Comments (9)
brianstock
commented on September 16, 2024
Yes, see the snail example:
https://github.com/brianstock/MixSIAR/blob/master/inst/example_scripts/mixsiar_script_snail.R.
That has only 1 isotope and 2 sources. The alligator ex has 2 sources and 2
isotopes. And some of the other examples have 3 sources, eg wolves.
…On Thu, Oct 27, 2022, 9:51 PM EmmiKurosawa ***@***.***> wrote:
Can we use only 3 food sources in MixSIAR? If less than 5 sources, I get
an error message when loading the source file. Please let me know.
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EmmiKurosawa
commented on September 16, 2024
Dear Brian,
Thanks for getting back to me promptly. When I have only two to foursources, I get the following error.
source <- load_source_data(filename="source_EH_SP_Ui_TEST2022.csv", source_factors=NULL, conc_dep=FALSE, data_type="means", mix)
Warning message:In read.table(file = file, header = header, sep = sep, quote = quote, : incomplete final line found by readTableHeader on 'source_EH_SP_Ui_TEST2022.csv'
When I make triplicates and have total of 6 sources, the program accepts the source table. Please let me know how I can make it work with just two sources. Below is the source table.
Sources Meand13C SDd13C Meand15N SDd15N n
Seston -28.78 0.12 0.99 0.17 5
Water -30.59 4.37 0.66 2.04 3
Thank you so much for your help!
Emmi Kurosawa
PhD candidate
Dept. of Molecular, Cellular, and Organismal Biology
University of Massachusetts Boston
USA
________________________________
From: Brian Stock ***@***.***>
Sent: Thursday, October 27, 2022 5:40 PM
To: brianstock/MixSIAR ***@***.***>
Cc: Emmi Kurosawa ***@***.***>; Author ***@***.***>
Subject: Re: [brianstock/MixSIAR] Can we use only 3 food sources in MixSIAR? If less than 5 sources, I get an error message when loading the source file. (Issue #324)
CAUTION: EXTERNAL SENDER
Yes, see the snail example:
https://github.com/brianstock/MixSIAR/blob/master/inst/example_scripts/mixsiar_script_snail.R.
That has only 1 isotope and 2 sources. The alligator ex has 2 sources and 2
isotopes. And some of the other examples have 3 sources, eg wolves.
On Thu, Oct 27, 2022, 9:51 PM EmmiKurosawa ***@***.***> wrote:
Can we use only 3 food sources in MixSIAR? If less than 5 sources, I get
an error message when loading the source file. Please let me know.
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brianstock
commented on September 16, 2024
Try reading in your csv without mixsiar, using read.csv(). Sometimes you
have an extra empty line in the CSV file, can open in excel and delete the
(blank) several rows below your data, re-save, and retry. Or maybe there
are extra blank columns - the error says something about readtableheader.
…On Fri, Oct 28, 2022, 1:48 AM EmmiKurosawa ***@***.***> wrote:
Dear Brian,
Thanks for getting back to me promptly. When I have only two to
foursources, I get the following error.
> source <- load_source_data(filename="source_EH_SP_Ui_TEST2022.csv",
source_factors=NULL, conc_dep=FALSE, data_type="means", mix)
Warning message:In read.table(file = file, header = header, sep = sep,
quote = quote, : incomplete final line found by readTableHeader on
'source_EH_SP_Ui_TEST2022.csv'
When I make triplicates and have total of 6 sources, the program accepts
the source table. Please let me know how I can make it work with just two
sources. Below is the source table.
Sources Meand13C SDd13C Meand15N SDd15N n
Seston -28.78 0.12 0.99 0.17 5
Water -30.59 4.37 0.66 2.04 3
Thank you so much for your help!
