Yuan Chun Ding
2024-Jun-12 18:03 UTC
[R] my R code worked well when running the first 1000 lines of R code
I am sorry that I know I should provide a dataset that allows to replicate my
problem.
It is a research dataset and quite large, so I can not share.
Both Bert and Tim guessed my problem correctly. I also thought about the
conflicting issue between different packages and function masking.
I just hope to that someone has similar experience, so providing me suggestion.
For conflicting issue,
What I tried was to add dplyr::pivot_longer or tidyr:: pivot_longer, but still
not resolved the problem.
I will restart from the first line my code, it will work again and then I will
track down.
Thank you,
Ding
From: CALUM POLWART <polc1410 at gmail.com>
Sent: Wednesday, June 12, 2024 10:52 AM
To: Yuan Chun Ding <ycding at coh.org>
Cc: r-help at r-project.org
Subject: Re: [R] my R code worked well when running the first 1000 lines of R
code
I sometimes think people on this list are quite rude to posters. I'm afraid
I'm likely to join in with some rudeness? 1. "Here is some code that
works but also doesn't" is probably not going to get you an answer 2. I
provide
I sometimes think people on this list are quite rude to posters.
I'm afraid I'm likely to join in with some rudeness?
1. "Here is some code that works but also doesn't" is probably not
going to get you an answer
2. I provide no information about the data it works on or doesn't
3. I tell you I'm using a load of dependencies, but don't tell you what
4. I refer to 2000 lines of code but probably means 2000 lines of data?
So. Please post a question someone can actually answer.
If the question is "why might code fail on a 2000 line dataset when it
works on 1000 line dataset" then here are some thoughts:
* Is the 1000 lines being run as dataset[1:1000,] or is it dataset1 and dataset2
?
* Is there a structural difference in the datasets - i.e. numbers, characters or
factors as columns. Often import functions guess a column type by reading the
first 500/1000 lines. If the data has numbers in column 1 for 1-1000 but on line
1999 has a letter... The data type may vary.
On Wed, 12 Jun 2024, 17:28 Yuan Chun Ding via R-help, <r-help at
r-project.org<mailto:r-help at r-project.org>> wrote:
Hi R users,
The following code worked well to summarize four data groups in a dataframe for
three variables (t_depth, t_alt_count, t_alt_ratio), 12 columns of summary, see
attached.
However, after running another 2000 lines of R codes using functions from more
than 10 other R libraries, then it only generated one column of summary.
Do you know why?
Thank you,
Yuan Chun Ding
summary_anno1148ft <- anno1148ft %>%
pivot_longer(c(t_depth, t_alt_count, t_alt_ratio), names_to =
"measure") %>%
group_by(dat, measure) %>%
summarize(minimum = min(value,na.rm=T),
q25 = quantile(value, probs = 0.25,na.rm=T),
med = median(value,na.rm=T),
q75 = quantile(value, probs = 0.75,na.rm=T),
maximum = max(value,na.rm=T),
average = mean(value,na.rm=T),
#standard_deviation = sd(value),
.groups = "drop"
)
summary_anno1148ft <-t(summary_anno1148ft)
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Rui Barradas
2024-Jun-12 18:29 UTC
[R] my R code worked well when running the first 1000 lines of R code
Hello, Inline. ?s 19:03 de 12/06/2024, Yuan Chun Ding via R-help escreveu:> I am sorry that I know I should provide a dataset that allows to replicate my problem. > > It is a research dataset and quite large, so I can not share. > > Both Bert and Tim guessed my problem correctly. I also thought about the conflicting issue between different packages and function masking. > I just hope to that someone has similar experience, so providing me suggestion. > > For conflicting issue, > > What I tried was to add dplyr::pivot_longer or tidyr:: pivot_longer,Do that to all functions comming from contributed packages. At least to those. summary_anno1148ft <- anno1148ft %>% tidyr::pivot_longer(c(t_depth, t_alt_count, t_alt_ratio), names_to = "measure") %>% dplyr::group_by(dat, measure) %>% dplyr::summarize(minimum = min(value,na.rm=T), q25 = quantile(value, probs = 0.25,na.rm=T), med = median(value,na.rm=T), q75 = quantile(value, probs = 0.75,na.rm=T), maximum = max(value,na.rm=T), average = mean(value,na.rm=T), #standard_deviation = sd(value), .groups = "drop" ) Or, simpler, no need to group_by anymore. It can be done in summarise. summary_anno1148ft <- anno1148ft %>% tidyr::pivot_longer(c(t_depth, t_alt_count, t_alt_ratio), names_to = "measure") %>% dplyr::summarize(minimum = min(value,na.rm=T), q25 = quantile(value, probs = 0.25,na.rm=T), med = median(value,na.rm=T), q75 = quantile(value, probs = 0.75,na.rm=T), maximum = max(value,na.rm=T), average = mean(value,na.rm=T), #standard_deviation = sd(value), .by = c(dat, measure), .groups = "drop" ) This is only a guess, the question cannot really be answered. Hope this helps, Rui Barradas but still not resolved the problem.