor(right/200) # rightmost x label
# draw graphs
for (i in 1:timemax) {
tiff(gname[i],width=480)
plot(gdata$Temps[right[i]:left[i]],gdata$RH_Xacc[right[i]:left[i]],col="red",type="l",ylim=c(-100,200),xlim=c(right[i],left[i]),xaxt="n",ylab="",xlab="time")
axis(1,at=seq(from=rightlab[i],to=leftlab[i],by=12))
lines(gdata$Temps[right[i]:i],gdata$RH_Xacc[right[i]:i])
dev.off(dev.cur())
}
# call FFMPEG and make the video
shell("C:/Users/victo/Downloads/ffmpeg/ffmpeg/bin/ffmpeg.exe -codecs -i g%d.tif -b:v 2048k gdata.mpg",mustWork=FALSE)
My code seems to work until the shell function. I don't get an error. The code just never stops running. I am not able to get the video with all the data. Can someone tell me where is the problem ? How can I get the video or if there is an other to get the same result ? I've tried the library gganimate but i didn't succeed either... I am doing this in Rstudio and using sweave.
Thanks a lot
Actually, the first thing you should do is probably run the command :
C:/Users/victo/Downloads/ffmpeg/ffmpeg/bin/ffmpeg.exe -codecs -i g%d.tif -b:v 2048k gdata.mpg directly and not with a calling shell from RStudio. You would have a more verbose output.
Original post
Do you have any CPU performance profiling tool ? I suspect that the shell command might take a lot of time to run on your computer since in your example : timemax<-151737 whereas the example has a shorter timemax timemax<-1000
Try your program with a low value of timemax (=1000) and time the execution of the code. I guess you could extrapolate the total time needed to execute multiplying by 150 (I am not an expert of ffmpeg, it might actually be longer)
I was making a package in R and would like it to make it as a trial version for a period of 30 days .
Well my question is how to make a code self destructive depends on number of days ??
I had played with time and date package for a while where i came to know ,
Sys.Date() could give todays date , so i get forard with something below
today=Sys.Date()
a=today
b=a+1
if(a==today)
{
print(paste("today is sunday"))
if(b==today){
print(paste("today is monday"))
}
I know it is stupid work whatever i had done , my sole idea was to fix the 1st use of package as starting day ,and every day it will increment till 30 days ,when it will reach the limit it will automatically destroy using
file.remove () <- through which I can remove some file ........
May be I am clear with my ideas .
Sorry for the novice question .
Add this condition to the license. ("30 days for free, after that you'll have to pay".) and expect users to comply with this.
There is really nothing else you can do.
Well, actually you can. For example, on the first occasion your code is run, save the current date to a file in a certain location (say, "~/.datetocheck"). Then every time your code is run, check for the existence of this file, and if it exists, compare the dates. If more than 30 days have passed, give an error message:
stop("Time is over! You have to pay!")
The problem is that nothing prevents the user from simply deleting this file.
I'm writing a program that performs several tests on a hardware unit, and logs both the results of each test and the steps taken to perform the test. The trick is that I want the program to log these results to a text file as they become available, so that if the program crashes the results that had been obtained are not lost, and the log can help debug the crash.
For example, assume a program consisting of two tests. If the program has finished the first test and is working on the second, the log file would look like:
Results:
Test 1 Result A: Passed
Test 1 Result B: 1.5 Volts
Log:
Setting up instruments.
Beginning test 1.
[Steps in test 1]
Finished test 1.
Beginning test 2.
[whatever test 2 steps have been completed]
Once the second test has finished, the log file would look like this:
Results:
Test 1 Result A: Passed
Test 1 Result B: 1.5 Volts
Test 2 Result A: Passed
Test 2 Result B: 2.0 Volts
Log:
Setting up instruments.
Beginning test 1.
[Steps in test 1]
Finished test 1.
Beginning test 2.
[Steps in test 2]
Finished test 2.
All tests complete.
How would I go about doing this? I've been looking at the help files for QFile and QTextStream, but I'm not seeing a way to insert text in the middle of existing text. I don't want to create separate files and merge them at the end because I'd end up with separate files in the event of a crash. I also don't want to write the file from scratch every time a change is made because it seems like there should be a faster, more elegant way of doing this.
QFile.readAll will read the entire file into a QByteArray.
On the QByteArray you can then use insert to insert text in the middle,
and then write it back to file again.
Or you could use the classic c style that can modify files in the middle with the help of filepointers.
As #Roku pointed out, there is no built in way to insert data in a file with a rewrite. However if you know the size of the region, i.e., if the text you want to write has a fixed length, then you can write an empty space in the file and replace it later. Check
this discussion in overwriting part of a file.
I ended up going with the "write the file from scratch" method that I mentioned being hesitant about in my question. The benefit of this technique is that it results in a single file, even in the event of a crash since the log and the results are never placed in different files to begin with. Additionally, rewriting the file only happens when adding new results (an infrequent occurrence), whereas updating the log means simply appending text to the file as usual. I'm still a bit surprised that there isn't a way to have the OS insert text into a file for you.
Oh, and for those of you who absolutely must have this functionality as efficiently as possible, the following might be of use:
http://www.codeproject.com/Articles/17716/Insert-Text-into-Existing-Files-in-C-Without-Temp
You just cannot add more stuff in the middle of a file. I would go with two separate files, another for the results and another for the logs.