DHIS2 User Manual
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DHIS2 User Manual

DHIS2 Documentation Team

2.11

Copyright © 2006-2013

Warranty:  THIS DOCUMENT IS PROVIDED BY THE AUTHORS ''AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS MANUAL AND PRODUCTS MENTIONED HEREIN, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

License:  Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the source of this documentation, and is available here online: http://www.gnu.org/licenses/fdl.html.

Revision History
Revision 739
Version 2.11 2013-05-23 19:11:43

Table of Contents

About this guide
1. What is DHIS 2?
1.1. DHIS 2 Background
1.2. Key features and purpose of DHIS 2
1.3. Use of DHIS 2 in HIS: data collection, processing, interpretation, and analysis.
1.4. Technical background
1.4.1. DHIS as a platform
1.4.2. Understanding platform independence
1.4.3. Deployment strategies - online vs offline
1.5. Difference between Aggregated and Patient data in a HIS
1.6. Free and Open Source Software (FOSS): benefits and challenges
2. Getting started with DHIS 2
2.1. Getting started with DHIS 2
2.1.1. Prerequisites
2.1.2. Starting the DHIS 2 Live package
2.1.3. Working directly with the H2 database
2.1.4. Downloading and installing the server version
2.2. Logging on to DHIS 2
2.3. Creating new users and roles
2.3.1. Open User Menu
2.3.2. Define a new role
2.3.3. Add New User
2.4. Logging out of DHIS 2
2.5. Quick intro to designing a DHIS 2 database
2.5.1. The organisational hierarchy
2.5.2. Data Elements
2.5.3. Datasets and data entry forms
2.5.4. Validation rules
2.5.5. Indicators
2.5.6. Report tables and reports
2.5.7. GIS
2.5.8. Charts and dashboard
3. Organisation units
3.1. The organisational hierarchy
3.2. Organisation unit maintenance
3.2.1. Organisation units
3.2.2. Organisation unit group sets
3.2.3. Organisation unit groups
3.2.4. Organisation unit level
3.2.5. Hierarchy operations
4. Data elements
4.1. Data element maintenance
4.1.1. Data elements
4.1.2. Data element groups
4.1.3. Data element group editor
4.1.4. Data element group sets
4.1.5. Data element categories
4.1.6. Data element category combinations
4.1.7. Data dictionaries
4.1.8. Translations
5. Data sets and data entry forms
5.1. Data sets
5.1.1. Data set management
5.2. Data Entry Forms
5.2.1. Section forms
5.2.2. Adding a new section form
5.2.3. Custom Forms
5.2.4. Data set assignment editor
6. User management
6.1. Creating new users and roles
6.1.1. User maintenance
6.1.2. User role management
6.1.3. User management
6.1.4. User group management
6.1.5. User by organisation unit
7. Sharing
7.1. Sharing of objects
7.2. Sharing and access control
7.3. Sharing applied
8. Dashboards
8.1. Setting up the dashboard
8.2. Messages and feedback
9. Data entry
9.1. Learning Objectives
9.2. Data entry with DHIS 2
9.2.1. Selecting the data entry form
9.2.2. Entering data
9.2.3. Validating data in the form
9.2.4. Offline data entry
9.2.5. Multi-organisation unit data entry
10. Using Data Quality functionality
10.1. Overview of data quality checks
10.2. Data quality checks
10.3. Running Validation Rule Analysis
10.4. Std Dev Outlier Analysis
10.5. Min-Max Outlier Analysis
10.6. Gap Analysis
10.7. Follow-Up Analysis
11. Setting up Data Quality functionality
11.1. Learning Objectives
11.2. Overview of data quality check
11.3. Data quality checks
11.4. Data quality check at the point of data entry
11.4.1. Setting the minimum and maximum value range manually
11.4.2. Generated min-max values
11.5. Validation Rule
11.6. Validation Rule Group
12. Indicators
12.1. Indicator maintenance
12.1.1. Indicators
12.1.2. Indicator types
12.1.3. Indicator groups
12.1.4. Indicator group editor
12.1.5. Indicator group sets
13. Using reporting functionality
13.1. Reporting functionality in DHIS 2
13.2. Using standard reports
13.3. Using report tables
13.4. Using dataset reports
13.5. Using resources
13.6. Using data visualizer
13.7. Using the dashboard
13.8. Using reporting rate summary
13.9. Using organisation unit distribution reports
13.10. Using web pivot table
13.11. Using data mart management
14. Setting up report functionality
14.1. Data sources for reporting
14.1.1. Types of data and aggregation
14.1.2. Data mart
14.1.3. Resource tables
14.1.4. Report tables
14.2. How to create report tables
