DHIS2 User Manual
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DHIS2 User Manual

DHIS2 Documentation Team

2.8-SNAPSHOT

Copyright © 2006-2012

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 525
Version 2.8-SNAPSHOT 2012-05-17 12:32:05

Table of Contents

About this guide
1. What is DHIS 2?
1.1. Background of The District Health Information Software – Version 2
1.2. Purpose of DHIS2
1.3. Difference between Aggregated and Patient data in a HMIS
1.4. Use of DHIS2 in HMIS: data collection, processing, interpretation, and analysis.
1.5. Overview of DHIS2
1.5.1. Overview of DHIS2 modules
1.5.2. Web-based versus standalone HMIS and their suitability
1.5.3. Free and Open Source Software (FOSS): benefits and challenges
1.5.4. Understanding platform independence
1.5.5. Auxiliary software that can be used with DHIS2
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. Datasets and data entry forms
5.1. Datasets
5.1.1. Dataset 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. Dashboards
7.1. Setting up the dashboard
7.2. Messages and feedback
8. Data entry
8.1. Learning Objectives
8.2. Data entry with DHIS 2
8.2.1. Selecting the data entry form
8.2.2. Entering data
8.2.3. Validating data in the form
8.2.4. Offline data entry
9. Using Data Quality functionality
9.1. Overview of data quality checks
9.2. Data quality checks
9.3. Running Validation Rule Analysis
9.4. Std Dev Outlier Analysis
9.5. Min-Max Outlier Analysis
9.6. Gap Analysis
9.7. Follow-Up Analysis
10. Setting up Data Quality functionality
10.1. Learning Objectives
10.2. Overview of data quality check
10.3. Data quality checks
10.4. Data quality check at the point of data entry
10.4.1. Setting the minimum and maximum value range manually
10.4.2. Generated min-max values
10.5. Validation Rule
10.6. Validation Rule Group
11. Indicators
11.1. Indicator maintenance
11.1.1. Indicators
11.1.2. Indicator types
11.1.3. Indicator groups
11.1.4. Indicator group editor
11.1.5. Indicator group sets
12. Using reporting functionality
12.1. Reporting functionality in DHIS 2
12.2. Using standard reports
12.3. Using report tables
12.4. Using dataset reports
12.5. Using resources
12.6. Using data visualizer
12.7. Using the dashboard
12.8. Using reporting rate summary
12.9. Using organisation unit distribution reports
12.10. Using web pivot table
12.11. Using data mart management
13. Setting up report functionality
13.1. Data sources for reporting
13.1.1. Types of data and aggregation
13.1.2. Data mart
13.1.3. Resource tables
13.1.4. Report tables
13.2. How to create report tables
13.2.1. General options
13.2.2. Selecting data
13.2.3. Selecting report parameters
13.2.4. Data element dimension tables
13.2.5. Report table - best practices
13.3. Report table outcome
13.4. Standard reports
13.4.1. What is a standard report?
13.4.2. Designing Standard reports in iReport
14. Using Data Visualizer
14.1. Data Visualizer overview
14.2. Selecting chart type
14.3. Selecting series, category and filter
14.4. Selecting indicators and data elements
14.5. Selecting reporting rates
14.6. Selecting periods
14.7. Selecting organisation units
14.8. Selecting chart options
14.9. Displaying a chart
14.10. Displaying a data table
14.11. Downloading chart as image or PDF
14.12. Saving chart as favorite
14.13. Exiting the data visualizer module
15. Using GIS
15.1. GIS module overview
15.2. Thematic mapping
15.2.1. Thematic layer 1 and 2
15.2.2. Facility layer
15.2.3. Symbol layer
15.3. Tools
15.3.1. Register favorite map views
15.3.2. Register legend sets
15.3.3. Exporting/saving map images
15.3.4. Measure distance
16. Setting up GIS
16.1. Context
16.2. Importing coordinates
16.3. Administering the GIS module
16.3.1. Register overlays
17. Import and export
17.1. What is import and export?
17.2. Exporting data
17.2.1. Exporting from DHIS 2
17.2.2. Exporting data to other DHIS 2 systems
17.2.3. Exporting metadata to other DHIS 2 systems
17.2.4. DHIS 1.4 Metadata export