Emmi Kurosawa
PhD candidate
Dept. of Molecular, Cellular, and Organismal Biology
University of Massachusetts Boston
USA
________________________________
From: Brian Stock ***@***.***>
Sent: Thursday, October 27, 2022 5:40 PM
To: brianstock/MixSIAR ***@***.***>
Cc: Emmi Kurosawa ***@***.***>; Author ***@***.***>
Subject: Re: [brianstock/MixSIAR] Can we use only 3 food sources in
MixSIAR? If less than 5 sources, I get an error message when loading the
source file. (Issue #324)
CAUTION: EXTERNAL SENDER
Yes, see the snail example:
https://github.com/brianstock/MixSIAR/blob/master/inst/example_scripts/mixsiar_script_snail.R
.
That has only 1 isotope and 2 sources. The alligator ex has 2 sources and 2
isotopes. And some of the other examples have 3 sources, eg wolves.
On Thu, Oct 27, 2022, 9:51 PM EmmiKurosawa ***@***.***> wrote:
> Can we use only 3 food sources in MixSIAR? If less than 5 sources, I get
> an error message when loading the source file. Please let me know.
>
> —
> Reply to this email directly, view it on GitHub
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EmmiKurosawa
commented on September 16, 2024
Dear Brian,
Thank you for pointing this out. As you said, it was a problem with my file, not MixSIAR. In short, I was able to fix the problem. However, I am writing the following message for those who might have the similar problem in the future.
The error message I get when I load my source data file (it reliably occurs only when I have less than 5 sources) was:
Warning message: In read.table(file = file, header = header, sep = sep, quote = quote, : incomplete final line found by readTableHeader on 'my_data.csv'
This site tells us how to fix the error. https://www.statology.org/r-incomplete-final-line-found-by-readtableheader/. Some other sites also mentioned the same way = Press "enter" the last line in your csv. to insert a blank line. In my case, it did nothing.
But I found that the file was actually loaded correctly despite the warning. So I simply ignored the warning, and proceeded forward with MixSIAR script. I was able to get the source proportions without a problem.
[https://www.statology.org/wp-content/uploads/2022/06/incomp1.jpg]<https://www.statology.org/r-incomplete-final-line-found-by-readtableheader/>
How to Fix in R: incomplete final line found by readTableHeader<https://www.statology.org/r-incomplete-final-line-found-by-readtableheader/>
One warning you may encounter in R is: Warning message: In read.table(file = file, header = header, sep = sep, quote = quote, : incomplete final line found by readTableHeader on 'my_data.csv'
www.statology.org
Emmi Kurosawa
PhD candidate
Dept. of Molecular, Cellular, and Organismal Biology
University of Massachusetts Boston
USA
![https://www.statology.org/wp-content/uploads/2022/06/incomp1.jpg]<https://www.statology.org/r-incomplete-final-line-found-by-readtableheader/](https://www.statology.org/wp-content/uploads/2022/06/incomp1.jpg%5D<https://www.statology.org/r-incomplete-final-line-found-by-readtableheader/){kind=link}
________________________________
From: Brian Stock ***@***.***>
Sent: Friday, October 28, 2022 1:09 AM
To: brianstock/MixSIAR ***@***.***>
Cc: Emmi Kurosawa ***@***.***>; Author ***@***.***>
Subject: Re: [brianstock/MixSIAR] Can we use only 3 food sources in MixSIAR? If less than 5 sources, I get an error message when loading the source file. (Issue #324)
CAUTION: EXTERNAL SENDER
Try reading in your csv without mixsiar, using read.csv(). Sometimes you
have an extra empty line in the CSV file, can open in excel and delete the
(blank) several rows below your data, re-save, and retry. Or maybe there
are extra blank columns - the error says something about readtableheader.
On Fri, Oct 28, 2022, 1:48 AM EmmiKurosawa ***@***.***> wrote:
Dear Brian,
Thanks for getting back to me promptly. When I have only two to
foursources, I get the following error.
