R Usage
All the R commands that perform search return data frames. The query parameter that can be passed as an argument is the one that can be copied from the search page.
Connection
# Load library
library(micar)
# Open connection
m <- mica.login(url="https://mica-demo.obiba.org")
# Make queries
# ...
# Close connection
mica.logout(m)
Search
A unified search service allows to get any kind of document type, the search criteria can be applied to same or other document types. Only the published documents can be searched.
Networks
Search for published networks.
mica.networks(m)
mica.networks(m, query="network(in(Mica_network.studyIds,clsa))")
mica.networks(m, query="variable(in(Mlstr_area.Lifestyle_behaviours,Drugs))", locale="en", from=0, limit=10)
Studies
Search for studies, populations and data collection events.
mica.studies(m)
mica.studies(m, query="study(in(Mica_study.methods-design,cohort_study))")
mica.studies(m, query="variable(in(Mlstr_area.Lifestyle_behaviours,Drugs))", locale="en", from=0, limit=10)
mica.study.populations(m)
mica.study.dces(m)
Datasets
Search for datasets.
mica.datasets(m)
mica.datasets(m, query="dataset(in(Mica_dataset.className,HarmonizationDataset))")
mica.datasets(m, query="variable(in(Mlstr_area.Lifestyle_behaviours,Drugs))")
Variables
Search for variables.
mica.variables(m)
mica.variables(m, query="variable(in(Mlstr_area.Lifestyle_behaviours,Drugs))")
mica.variables(m, query="dataset(in(Mica_dataset.className,HarmonizationDataset))")
Taxonomies
The taxonomies describe the variable annotations and are also used to build the search criteria.
# Get taxonomies, vocabularies, terms
mica.taxonomies(m,target="variable")
mica.taxonomies(m,target="variable", query="sex", locale="en", taxonomies = list("Mlstr_area", "Mlstr_additional"))
mica.taxonomies(m,target="study")
mica.vocabularies(m,target="variable", query="cancer", locale = "en")