Hi Rui,
Thank you very much!
Yes, I verified using real data, it worked correctly as expected after adding
tidyr:: to the pivot_longer function and dplyr:: to the group_by and summarize
Function.
I did not know how to assign the tidyr and dplyr to the three functions because
I do not really understand well the three functions and just got the code from
a google search.
I also tried your simplified code, but got the following error
Error in `dplyr::summarize()`:
! Can't supply both `.by` and `.groups`.
Run `rlang::last_trace()` to see where the error occurred.
Ding
From: Rui Barradas <ruipbarra...@sapo.pt>
Sent: Wednesday, June 12, 2024 11:29 AM
To: Yuan Chun Ding <ycd...@coh.org>; CALUM POLWART <polc1...@gmail.com>
Cc: r-help@r-project.org
Subject: Re: [R] my R code worked well when running the first 1000 lines of R
code
Hello, Inline. Às 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. >
Hello,
Inline.
Às 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 <polc1...@gmail.com<mailto:polc1...@gmail.com>>
> Sent: Wednesday, June 12, 2024 10:52 AM
> To: Yuan Chun Ding <ycd...@coh.org<mailto:ycd...@coh.org>>
> Cc: r-help@r-project.org<mailto:r-help@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@r-project.org<mailto:r-help@r-project.org<mailto:r-help@r-project.org%3cmailto:r-help@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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