17.2.5. DHIS 1.4 Detailed Metadata Export
17.2.6. PDF Metadata Export
17.3. Importing data
17.3.1. Importing data from another DHIS 2 instance
17.3.2. Importing data from DHIS 1.4
17.4. Importing CSV data
17.5. Importing XML data
18. Data Administration
18.1. Data browser
18.2. Data integrity
18.2.1. Data elements without data set
18.2.2. Data elements without groups
18.2.3. Data elements violating exclusive group sets
18.2.4. Data elements assigned to data sets with different period types
18.2.5. Data sets not assigned to organisation units
18.2.6. Indicators with identical formulas
18.2.7. Indicators without groups
18.2.8. Invalid indicator numerators
18.2.9. Invalid indicator denominators
18.2.10. Indicators violating exclusive group sets
18.2.11. Organisation units with cyclic references
18.2.12. Orphaned organisation units
18.2.13. Organisation units without groups
18.2.14. Organisation units violating compulsory group sets
18.2.15. Organisation units violating exclusive group sets
18.2.16. Organisation unit groups without group sets
18.2.17. Validation rules without groups
18.2.18. Invalid validation rule left side expressions
18.2.19. Invalid validation rule right side expressions
18.3. Data Archive
18.4. Beneficiary Data Archive
18.5. Maintenance
18.6. Resource tables
18.7. SQL View
18.7.1. Creating a new SQL view
18.7.2. SQL View management
18.8. Organisation unit merge
18.9. Duplicate data elimination
18.10. Data statistics
18.11. Lock exceptions
18.12. Zero value storage
18.13. Organisation unit pruning
18.14. Min-Max Value Generation
18.15. Constant
18.16. Option sets
18.17. Cache Statistics
18.18. Dynamic attributes
18.19. Scheduling
19. Settings
19.1. User settings
19.1.1. User general settings
19.1.2. User message settings
19.2. System settings
19.2.1. System general settings
19.2.2. System appearance settings
19.2.3. System email settings
20. DHIS Mobile
20.1. Introduction
20.2. Mobile browser based data entry
20.2.1. Getting started with mobile browser data entry
20.3. J2ME GPRS/3G Client
20.3.1. Data connection availability
20.3.2. J2ME GPRS 3G facility reporting client
20.3.3. J2ME GPRS 3G program reporting client
20.3.4. Detailed configuration of data sets and reporting forms
20.3.5. Mobile application setup
20.4. Legacy J2ME client with SMS transport
20.4.1. Build DHIS2 with the dhis-web-mobile module
20.4.2. Install the GSM modem
20.4.3. Register users
20.4.4. Install the mobile application on a phone
20.4.5. Using the system
21. Data dimensions in DHIS2
21.1. The core building blocks describing the data
21.2. The data element dimension
21.2.1. Data element categories
21.2.2. Data element group sets
21.3. The organisation unit dimension
21.3.1. Organisation unit group sets and groups
21.3.2. Best practice on the use of group sets and groups
21.4. The time (period) dimension
21.4.1. Period Types
21.4.2. Relative periods
21.4.3. Aggregation of periods
21.5. Data collection vs. data analysis
21.5.1. Data collection and storage
21.5.2. Input != Output
21.6. Some more examples
21.7. How this works in pivot tables
21.8. From paper for to multidimensional datasets - lessons learned
21.8.1. From tables to category combinations - designing multidimensional data sets
22. Web API
22.1. Introduction
22.2. Authentication
22.3. Date and period format
22.4. Example: Sending data values
22.5. Example: Sending large bulks of data values
22.6. Example: Reading data values
22.7. Example: Writing and reading messages
22.8. Example: Embedding reports in web pages
22.9. Example: Embedding charts with the Visualizer Plugin
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
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

17.1. CSV format of DHIS 2
20.1.
21.1.
21.2. 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)
21.3.
21.4.
21.5.
22.1. Period format
22.2. Import parameters
22.3. Data value set query parameters
22.4. Visualizer plugin configuration
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