uploadEnvDataRequest: Upload an Env-Data request for Annotation

In ABoVE-AotM/above: Functions and methods for the Animals on the Move project of the Arctic Boreal Vulnerability Experiment (ABoVE - NASA).

Description

Upload an Env-Data request for Annotation

Usage

uploadEnvDataRequest(
  csv.file,
  xml.file,
  login = NULL,
  password = NULL,
  link.file = "annotation_status_link.url"
)

Arguments

csv.file	Location and name of .csv file to annotate, either a MoveBank track or file generated by createEnvDataGrid
xml.file	Location and name of .xml file that contains the request instructions - almost certainly generated by createEnvDataRequest
link.file	name of link to access status and final annotated data
login, password	login and password for EnvData (NOT the same as MoveBank login and password)

Details

The function will fill out the data annotation form on the EnvData annotation tool at http://www.bioinfo.mpg.de/orn-gateway/services2.jsp. It will also create a link to the status report of the annotation request, and will attempt to automatically open that page.

Examples

# specify names of data file to annotate (e.g. output of grid) and xml file with the request

csv.file <- "../sandbox/testdata.csv"
xml.file <- "../sandbox/testrequest.xml"

# create a gridded dataset

lats <- seq(38.8, 39.0, length = 40)
lons <- seq(-77.12, -76.91, length = 40) 
start <- ymd("2014-01-01")
finish <- ymd("2014-01-01")

createEnvDataGrid(lats, lons, start, finish, 0, 
                  savefile = TRUE, 
                  fileout = csv.file)

# create an xml request
createEnvDataRequest(request_name = "TestRequest", 
                     type_name = "aster/ASTGTM2", 
                     variable_name = "dem",  
                     interpolation_type = "bilinear",
                     dist_func_spatial="geodetic",
                     email = email,
                     savefile = TRUE, 
                     fileout = xml.file)

# send the request to the server
uploadEnvDataRequest(csv.file, xml.file, 
                     link.file = "annotation_status_link.url")

ABoVE-AotM/above documentation built on May 28, 2020, 6:08 a.m.