14.2.1. General options
14.2.2. Selecting data
14.2.3. Selecting report parameters
14.2.4. Data element dimension tables
14.2.5. Report table - best practices
14.3. Report table outcome
14.4. Standard reports
14.4.1. What is a standard report?
14.4.2. Designing Standard reports in iReport
14.4.3. Designing SQL based standard reports
14.4.4. Designing HTML based standard reports
15. Using Pivot Table
15.1. Pivot Table overview
15.2. Selecting dimension items
15.3. Arranging the table layout
15.4. Using table options
15.5. Creating a favorite
15.6. Downloading data
15.7. Constraints
16. Using Data Visualizer
16.1. Data Visualizer overview
16.2. Selecting chart type
16.3. Selecting series, category and filter
16.4. Selecting indicators and data elements
16.5. Selecting reporting rates
16.6. Selecting relative periods
16.7. Selecting fixed periods
16.8. Selecting organisation units
16.9. Selecting organisation unit groups
16.10. Selecting chart options
16.11. Displaying a chart
16.12. Displaying a data table
16.13. Downloading chart as image or PDF
16.14. Saving chart as favorite
16.15. Sharing interpretations
16.16. Exiting the data visualizer module
17. Using GIS
17.1. GIS module overview
17.2. Thematic mapping
17.2.1. Boundary layer
17.2.2. Thematic layer 1 and 2
17.2.3. Facility layer
17.3. Tools
17.3.1. Favorite maps
17.3.2. Create predefined legend sets
17.3.3. Download map as image
17.3.4. Share map interpretation
18. Setting up GIS
18.1. Context
18.2. Importing coordinates
19. Import and export
19.1. What is import and export?
19.2. Exporting data
19.2.1. Exporting from DHIS 2
19.2.2. Exporting data to other DHIS 2 systems
19.2.3. Exporting metadata to other DHIS 2 systems
19.2.4. DHIS 1.4 Metadata export
19.2.5. DHIS 1.4 Detailed Metadata Export
19.2.6. PDF Metadata Export
19.3. Importing data
19.3.1. Importing data from another DHIS 2 instance
19.3.2. Matching identifiers in DXF2
19.3.3. Importing data from DHIS 1.4
19.4. Importing CSV data
19.5. Importing XML data
20. Data Administration
20.1. Data browser
20.2. Data integrity
20.2.1. Data elements without data set
20.2.2. Data elements without groups
20.2.3. Data elements violating exclusive group sets
20.2.4. Data elements assigned to data sets with different period types
20.2.5. Data sets not assigned to organisation units
20.2.6. Indicators with identical formulas
20.2.7. Indicators without groups
20.2.8. Invalid indicator numerators
20.2.9. Invalid indicator denominators
20.2.10. Indicators violating exclusive group sets
20.2.11. Organisation units with cyclic references
20.2.12. Orphaned organisation units
20.2.13. Organisation units without groups
20.2.14. Organisation units violating compulsory group sets
20.2.15. Organisation units violating exclusive group sets
20.2.16. Organisation unit groups without group sets
20.2.17. Validation rules without groups
20.2.18. Invalid validation rule left side expressions
20.2.19. Invalid validation rule right side expressions
20.3. Data Archive
20.4. Beneficiary Data Archive
20.5. Maintenance
20.6. Resource tables
20.7. SQL View
20.7.1. Creating a new SQL view
20.7.2. SQL View management
20.8. Organisation unit merge
20.9. Duplicate data elimination
20.10. Data statistics
20.11. Lock exceptions
20.12. Zero value storage
20.13. Organisation unit pruning
20.14. Min-Max Value Generation
20.15. Constant
20.16. Option sets
20.17. Cache Statistics
20.18. Dynamic attributes
20.19. Scheduling
21. Settings
21.1. User settings
21.1.1. User general settings
21.2. System settings
21.2.1. General settings
21.2.2. Appearance settings
21.2.3. Email settings
21.2.4. Access settings
22. Mobile
22.1. Introduction
22.2. Mobile browser based data entry
22.2.1. Getting started with mobile browser data entry
22.3. J2ME GPRS/3G Client
22.3.1. Data connection availability
22.3.2. J2ME GPRS 3G facility reporting client
22.3.3. J2ME GPRS 3G program reporting client
22.3.4. Detailed configuration of data sets and reporting forms
22.3.5. Mobile application setup
22.4. Legacy J2ME client with SMS transport
22.4.1. Build DHIS2 with the dhis-web-mobile module
22.4.2. Install the GSM modem
22.4.3. Register users
22.4.4. Install the mobile application on a phone
22.4.5. Using the system
23. Data dimensions in DHIS2
23.1. The core building blocks describing the data
23.2. The data element dimension
