R help - Jun 2024 - my R code worked well when running the first 1000 lines of R code

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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I am assuming from your message that *exactly* the same code you show was
rerun and yielded different results. If that be so, I doubt that this can
be answered without knowing what that other R code did -- and perhaps not
even then -- and/or whether any of that code changed your data frame.
Another guess is that one of those other R packages may have replaced the
summarize method you used with another (customized) method.

Hopefully, someone else may have more insight than I, though.

-- Bert

On Wed, Jun 12, 2024 at 9:28?AM Yuan Chun Ding via R-help <
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
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> sender that you do not wish to receive further e-mail from the sender.
> (LCP301)
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> 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.
>
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Hi Yuan,
   When you load some packages do you get messages saying that some function is
being masked? What can happen is that one package has a function with the same
name as another package. The conflict is resolved by having one package mask the
other. However, this can cause conflicts if your code uses the function in a way
that is only supported in the masked package.

Tim

-----Original Message-----
From: R-help <r-help-bounces at r-project.org> On Behalf Of Yuan Chun Ding
via R-help
Sent: Wednesday, June 12, 2024 12:28 PM
To: r-help at R-project.org (r-help at r-project.org) <r-help at
r-project.org>
Subject: [R] my R code worked well when running the first 1000 lines of R code

[External Email]

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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------------------------------------------------------------
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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 receive
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 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.

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>
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 receive 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 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.
>
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