> > > > I will restart from the first line my code, it will work again and then I will track down. > > > > Thank you, > > Ding > > > From: CALUM POLWART <polc1410 at gmail.com> > Sent: Wednesday, June 12, 2024 10:52 AM > To: Yuan Chun Ding <ycding at coh.org> > Cc: r-help at r-project.org > Subject: Re: [R] my R code worked well when running the first 1000 lines of R code > > I sometimes think people on this list are quite rude to posters. I'm afraid I'm likely to join in with some rudeness? 1. "Here is some code that works but also doesn't" is probably not going to get you an answer 2. I provide > > > I sometimes think people on this list are quite rude to posters. > > I'm afraid I'm likely to join in with some rudeness? > > 1. "Here is some code that works but also doesn't" is probably not going to get you an answer > 2. I provide no information about the data it works on or doesn't > 3. I tell you I'm using a load of dependencies, but don't tell you what > 4. I refer to 2000 lines of code but probably means 2000 lines of data? > > So. Please post a question someone can actually answer. > > If the question is "why might code fail on a 2000 line dataset when it works on 1000 line dataset" then here are some thoughts: > > * Is the 1000 lines being run as dataset[1:1000,] or is it dataset1 and dataset2 ? > * Is there a structural difference in the datasets - i.e. numbers, characters or factors as columns. Often import functions guess a column type by reading the first 500/1000 lines. If the data has numbers in column 1 for 1-1000 but on line 1999 has a letter... The data type may vary. > > On Wed, 12 Jun 2024, 17:28 Yuan Chun Ding via R-help, <r-help at r-project.org<mailto:r-help at r-project.org>> wrote: > Hi R users, > > The following code worked well to summarize four data groups in a dataframe for three variables (t_depth, t_alt_count, t_alt_ratio), 12 columns of summary, see attached. > However, after running another 2000 lines of R codes using functions from more than 10 other R libraries, then it only generated one column of summary. > Do you know why? > > Thank you, > > Yuan Chun Ding > > summary_anno1148ft <- anno1148ft %>% > pivot_longer(c(t_depth, t_alt_count, t_alt_ratio), names_to = "measure") %>% > group_by(dat, measure) %>% > summarize(minimum = min(value,na.rm=T), > q25 = quantile(value, probs = 0.25,na.rm=T), > med = median(value,na.rm=T), > q75 = quantile(value, probs = 0.75,na.rm=T), > maximum = max(value,na.rm=T), > average = mean(value,na.rm=T), > #standard_deviation = sd(value), > .groups = "drop" > ) > summary_anno1148ft <-t(summary_anno1148ft) > > > > ---------------------------------------------------------------------- > ------------------------------------------------------------ > -SECURITY/CONFIDENTIALITY WARNING- > > This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to rec > eive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301) > ------------------------------------------------------------ > ______________________________________________ > R-help at r-project.org<mailto:R-help at r-project.org> mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help<https://urldefense.com/v3/__https:/stat.ethz.ch/mailman/listinfo/r-help__;!!Fou38LsQmgU!p3fE1cCl7_IxAOT0Fvr1vPWF3xDeYl1FCDaqXi4Z6HH7tOMmDULawS8DAa7XcG5s5PrfqmeMC0XA$> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html<https://urldefense.com/v3/__http:/www.R-project.org/posting-guide.html__;!!Fou38LsQmgU!p3fE1cCl7_IxAOT0Fvr1vPWF3xDeYl1FCDaqXi4Z6HH7tOMmDULawS8DAa7XcG5s5Prfqhxs3su7$> > and provide commented, minimal, self-contained, reproducible code. > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.-- Este e-mail foi analisado pelo software antiv?rus AVG para verificar a presen?a de v?rus. www.avg.com
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