jorgeassis / marineforestsdb

A fine-tuned global distribution dataset of marine forests

A fine-tuned global distribution dataset of marine forests

J. Assis, E. Fragkopoulou, D. Frade, J. Neiva, A. Oliveira, D. Abecasis, S. Faugeron, E.A. Serrão

Abstract

Species distribution records are a prerequisite to follow climate-induced range shifts across space and time. However, synthesizing information from various sources such as peer-reviewed literature, herbaria, digital repositories and citizen science initiatives is not only costly and time consuming, but also challenging, as data may contain thematic and taxonomic errors and generally lack standardized formats. We address this gap for important marine ecosystem-structuring species of large brown algae and seagrasses.

We gathered distribution records from various sources and provide a fine-tuned dataset with ~2.8 million dereplicated records, taxonomically standardized for 682 species, and considering important physiological and biogeographical traits. Specifically, a flagging system was implemented to sign potentially incorrect records reported on land, in regions with limiting light conditions for photosynthesis, and outside the known distribution of species, as inferred from the most recent published literature.

We document the procedure and provide a dataset in tabular format based on Darwin Core Standard (DwC), alongside with a set of functions in R language for data management and visualization.

Raw data permanent identifier: 10.6084/m9.figshare.7854767

R functions for data management and visualization

We provide a set of functions in R language to facilitate extraction, listing and visualization of occurrence records. The functions can be easily installed by entering the following line into the command prompt:

source("https://raw.githubusercontent.com/jorgeassis/marineforestsDB/master/sourceMe.R")

Table. List of functions available for management and visualization.

Function	Description	Arguments
extractDataset()	Imports data to R environment	group (character), pruned (logical)
listTaxa()	Lists available taxa	--
listData()	Lists data available in a dynamic table	extractDataset object name (character), taxa (character), status (character)
listDataMap()	Lists data available in a map	extractDataset object name (character), taxa (character), status (character),radius (integer), color (character), zoom (integer)
subsetDataset()	Subsets available data to a specific taxon	extractDataset object name (character), taxa (character), status (character)
exportData()	Exports available data to a text delimited file or shapefile (geospatial vector data for geographic information systems)	extractDataset object name (character), taxa (character), status (character), file type (character), file name (character)

Example of main functions use

1. dataset <- extractDataset("brownAlgae",pruned=TRUE)
   
2. getTaxonomyWorms("Laminaria digitata")
   
3. listData(dataset,taxa="Laminaria digitata",status="accepted")
   
4. listDataMap(dataset,taxa="Laminaria digitata",status="accepted",radius=2,color="Black",zoom=2)
   
5. exportData(dataset,taxa="Laminaria digitata",status="accepted",type="csv",file="myfile.csv")

1. listTaxa()
2. dataset <- extractDataset("seagrasses",pruned=TRUE)
   
3. getTaxonomyWorms("Zostera marina")
   
4. listData(dataset,taxa="Zostera marina",status="unaccepted")
   
5. listDataMap(dataset,taxa="Zostera marina",status="unaccepted",radius=3,color="Black",zoom=2)
   
6. exportData(dataset,taxa="Zostera marina",status="unaccepted",type="shp",file="myfile")

1. dataset <- extractDataset("brownAlgae",pruned=TRUE)
   
2. getTaxonomyWorms("Laminaria digitata")
   
3. myDataFrame <- subsetDataset(dataset,taxa="Laminaria digitata",status="accepted")

License

The content on this repository is licensed under a Creative Commons Attribution 4.0 International license.

Appropriate credits

Assis, J., Fragkopoulou, E., Frade, D., Neiva, J., Oliveira, A., Abecasis, D., Faugeron, A., Serrão, E.A. (2019) A fine-tuned global distribution dataset of marine forests. Scientific Data

marineforestsdb's Issues

Mapping multiple species

Dear Jorge

Thank you for this incredible resource, I am so impressed.

I would like to make a distribution map for multiple kelp species. Is this possible?
If so, what arguments can I use in the 'listDataMap' function to specify multiple taxa:

listData(dataset,taxa="Laminaria hyperborea","Laminaria ochroleuca","Saccharina latissima" status="accepted")

I have tried to a few variations switching between ',' and '+' but the R error messages returns a

'non-numeric argument to binary operator'.

Thank you in advance for your response,

Nadia