> source <- load_source_data(filename="source_EH_SP_Ui_TEST2022.csv",
source_factors=NULL, conc_dep=FALSE, data_type="means", mix)
Warning message:In read.table(file = file, header = header, sep = sep,
quote = quote, : incomplete final line found by readTableHeader on
'source_EH_SP_Ui_TEST2022.csv'
When I make triplicates and have total of 6 sources, the program accepts
the source table. Please let me know how I can make it work with just two
sources. Below is the source table.
Sources Meand13C SDd13C Meand15N SDd15N n
Seston -28.78 0.12 0.99 0.17 5
Water -30.59 4.37 0.66 2.04 3
Thank you so much for your help!
Emmi Kurosawa
PhD candidate
Dept. of Molecular, Cellular, and Organismal Biology
University of Massachusetts Boston
USA
________________________________
From: Brian Stock ***@***.***>
Sent: Thursday, October 27, 2022 5:40 PM
To: brianstock/MixSIAR ***@***.***>
Cc: Emmi Kurosawa ***@***.***>; Author ***@***.***>
Subject: Re: [brianstock/MixSIAR] Can we use only 3 food sources in
MixSIAR? If less than 5 sources, I get an error message when loading the
source file. (Issue #324)
CAUTION: EXTERNAL SENDER
Yes, see the snail example:
https://github.com/brianstock/MixSIAR/blob/master/inst/example_scripts/mixsiar_script_snail.R
.
That has only 1 isotope and 2 sources. The alligator ex has 2 sources and 2
isotopes. And some of the other examples have 3 sources, eg wolves.
On Thu, Oct 27, 2022, 9:51 PM EmmiKurosawa ***@***.***> wrote:
> Can we use only 3 food sources in MixSIAR? If less than 5 sources, I get
> an error message when loading the source file. Please let me know.
>
> —
> Reply to this email directly, view it on GitHub
> <#324>, or unsubscribe
> <
https://github.com/notifications/unsubscribe-auth/ABHDA46XDULHGI5YLLY6CB3WFLMKXANCNFSM6AAAAAARQMZXMI
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EmmiKurosawa
commented on September 16, 2024
Dear Brian,
After running output_JAGS, I often get an error message: “Error in UseMethod("depth"): no applicable method for 'depth' applied to an object of class "NULL", and won't be able to get the output. It’s devastating after 5 hrs of running MCMC. Sometimes if I ignore the error message and repeat the command "output_JAGS", it gives me the output. However, when I run more complicated models, once I get the error message, no matter how many times I repeat the command, the same error message appears. I ran R 4.0.3 on Ventura 13.1 on Mac. Please help me solve this issue.
Kind regards,
…-Emmi
Emmi Kurosawa
PhD candidate
Dept. of Molecular, Cellular, and Organismal Biology
University of Massachusetts Boston
USA
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brianstock
commented on September 16, 2024
Sorry, I haven't seen this before and there isn't enough information here to help...
If your models take 5 hours to run I suggest writing your script so that it saves the fit model object immediately afterward.
R 4.0.3 sounds pretty old (years?). You could try updating R and reinstalling the latest MixSIAR version:
install.packages("devtools")
remotes::install_github("brianstock/MixSIAR", dependencies=T)
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EmmiKurosawa
commented on September 16, 2024
Dear Brian,
Thank you for getting back to me.
Could you kindly tell me the code to save the fit model object immediately afterwards?
I was afraid to upgrade R studio, because then I'd have to upgrade all my libraries to work properly. And I was afraid that might introduce unknown complications for running MixSIAR etc. Which R version do you use? Have you come across any complications after upgrading R?
Please let me know.
Kind regards,
Emmi Kurosawa
PhD candidate
Biology Dept.
University of Massachusetts Boston
USA
…________________________________
From: Brian Stock ***@***.***>
Sent: Saturday, April 1, 2023 4:25 PM
To: brianstock/MixSIAR ***@***.***>
Cc: Emmi Kurosawa ***@***.***>; Author ***@***.***>
Subject: Re: [brianstock/MixSIAR] Can we use only 3 food sources in MixSIAR? If less than 5 sources, I get an error message when loading the source file. (Issue #324)
CAUTION: EXTERNAL SENDER
Sorry, I haven't seen this before and there isn't enough information here to help...
