Tasks - Zootraits Review Panel

[beatrizmilz]

Temporary deploy: https://beatriz-milz.shinyapps.io/zootraits/

• [x] Set up the first version of the repository
• [x] Write a first draft of the README file @thiagotoyoyo [by 15 de junho]
• [x] Set a LICENSE (ask Thiago which license to use: for now, it's MIT @thiagotoyoyo ) - https://choosealicense.com/ ; attribution to the paper
• [x] Add favicon: https://seas.umich.edu/globalchangebiology - https://seas.umich.edu/themes/custom/creative/favicon.ico
• [x] Ask Thiago what he wants to add in the footer (logo? email?): link to the paper; logo of the founder
• It would be nice to have a logo for the project!
• [x] Ideia: home page

Data

• [x] Create a dataset for the team
• [ ] add ORCID/GOOGLE SCHOLAR/homepage in the team dataset @thiagotoyoyo [by 15 de junho]
• [x] Add ZooTraits dataset

About page

• [x] Add a text about the project @thiagotoyoyo (it can be the same used in the README section)
• [x] Add a table of authors/team
• [x] Map of authors/team?
• [x] Add a list of institutions - with logos

Zootraits review dataset

• [x] Add filters

  • [x] Taxonomic unit [remover]
  • [x] Taxonomic Level [remover]
  • [x] Taxonomic group
  • [x] Ecosystem
  • [x] ~Geographical region - studied sites (column to use: where? is not standardized) @thiagotoyoyo ~
  • [x] Geographical region - Studied scale
  • [x] Traits: (create tables and maps from this information)
    • [x] trait type
    • [x] trait dimension,
    • [x] intraspecific data

• [x] Table

  • [x] improve front end
  • [x] As Thiago: which columns to add to the table?
  • [x] implement download button
    • [x] talk to Thiago: wide or long format to download?

• [x] Visualizations

  • [x] Add tree map

[beatrizmilz]

Ignore column "conclusion"

[beatrizmilz]

Remove "code" from table

[beatrizmilz]

• [x] Check 404 in the DOI URL

[beatrizmilz]

https://r-graph-gallery.com/treemap.html - see paper

[beatrizmilz]

download graphs

[beatrizmilz]

download report: table of articles, plots

[beatrizmilz]

metadata-raw.xlsx @thiagotoyoyo I created a template for the metadata information, so it is easier to add to the page! Do you have a description of the columns somewhere?

[thiago-goncalves-souza]

code can be ignored. I added a description of each column in the file ZooTraits_review_data_may23 in METADATA. Let me know if you need more details. Thanks!

[thiago-goncalves-souza]

FunctionalTraitData_regional.csv FunctionalTraitData_local.csv FunctionalTraitData_global.csv

@beatrizmilz Não sei se fica claro pra você, mas tivemos que separar os dados assim. O CODE é aquele que falei que é o agregador. O local tem a lat-long do local de coleta. O regional tem o país escrito exatamente com o nome do pais que o R usa. O global são os trabalhos que não tinhamos controle. No mapa original simplesmente adicionamos um ponto no canto esquerdo do mapa. Os trabalhos que fizeram estudos em oceano nós inserimos manualmente (naquele tempo, não descobrimos um jeito fácil de fazer pois somos noob )

[thiago-goncalves-souza]

Potential datasets to add to Open Trait (app 2)

https://figshare.com/articles/dataset/AVONET_morphological_ecological_and_geographical_data_for_all_birds_Tobias_et_al_2021_Ecology_Letters_/16586228

https://github.com/RS-eco/traitdata

https://esajournals.onlinelibrary.wiley.com/doi/10.1890/13-1917.1

https://figshare.com/articles/dataset/TetraDENSITY_Population_Density_dataset/5371633?file=11358218

Algumas delas provavelmente já estão dentro do OpenTraits

[beatrizmilz]

code can be ignored. I added a description of each column in the file ZooTraits_review_data_may23 in METADATA. Let me know if you need more details. Thanks!

