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EcologicalTraitData / traitdataform

A package to manage and compile functional trait data into predefined templates
https://ecologicaltraitdata.github.io/traitdataform/
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pulldata("pantheria") not working #43

Closed rplewes closed 2 years ago

rplewes commented 3 years ago

There is an error in pantheria.R code that is causing pulldata("pantheria") not to work.

amniota needs to be changed to pantheria and read.csv needs to be changed to read.delim

amniota <- utils::read.csv("PanTHERIA_1-0_WR05_Aug2008.txt", fileEncoding = "UTF-8", stringsAsFactors = FALSE)

pantheria <- utils::read.delim("PanTHERIA_1-0_WR05_Aug2008.txt", fileEncoding = "UTF-8", stringsAsFactors = FALSE)

JELLY1 commented 2 years ago

mammaldiet is also not working

# to import a dataset pulldata("mammaldiet")

I get the following error: Direct call to data source failed. Please check internet connectivity and re-load data!

My internet connection is fine and I was able to load 'carabids'

fdschneider commented 2 years ago

As described in #47, those data URLs at Dryad are highly unstable and may break once in a while. Apparently they changed their API again. The original dataset is found at http://doi.org/10.5061/dryad.6cd0v.

The call for the carabids dataset employs the package suppdata, which takes care of changing URLs.

I just updated this for mammaldata, but it is not on CRAN, so you would need to re-install the development version using devtools::install_github('EcologicalTraitData/traitdataform').

JELLY1 commented 2 years ago

Thank you very much.

On Wed, Feb 2, 2022 at 2:38 AM Florian Schneider @.***> wrote:

As described in #47 https://github.com/EcologicalTraitData/traitdataform/issues/47, those data URLs at Dryad are highly unstable and may break once in a while. Apparently they changed their API again. The original dataset is found at http://doi.org/10.5061/dryad.6cd0v.

The call for the carabids dataset employs the package suppdata https://github.com/ropensci/suppdata, which takes care of changing URLs. Also it is not stored on Dryad.

I just updated this for mammaldata, but it is not on CRAN, so you would need to re-install the development version using devtools::install_github('EcologicalTraitData/traitdataform').

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fdschneider commented 2 years ago

Also, since the original issue topic was still unanswered, @rplewes @lauterbur, I fixed the pantheria script, too (e9c52fd). But since the pantheria dataset is very complex, further attributes and an extended thesaurus for mapping the traits would be required to enable the handling of this dataset into a standardised form. Pull requests to fill this gap are welcome (see how it is done for arthropodtraits). Otherwise I will remove those additional data from the package in the long run.