fisw10
commented
5 months ago Dear Lucia,
Thank you for your interest in BHPMF. I am sorry to hear you have had issues. The problems you describe are quite common and usually due to some structural issues in your data. Could it be that, e.g. you don't have the required levels of taxonomy (maybe try changing your int ID column to Factor), there are some cases where the same species has different genus or family names, some of the number formatting is not correct? If you would check these cases and come back to me on whether or not that worked, I'm happy to try and help you further.
Best wishes, Franziska
Dr. Franziska Schrodt FHEA (she/her)
Associate Professor
Director of Global Engagement, Geography
Editor Remote Sensing
Associate Editor Global Ecology and Biogeography
IAPB Measurements workstream technical co-lead
Working groups:
IMPACTS<https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/impacts/>: French biodiversity in the Anthropocene - impacts and drivers of spatial and temporal response (CESAB)
sTeTra<https://www.idiv.de/en/stetra.html>: Quantifying temporal change in traits across taxa and the globe (iDiv)
sMiLE<https://www.idiv.de/en/smile.html>: Synthesising plant Metabolomics into biodiversity, Life history & Ecology (iDiv)
Selected recent publications (Google scholar<https://scholar.google.com/citations?hl=en&user=0gjeygkAAAAJ&view_op=list_works>):
* Schrodt, F. et al. (2024) The status and future of Essential Geodiversity Variables. Proc. Roy. Soc. A. (accepted) https://doi.org/10.1098/rsta.2023.0052
* Walker, T.W.N., Schrodt, F., et al. (2023) Leaf metabolic traits reveal hidden dimensions of plant form and function. Science advances (accepted, preprint: https://doi.org/10.1101/2023.03.08.531692)
* Martin, I., Schrodt, F. et al. (2023) Widespread reductions in body size are paired with stable assemblage biomass. Science 381: 1067-1071. https://doi.org/10.1126/science.adg6006
* Xu, W.-B., Go, W.-J., Sierra-Diaz, J. M., Schrodt, F. et al. (2023) Global beta-diversity of angiosperm trees is shaped by Quaternary climate change, Science Advances. https://doi.org/10.1126/sciadv.add85
* Sabatini F. M., ...., Schrodt, F. et al. (2022) Global patterns of vascular plant alpha diversity. Nature Ecology & Evolution. https://doi.org/10.1038/s41467-022-32063-z
* Guo, W.-Y., Serra-Diaz, J. M., Schrodt, F. et al (2022) High exposure of global tree diversity to human pressure. PNAS. https://doi.org/10.1073/pnas.202673311<https://doi.org/10.1073/pnas.2026733119>
School of Geography
University of Nottingham, University Park
Nottingham, NG7 2RD, UK
Twitter: @fschrodt
Skype: fschrodt
LinkeIn: https://www.linkedin.com/in/franziska-schrodt/
________________________________
From: LuciaOliveiracruz ***@***.***>
Sent: 27 February 2024 14:03
To: fisw10/BHPMF ***@***.***>
Cc: Subscribed ***@***.***>
Subject: [fisw10/BHPMF] R session aborts (Issue #4)
Hi, every time I run GapFilling command, I encounter fatal error and R session aborts.
Can you please, help? We already checked some things, this is not a RAM problem.
The package is working on R version 4.2.2 (Windows), we used the GapFilling function on the data associated with the package and everthing is fine. However, the same script is not working with my data, I encounter a fatal error every time I use any functions of the package (GapFilling() ...).
My datasets are:
* hier: the taxonomy with 3 nested levels in a dataframe ( genus, sub-family, family as factors) and an index. There is no missing value for the 259 observations.
hier.png (view on web)<https://github.com/fisw10/BHPMF/assets/145551780/eac11870-63bc-4ca7-a8da-5fcad4387b47>
* trait_norm: the traits dataset, 6 quantitative traits with 20% of missing values. Traits values are normalized and are contained in a matrix. There are also 259 observations.
trait.png (view on web)<https://github.com/fisw10/BHPMF/assets/145551780/1f19a6bb-0144-4e24-b61c-cd4038944e37>
And this is the problematic code line:
GapFilling(trait_norm, hier,mean.gap.filled.output.path = paste0(tmp.dir,"/mean_gap_filled.txt"),
std.gap.filled.output.path = paste0(tmp.dir,"/std_gap_filled.txt"), tmp.dir = tmp.dir)
Can you please, help?
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LuciaOliveiracruz
Hi, every time I run GapFilling command, I encounter fatal error and R session aborts. Can you please, help? We already checked some things, this is not a RAM problem. The package is working on R version 4.2.2 (Windows), we used the GapFilling function on the data associated with the package and everthing is fine. However, the same script is not working with my data, I encounter a fatal error every time I use any functions of the package (GapFilling() ...).
My datasets are:
hier: the taxonomy with 3 nested levels in a dataframe ( genus, sub-family, family as factors) and an index. There is no missing value for the 259 observations.
trait_norm: the traits dataset, 6 quantitative traits with 20% of missing values. Traits values are normalized and are contained in a matrix. There are also 259 observations.
And this is the problematic code line: GapFilling(trait_norm, hier,mean.gap.filled.output.path = paste0(tmp.dir,"/mean_gap_filled.txt"), std.gap.filled.output.path = paste0(tmp.dir,"/std_gap_filled.txt"), tmp.dir = tmp.dir)
Can you please, help?