Do you have a description for the following columns? @thiago-goncalves-souza

taxon_higher_level_1 taxon_higher_level_2 body_size_undetermined

[thiago-goncalves-souza]

To pensando aqui que eles (taxon_higher_level_1, taxon_higher_level_2) podem sair. Poderia manter somente a coluna Taxonomic group que tá la no filter e ai aparece tbm no grafico de barras (primeiro da esquerda).

Body size undetermined -> Pode mudar parar "undetermined morphological traits": when authors used morphological traits without explicitly linking them to a specific trait dimension.

[thiago-goncalves-souza]

Some comments in the data exploration app:

• [x] General traits -> is it possible to export IMAGE and the data used for preparing that plot? this is basically a csv with the proportion that each trait was used in a specific taxonomic group

• [x] General traits -> I was planning to remove the trait "other" from the general traits category. This should not be there, as this column represents only the used traits. -> https://github.com/beatrizmilz/zootraits/issues/1#issuecomment-1620423117

• [ ] ~Global database -> maybe adding a "random small island" to aggregate them?~

[beatrizmilz]

General traits -> I was planning to remove the trait "other" from the general traits category. This should not be there, as this column represents only the used traits.

@thiago-goncalves-souza About this: I found 26 papers in the raw dataset that only has other traits. If we remove the "other" category, they won't appear in the app. Is that ok? papers_only_other_traits.xlsx

[thiago-goncalves-souza]

General traits -> I was planning to remove the trait "other" from the general traits category. This should not be there, as this column represents only the used traits.

@thiago-goncalves-souza About this: I found 26 papers in the raw dataset that only has other traits. If we remove the "other" category, they won't appear in the app. Is that ok? papers_only_other_traits.xlsx

• [x] I'd suggest replacing "other trait" per "undetermined trait" as the readers will understand these papers basically didn't name that trait

[thiago-goncalves-souza]

Two suggestions to the app:

• [x] in the general traits figure you could:

  • [x] (1) replace general trait by TRAIT and
  • [x] (2) select only a color-blind safe palette using only 4 colors. Actually, we don't need to have multiple colours to understand which traits are more or less used.

• [x] Another suggestion is about the name of the countries in the map. Although I thought really nice to have the country with its local language it is difficult for a "general reader" to understand other languages. So, everything could be in english, although we want to translate this app to other languages

[beatrizmilz]

• [x] Update the dataset - sent by @thiago-goncalves-souza to my email

[beatrizmilz]

• [x] Check on https://docs.google.com/document/d/1uQhp42R2G2tf9jbUHgwG5vhW7Nw1zrkCIxlcQh0MsAs/edit what we can use on the app (ex. in the README file, on the homepage, etc.)

[beatrizmilz]

Updated the deployed version: https://beatriz-milz.shinyapps.io/zootraits/

[beatrizmilz]

I had to change the map provider in order to change everything to English (now is using Esri)

[beatrizmilz]

• [ ] Thiago's team is going to complete the lat/long
• [x] map : add more tile options, like sattelite and open street map

[beatrizmilz]

• [ ] @thiago-goncalves-souza review information on metadata

[beatrizmilz]

New changes in the "about" page:

• Added Thiago as the corresponding author (so is easier for anyone who wants to get in touch about the app to know who to reach for)
• Added a table for the "Contributors to the Review Dataset": Will be more easy to understand that as soon as we have contributions from the community.
• Added a small section for the "Authors of the Open Traits Network", linking their website
• Added a section about the app: added the name of the developer and tools that we used.
• Added a section "how to cite"

New changes on the homepage:

• Added a section "how to cite"

[beatrizmilz]

About the license: I think the most apropriate is this https://creativecommons.org/licenses/by-nc-sa/4.0/

[thiago-goncalves-souza]

About the license: I think the most apropriate is this https://creativecommons.org/licenses/by-nc-sa/4.0/

Concordo com você