Links

- Plant Databases

• Missouri Botanical Garden's Tropicos: MOBOT

• Field Museum of Chicago: Tropical Plant Guides

• New York Botanical Garden Virtual Herbarium: NYBG

• Sistema de Informacion de la Biodiversidad de Colombia (SIB)

• Herbario Amazonico Colombiano - COAH

• Flora of Brazil online database: Flora do Brasil

• SpeciesLink: Brazil

• Global Biodiversity Information Facility: GBIF

• Gentry's transect dataset (manipulated in R)

- Plant trait databases

• TRY-DB - plant traits database

• Kew SID - Kew seed information database

- Fossil databases

• Fossilworks

- Ecological Datasets

• NCEAS data repository

• Salvias plot inventory database (including Gentry's 0.1 plots)

• Global plant traits database: TRY

- GIS Tutorials

• GIS MOOCS and Tutorials

- Base maps

• Global administrative areas

• GIS data sources

• Amazon basin protected areas

• World Protected Areas

- Climate

• Global climatologies for bioclimatic modelling: CliMod

• Global potential evapotranspiration (Global-PET) and aridity index (Global-Aridity)

• Bioclimatic variables for mapping species distributions: Bioclim

• Global climate change scenarios 10 minute grid: 1901-2000

- Soil

• FAO Spatial Geonetwork

• Harmonized World Soil Database IIASA

• Global Soil Regions Map: FAO-UNESCO

• Global Soil Carbon, Nitrogen, Water profile: IGBP-DIS

• Global Soil Organic Carbon, Moisture, pH, Potential Evapo-transpiration: SAGE

• Soil and Terrain Database for Latin America and the Caribbean: SOTERLAC

• Global soil, climate, carbon, vegetation, canopy, wetland, geochemistry: ORLN DAAC

• Global soil water balance (GSWB)

• SoilGrids

• Soil exchangeable cation concentration map of Amazonia, link to GeoTif. University of Turku, PANGAEA

- Topographic maps

• Physical topographic maps

- Global seismic dataset

• Global seismic dataset

• Global landslide catalog

- Global Landslides

• Global landslide hazard

- Rainfall and flooding

• Global rainfall and flooding: TRMM

- Landcover map

• Global Land Cover 2000: GLC2000

- Satellite imagery

• Global Landcover Facility (GLCF): Global satellite imagery and elevation

• ORTHORECTIFIED LANDSAT ETM+ DATA FOR LEGAL AMAZON: LBA-ECO LC-10

• EarthExplorer

- Lidar

• Global scale mapping of canopy height and biomass in 3D: Lidar

- River, stream, water-related

• Stream dranaige Amazon river

• Amazon hydro datasets

• Amazon basin simulated discharge

• Amazon basin river discharge

• Hydroshed and Hydrobasin Amazon region

• HYBAM Amazon basin hydrography

• Amazon river routing and monthly river discharge

• Wetland, floodplain, inundation in the Amazon basin

• Freshwater ecoregions of the world

• Global freshwater biodiversity datasets

• GIEMS-15 Global inundation extent

• Global dataset of rivers, lakes, and reservoirs larger than 300 m width

- DEM (Digital Elevation Model)

• DEM CGIAR-CSI

• Free Digital Elevation Model (DEM) data

• Ecuador DEM

- Volcanos of the world

• Smithsonian's volcanos of the world dataset

- Basemaps

• Shapefiles of Global Protected Areas

• Shapefiles for freshwater and biodiversity research: Biofresh

• Large collection of shapefiles by country level: administrative, roads, elevation, population, land cover (DIVA-GIS)

• Global administrative areas: GADM

• Amazon basin hydrography

• Amazon basin drainage direction

• Ministerio de Transportes y Comunicaciones - Peru (red vial, etc.)

- Biodiversity datasets

• Global freshwater endemic species

- Online tools

• Taxonomic Name Resolution Service(TNRS): Standardizing plant names taxonomy datasets

- Python-related

• Python binaries (unofficial)

• Scipy topical software

• GIS with Python, Shapely, and Fiona

• Best Python editors: pyscripter, vim, notepad++

• Think Python

• Data science tutorials: Kaggle Wiki

• SeqTrace: Free DNA chromatogram editor

- Online datasets

• List of datasets

• Airport and their locations

- Bibliography manager

• Mastering Zotero

- Phylogenetics

• Tools and methods in applied phylogenetics

-R-related

+R basics

• A collection of R-tools and applications: R-project

• Customizing R Studio: IDE for R in Windows

• Google's R style guide

• R warnings

• Common R functions in Ecology and Evolution

• The very basics of R

• R basics

• List of functions in R

• Tutorials list

+R tutorials

• R tutorials: Quick R, R Cookbook, Kickstarter, R tutorial

• igraph

• R tutotial cyclismo

• R books

• R video tutorials

• R code school

• Code examples: example 1, Example 2, Example 3

• Data mining with R

• Creating R packages in Windows

• Eco-R

• Programming in R: Resource 1, Resource 2, Resource 3, Resource 4

+R graphics and labels

• Graphics and labels in R: Example 1, Example 2, Example 3, Example 4, Example 5

• R Graphics

+R in vegetation analysis

• Vegetation analysis in R, PCNM

• Taxize: Allows you to resolve plant taxonomic names using R environment

+R spatial analyses and maps

• Spatial analysis in R

• Geospatial analysis tools and resources

• How to create distribution maps in R: Example 1, Example 2, Example 3, Example 4, Example 5, Example 6

• Species richness map in R: Example 1, Example 2, Example 3

• R for geostatistical analysis: IntR, geoR, geoR tutorials, spatial R

• Ordinary Kriging in R: via texfile, using GRASS

• Species distribution with point records

• Geographic data analysis using R

• Gridding spatial data in R

+R and phylogenetic analyses

• Phylogenetic analysis using R

• Phylomatic in R

• Phylogenetic community structure using PGLMM

• R in Bioinformatics

• Accessing Genbank and Pubmed using R

• R-Phylo

-Web Utilities

• convert json file to csv: https://json-csv.com/

• compress image: https://tinypng.com/

• convert to PDF: https://convertio.co/epub-pdf/

• convert PDF to Excel: https://www.pdftoexcel.com/, https://smallpdf.com/pdf-to-excel

• OCR for image/PDFs to text: http://www.onlineocr.net/