If your models take 5 hours to run I suggest writing your script so that it saves the fit model object immediately afterward.
R 4.0.3 sounds pretty old (years?). You could try updating R and reinstalling the latest MixSIAR version:
install.packages("devtools")
remotes::install_github("brianstock/MixSIAR", dependencies=T)
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brianstock
commented on September 16, 2024
You can either save all objects in your workspace with save.image() or save individual objects with saveRDS.
https://stat.ethz.ch/R-manual/R-devel/library/base/html/save.html
https://stat.ethz.ch/R-manual/R-devel/library/base/html/readRDS.html
Keeping your version of R (RStudio is less important, just a user interface) and packages updated is a good idea. The current version is 4.2.3 so that is what I use. When developing packages, they are tested in the current R release and the in-progress next version.
R version history: https://cran.r-project.org/bin/windows/base/old/
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EmmiKurosawa
commented on September 16, 2024
Thanks, Brian. I will try!
Emmi Kurosawa
PhD candidate
Biology Dept.
University of Massachusetts Boston
USA
…________________________________
From: Brian Stock ***@***.***>
Sent: Monday, April 3, 2023 7:26 AM
To: brianstock/MixSIAR ***@***.***>
Cc: Emmi Kurosawa ***@***.***>; Author ***@***.***>
Subject: Re: [brianstock/MixSIAR] Can we use only 3 food sources in MixSIAR? If less than 5 sources, I get an error message when loading the source file. (Issue #324)
CAUTION: EXTERNAL SENDER
You can either save all objects in your workspace with save.image() or save individual objects with saveRDS.
https://stat.ethz.ch/R-manual/R-devel/library/base/html/save.html<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2FR-manual%2FR-devel%2Flibrary%2Fbase%2Fhtml%2Fsave.html&data=05%7C01%7Cemmi.kurosawa001%40umb.edu%7C318d9c9bf7744cebabfd08db34363943%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638161179728929674%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=t4Af1EJbqQ9X2dIFB2BVZyYrR%2BqAaHbN6Xrwk2PG498%3D&reserved=0>
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Keeping your version of R (RStudio is less important, just a user interface) and packages updated is a good idea. The current version is 4.2.3 so that is what I use. When developing packages, they are tested in the current R release and the in-progress next version.
R version history: https://cran.r-project.org/bin/windows/base/old/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.r-project.org%2Fbin%2Fwindows%2Fbase%2Fold%2F&data=05%7C01%7Cemmi.kurosawa001%40umb.edu%7C318d9c9bf7744cebabfd08db34363943%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638161179728929674%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=cLVLvzVB1MjhLUGn2ydymJY%2BekOM2syn3Wp9sXQa6x0%3D&reserved=0>
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Related Issues (20)
- Is it possible to have a different number of sources in different regions? HOT 1
- Can we include different sample sizes for each isotope in the source file?
- Problem installing GUI HOT 1
- "incorrect number of dimensions" error when running output_JAGS HOT 1
- How do you add more models to jags.mod without running every model over each time? HOT 1
- Modify output posterior continuous effect
- ILR slope terms are inconsistent with ggplot visual output HOT 1
- Warning message concerning deprecation of `..scaled..`, to use 'after_stat(scaled)' instead.
- Extract posterior estimates? HOT 1
- Continuous effect output options HOT 1
- Concentration dependence meaning in MixSIAR HOT 3
- include sampling precision error into MixSIAR model HOT 2
- Is it possible to define the order of categorial covariates? HOT 4
- Your 'iso_names' do not match column names HOT 1
- Isospace Plot Output Axis
- Error when using MixSIAR "dot-dot notation was deprecated HOT 5
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