add_functions {spiritR}

Add arms, interventions and outcomes to an existing xml document for upload to clinicaltrials.gov

Description

These functions add arms, interventions, primary and secondary outcomes as well as conditions and keywords to an xml document created using the create_ctxml() function. Calls to these functions should not be assigned to an object.

Usage

add_arm(ctxml, arm_label, arm_type, arm_desc)

add_intervention(ctxml, int_name, int_type, int_desc, arm_label)

add_pr_outcome(ctxml, name, time, description)

add_sec_outcome(ctxml, name, time, description)

add_condition(ctxml, condition)

add_keyword(ctxml, keyword)

Arguments

ctxml

A xml document generated from the create_ctxml() function

arm_label

Label assigned to arm of clinical trial. Arm means a pre-specified group or subgroup of participant(s) in a clinical trial assigned to receive specific intervention(s) (or no intervention).

arm_type

Either Experimental, Active comparator, Placebo Comparator, Sham Comparator, No Intervention, or Other.

arm_desc

Description of the arm.

int_name

Name of the intervention. For a drug, it is the generic name.

int_type

Drug, Device, Biological/Vaccine, Procedure/Surgery, Radiation, Behavioural, Genetic, Dietary Supplement, Combination Product, Diagnostic Test, or Other.

int_desc

Other details about the intervention not included in name.

name

Name of outome measure.

time

Time point(s) at which the measurement is assessed.

description

Other details about the outcome measure not included in the name

condition

MeSH term for condition being studied in the trial, or Focus of the Study

keyword

Words or phrases that best describe the protocol. Keywords help users find studies in the database.

Details

• add_arm(): Adds an xml nodespace containing information about the arm name, type and description to the xml document.

• add_intervention(): Adds an xml nodespace containing information about the intervention name, type, description and arm it is associated with to the xml document.

• add_pr_outcome(): Adds an xml nodespace containing information about the outcome name, time frame for measurement and additional descriptive details to the xml document.

• add_sec_outcome(): Adds an xml nodespace containing information about the outcome name, time frame for measurement and additional descriptive details to the xml document.

• add_condition(): Adds an xml nodespace containing a MeSH term for the condition being studied in the trial, or Focus of the Study to the xml document.

• add_keyword(): Adds an xml nodespace containing a Words or phrases that best describe the protocol. Keywords help users find studies in the database to the xml document.

Value

A xml document

Examples

args_ctxml <- list(
org_name = "UHNToronto",
org_study_id = "Foo trial 20190806",
brief_title = "Foo trial to test auto upload 20190806",
study_acronym = "N/A",
official_title = "Foo trial to test auto upload: A randomized trial new 20190806",
agency  = "Aaron Conway",
resp_party_type = "Sponsor-Investigator",
investigator_username = "aconway",
investigator_title ="Assistant Professor",
brief_summary = "Lay summary here",
start_date = "2019-10",
primary_compl =  "2020-12",
study_compl = "2020-12",
int_subtype = "Health Services Research",
phase = "N/A",
assignment = "Parallel",
allocation = "Randomized",
no_masking =  "False",
masked_subject = "True",
masked_caregiver = "True",
masked_investigator = "True",
masked_assessor = "True",
number_arms = 2,
sample_size = "40",
eligibility_criteria = "Inclusion Criteria
- Adults
Exclusion Criteria
- Children",
healthy_volunteers = "No",
genders_included = "Both",
gender_based = "No",
min_age = "1 years",
max_age = "N/A",
#Central contact
contact_first_name = "Aaron",
contact_last_name = "Conway",
contact_degrees = "PhD",
contact_phone = "649-728-8499",
contact_email = "[e-mail]",
#Overall official
official_first_name = "Aaron",
official_last_name ="Conway",
official_degrees = "PhD",
official_affiliation = "UHN",
official_role = "Study Principal Investigator",
#Sharing statements
ipd_sharing = "Yes",
ipd_description = "details",
ipd_protocol =  "True",
ipd_sap = "True",
ipd_icf = "True",
ipd_csr = "True",
ipd_code = "True",
ipd_time = "details",
ipd_criteria = "details",
ipd_url = "http://www.aaronconway.info"
)

ctxml <- do.call(create_ctxml, args_ctxml)


 add_arm(ctxml = ctxml, 
         arm_label = "Standard", 
         arm_type =  "Active Comparator", 
         arm_desc = "Manual upload to registry")

add_intervention(ctxml = ctxml, 
                 int_type =  "Device", 
                 int_name = "Registry entry",
                 int_desc = "The usual way to enter to the registry",
                 arm_label = "Standard")

add_pr_outcome(ctxml = ctxml,
               name = "correct upload",
               time = "As measured",
               description = "Insert description about the measure.")

add_sec_outcome(ctxml = ctxml,
                name = "time to upload",
                time = "As measured",
                description = "Insert description about the measure.")

add_condition(ctxml = ctxml,
              condition = "Cardiac")

add_keyword(ctxml = ctxml,
            keyword = "sedation")