obm.r

R package for connecting and retreive data from OpenBioMaps servers

For shiny data exploration, see the OBM Insight R-Shiny app: http://computation.openbiomaps.org

install from github

library("devtools")

install_github('OpenBioMaps/obm.r')

load library

library(obm)

usage examples

initialize connection to dead_animals database on openbiomaps.org. If the database is registered in openbiomaps.org it might be works without the url param

obm_init('dead_animals')

initialize connection to dead_animals database on a specified server

obm_init('dead_animals','https://somewhere.something')

initialize connection without parameters

obm_init()

authenticating without parameters

obm_auth()

query a range of data from the main table. Returns obm_class

data <- obm_get('get_data','39980:39988')

query all data from the main table. Returns obm_class

data <- obm_get('get_data','*')

query all data from an additional data table. Returns obm_class

data <- obm_get('get_data','*',table='buildings')

query data based on column filter. Returns obm_class

data <- obm_get('get_data','filter=species=Parus palustris')

get avilable forms

form_list <- obm_get('get_form_list')

get form data

form_data <- obm_get('get_form_data',73)

offline form fill - THIS FUNCTION IS NOT READY

obm_form_fill(form_data)

upload data

obm_put(...)

upload tracklog recorded with the mobile app

trl <- '{"trackLogId":"...","trackLogArray":[{...}], ... }' res <- obm_put(scope="tracklog", tracklog=trl)

perform stored query

the last label points an SQL query which stored on the server. These queries connected with the users.

The users can create and save custom queries with custom labels.

obm_get('get_report','last')

Create datatable using a csv file

creates an sql file which can be used in the obm web interface for creating a new table, or add several new columns to an existing table

create_table(file='foo.csv',[data=, sep=',' , quote="'", create-table=F, project=F, table='']

Example:

create_table(file='database_example_rows.csv',quote='"',table='butterfly')

repository function

If the OBM project has a repository connection, the following function will be available

Create dataverse, dataset, add files to dataset

Get info about dataverses, datasets, files

Publish datasets

Delete files, datasets, dataverse

obm_repo('get|put',params=list())

Capture-recapture data processing

library(obm)

mark_transform(file='Urhanya2017.csv')

...answer questions...

look for output files in you working folder:

-rw-r--r-- 1 banm banm 1157626 febr   8 19.11 Urhanya2017.csv
-rw-r--r-- 1 banm banm   16733 febr   8 19.15 errors.txt
-rw-r--r-- 1 banm banm   90986 febr   8 19.15 nau_results.csv
-rw-r--r-- 1 banm banm   29187 febr   8 19.15 nau_input.inp
-rw-r--r-- 1 banm banm   80159 febr   8 19.15 tel_results.csv
-rw-r--r-- 1 banm banm   25645 febr   8 19.15 tel_input.inp