uRsal

repo for development of package to retrieve, clean and validate herbarium records Using R for South American Localities

INPUT, OUTPUT AND ACCESSORY FILES

Search input: vector of species name(s), genus or families (default = NULL: no name filtering) and vector of collection acronym (default = NULL: all collections available)

Data output: cbind(input data table, new columns related to the string editing and to geographical, taxonomical and duplicate-search information and validation/flagging)

Accessory files: Gazeetter (download from a given website or github)

STEP BY STEP - DATA CLEANING

0. Data download (or data entry?)

0.1 List of collections available for download

0.2 Obtaining the links for the DwC, EML and RTF files and other collection metadata

0.3 Downloading the content for each collection

0.3.1 speciesLink
	
0.3.2 Jabot
	
0.3.3 GBIF

0.4. Filtering of the downloaded data? By names or other fields...

Notas:

• Deixar esse passo para o fim: vale a pena investir nisso ou o usuário irá fornecer a lista de entrada para verificação?

• Se quisermos incluir esse passo, será necessário a consulta com speciesLink e Jabot sobre a possibilidade de consulta direta aos servidores deles para download das coleções disponíveis

• Marinez perguntar para Sidnei: podemos usar em um pacote de download de dados os links das coleções fornecidos ao Renato Lima (http://ipt1.cria.org.br/ipt/)

• Marinez vai falar com Luis Alexandre sobre como usar o ipt do JABOT tb

1. Data editing - names and collector number

1.1 Editing collectors and determiners names

1.1.1 Getting the first author/determiners for multiple authors

1.1.2 Removing unwanted characters and expressions (e.g. “et al.”)
	
1.1.3 Resolve encoding problems
	
1.1.4 Editing compound names (e.g. “Leitão-Filho”)

1.1.5 Editing/removing prefixes or prepositions (e.g. de, do, dos, da…)

1.1.6 Assigning occurrences with no collector information

1.1.7 Getting the names in the standardized TDWG format

Functions format.name and format.name

1.1.8 Getting authors/determiners last name

Function last.name adapted from Hans ter Steege function

1.2 Editing collectors numbers

	1.2.1 Removing unwanted characters, letters and expressions

Notas:

• Atualmente Renato está fazendo a rotina de edição separada para os dados de cada rede (speciesLink, JABOT, GBIF). Pensar em maneiras de padronizar os campos e nomes dos cabeçalhos de cada rede para ter uma função única.

2. Data editing - locality info and geographical coordinates

   2.1 Editing and standardization of locality names (country, state and county)

   2.1.1 correct common typos

   2.1.2 removing unwanted characters and solving encoding problems

   2.1.3 Creating the locality strings: Country_State_County_Locality_Sublocality

   2.1.4 Remove prefixes or prepositions (e.g. de, do, dos, da…) from the strings

2.2 Get coordinates from the gazetteer (county level)

2.3 Get coordinates from the gazetteer (locality level)

2.4 Downgrading the resolution for the localities not found in the gazetteer

2.5 Editing coordinates and defining the working coordinates

    2.5.1 Plain zero coordinates as missing coordinates 

    2.5.2 One of the coordinates missing as missing coordinates

    2.5.3	Possible problems with decimal division (e.g. commas instead of points) 
    
    2.5.4 Any coordinate on non-decimal degrees format?	

    2.5.5	Create the working coordinates and define the origin (original vs. gazetteer) and resolution the information (no minutes, no seconds) 
    
    2.5.6	Detecting probable rounding issues	
    
    2.5.7	Removing problematic coordinates still in the mix (e.g. lat>abs(90))

2.6 Replacing missing coordinates by the county coordinates from the gazetteer

Notas:

• Gazetteer precisa ser revisto quanto a nomenclatura das divisões administrativas entre países (e.g. Peru has region, province (estado?), distritos (municípios?))