23.2.1. Data element categories
23.2.2. Data element group sets
23.3. The organisation unit dimension
23.3.1. Organisation unit group sets and groups
23.3.2. Best practice on the use of group sets and groups
23.4. The time (period) dimension
23.4.1. Period Types
23.4.2. Relative periods
23.4.3. Aggregation of periods
23.5. Data collection vs. data analysis
23.5.1. Data collection and storage
23.5.2. Input != Output
23.6. Some more examples
23.7. How this works in pivot tables
23.8. From paper for to multidimensional datasets - lessons learned
23.8.1. From tables to category combinations - designing multidimensional data sets
24. Tracker
24.1. Introduction
24.1.1. Background
24.1.2. Getting started with tracker
24.2. User guide
24.2.1. Persons and Programs maintenance
24.2.2. Individual records module
25. Web API
25.1. Introduction
25.2. Authentication
25.3. Date and period format
25.4. Browsing the Web API
25.5. Working with the meta-data API
25.6. Sending data values
25.7. Sending data values using SDMX-HD
25.8. Sending large bulks of data values
25.9. Reading data values
25.10. Reading large bulks of data values
25.11. Writing and reading messages
25.12. Writing interpretations
25.13. Embedding reports in web pages
25.14. Embedding charts with the Visualizer chart plug-in
25.15. Creating a chart carousel with the carousel plug-in
25.16. Embedding report tables with the table plug-in
25.17. Working with SQL views
25.18. Analytics
25.18.1. Request query parameters
25.18.2. Response formats
25.18.3. Constraints
25.19. Generating resource, analytics and data mart tables
25.20. FRED API
26. Integration Engine
26.1. Introduction
26.2. Synchronising orgunits - an XML route
26.3. Loading an XML route
26.4. Transforming data - a Java route
A. DHIS 2 Documentation Guide
A.1. DHIS 2 Documentation System Overview
A.2. Introduction
A.3. Getting started with Launchpad
A.4. Getting the document source
A.5. Editing the documentation
A.6. Using images
A.7. Linking documents together
A.8. Handling multilingual documentation
A.9. Building the documentation
A.9.1. Building the documentation with Apache maven
A.9.2. Building with xmlto
A.10. Committing your changes back to Launchpad
B. MyDatamart User Manual
B.1. Overview
B.2. Installation
B.3. The Mydatamart application
B.3.1. Maintaining the local datamart
B.3.2. Working with Excel
B.3.3. Troubleshooting
B.3.4. History and Background
C. R and DHIS 2 Integration
C.1. Introduction
C.2. Using ODBC to retrieve data from DHIS2 into R
C.3. Using R with MyDatamart
C.4. Mapping with R and Postgresql
C.5. Using R, DHIS2 and the Google Visualization API
C.6. Using PL/R with DHIS2
C.7. Using this DHIS2 Web API with R
D. DHIS 2 Workbook
D.1. Introduction
D.2. Data Visualizer
E. DHIS Technical Architecture Guide
E.1. Overview
E.2. Technical Requirements
E.3. Project Structure
E.4. The Data Model
E.5. The Persistence Layer
E.6. The Business Layer
E.6.1. The JDBC Service Project
E.6.2. The Import-Export Project
E.6.3. The Data Mart Project
E.6.4. The Reporting Project
E.6.5. The System Support Project
E.7. The Presentation Layer
E.7.1. The Portal
E.8. Framework Stack
E.8.1. Application Frameworks
E.8.2. Development Frameworks
DHIS2 Glossary
Bibliography
Index

List of Figures

1.1. The health information cycle
B.1. Mydatamart desktop icon
B.2. Mydatamart on first open
B.3. Creating a new datamart
B.4. Logging in to dhis2 server
B.5. Setting analysis parameters
B.6. Downloading data
B.7. Selecting views
B.8. Datamart connections
B.9. Pivot report wizard
B.10. Data flows using DHIS2
B.11. Using a local datamart
E.1. Data value structure

List of Tables

19.1. CSV format of DHIS 2
22.1.
23.1.
23.2. Example of detailed storage of data values when using data element categories "Place of Service" and "Age" (simplified for readability compared to the actual database table)
23.3.
23.4.
23.5.
25.1. Period format
25.2. Query parameters
25.3. Available Content-Types
25.4. Available Query Filters
25.5. Import parameters
25.6. Data value set query parameters
25.7. Data value set query parameters
25.8. Visualizer chart plug-in configuration
25.9. Table plug-in configuration
25.10. Link plug-in (additional) configuration
25.11. Dimensions and dimension items
25.12. Query parameters
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