[R] my R code worked well when running the first 1000 lines of R code
Rui Barradas
ru|pb@rr@d@@ @end|ng |rom @@po@pt
Wed Jun 12 20:29:19 CEST 2024
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 <polc1410 using gmail.com>
> Sent: Wednesday, June 12, 2024 10:52 AM
> To: Yuan Chun Ding <ycding using coh.org>
> Cc: r-help using 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 using r-project.org<mailto:r-help using 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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