• Como a inclusão no gazetteer de localidades e sub-localidades é uma novidade, ainda não há uma rotina de padronização dos nomes de localidade (e.g. Parque Nacional => PARNA ou vice-versa)

• Há várias alterações e correções que são feitas quase manualmente. Pensar em criar um dicionário para as principais correções dos campos localidade (e.g. “S. José” => “São José”

• A edição dos dados de localidade do GBIF inclui uma padronização dos nomes dos estados (e.g. RJ => rio de janeiro)

3. Geographical validation

(Incluir aqui os passos que o Diogo já destrinchou)

4. Taxonomic validation

4.1 Standardize the nomenclature (synonyms, typos) to get only valid names for all occurrences

4.2 Consider all names at infraspecific level at specific level (e.g. remove ‘var.’, ‘subsp.’, ‘forma’, etc)

4.3 Edit family names (i.e. making sure that family in the record and in the taxonomists dictionary is the same). Step done using ‘flora’ package.

4.4 Cross the unique string of family-specialist combinations from the taxonomist dictionary and the family-determiner from the record

4.5 Validating all type specimens (isotype, paratypes, holotypes, etc)

Notas:

• Hoje, a atribuição do mesmo nome válido para todos os nomes encontrados nos herbários é feito pelo meu dicionário de nomes. Mas para o pacote essa atribuição tem que ser automatizada (pacote ‘flora’ ou ‘taxize’?) ou baseada em uma lista fornecida pelo usuário.

• Por uma decisão minha, faço a checagem taxonômica (e as análises posteriores apenas ao nível específico), mas acho que esse passo é opcional e talvez desnecessário em um contexto de um pacote mais abrangente

5. Duplicate search

5.1 Create the tree strings to be used in the duplicate search (e.g. Family_Author_collectionNumber_County)

5.2 Flagging the existence of duplicates (top down and bot down)

5.3 Merge best-resolution info from each duplicate?

Notas:

• A fusão das informações das duplicatas é opcional mas creio que ela aportará muitas ocorrências taxonomicamente validadas para a análise Renato ainda vai finalizar esse código...

SUPPORTING FILES

gazetteer.csv

Good to use at county level (or best resolution available from GDAM 3.6 - state, country) for all Latin American countries

Renato completed to add localities from TreeCo, CNCFlora and IBGE. Done by Renato!

Now that we have a gazetteer at locality level, we need to re-assess the resolution of some localities in the gazetteer. Some coordinates at locality level were assigned at county level previously (e.g. Brazil, Rio de Janeiro, Barra da Tijuca (locality within the city) was assigned to Brazil, Rio de Janeiro, Rio de Janeiro).

Renato obtained >1 million locality names from geonames for all Latin American countries, but this need checking before entering the gazetteer - needs to be discussed

Need to add more possible orthographic variants for counties and localities

Need to build a database of federal, state and municipal UCS and extract/add localities from UCs centroids for each county in the gazetteer - Volunteers?

Need to extract to a different file the info of the localities (e.g. biome) and store it separately (e.g. gazetteer_metada.csv)

Need to check problems with county-disagreement between IBGE and GDAM - Done by Renato!

Need to define:

1. How to deal with multiple locality entries with different coordinates (within and between coordinate sources)? Return average coordinates or remove duplicates?

Contact people from other countries to have, in the mid term, localities for other countries of Latin America. Already contact Hans ter Stegge that has a gazetteer for the Guyanas (GF, GU, and SR)

autores.csv

Ready to use!

Need to cross-check with Flora do Brasil family specialists

Simplify the number of fields, store authors/taxonomist info separately (e.g. autores_metadata.csv)

Include a more international ID for each name taxonomist (e.g. ORCID)

collections.csv In progress. Renato have a preliminary list of many herbaria available in speciesLink, JABOT and GBIF that can be used as a start list of collections available for download

species.csv ?? Non existent: list of synonyms and basionyms per valid name??

Table with county-specific threshold for the maximum distance between the original coordinate and the centroid of the county?

Shape file with edited fields (fields and format matching the gazetteer) for the validation of geographical coordinates? Many discordances between county names from GDAM and IBGE, with some errors as well...