Calculation of Demographic Parameters in Tropical Livestock Herds

1. Introduction
1.1. Background and objectives
1.2. Animal-based monitoring
1.3. A selection of parameters
1.4. Organization of the handbook
 

2. Grouping demographic data
2.1. Cohort splitting
2.1.1. Horizontal and vertical cells
2.1.2. Aggregation of cells
2.2. Pseudo-cohort splitting
2.2.1. Columns of cells
2.2.2. Other types of cells

3. Mortality and offtake rates
3.1. One type of removal
3.1.1. Probabilistic models
3.1.2. Calculations over subperiods
3.1.3. Mean size approximation
3.2. Case with two types of removal
3.2.1. Crude probabilities
3.2.2. Hazard rates
3.2.3. Relations between crude probabilities and hazard rates
3.2.4. Competing risks and interferences
3.2.5. Corrected probability of death
3.3. Additional points
3.3.1. Calculations with intake
3.3.2. Non-constant rates
3.3.3. Case with more than two types of events

4. Other demographic rates
4.1. Reproduction rates
4.1.1. Parturition and abortion rates
4.1.2. Prolificacy, stillbirth and female-at-birth rates
4.2. Synthetic rates
4.3. Global demographic rates
4.3.1. Herd dynamics
4.3.2. Production
 

5. Package laserdemog
5.1. R software
5.2. Functions in laserdemog
5.2.1. Data importation
5.2.2. Data splitting
5.2.3. Calculation of the parameters
5.3. Additional points
5.3.1. Arguments ini and end
5.3.2. Codes for exits and entries
5.3.3. Global dynamics and production rates
 

6. Numerical examples
6.1. Example 1 – Overall description
6.1.1. Data importation and splitting
6.1.2. Herd sizes and structures
6.1.3. Demographic rates
6.2. Example 2 – More on reproduction rates
6.3. Example 3 – Test of a treatment on mortality
6.3.1. Data importation and splitting
6.3.2. Descriptive analysis of the treatment effect
6.3.3. Test of the treatment effect
 

7. Annexes
7.1. Rates p and h in survival analyses
7.1.1. One cause of removal
7.1.2. Two causes of removal
7.2. R materials
7.3. Structure of tables generated by hsplit and vsplit
 

8. Bibliography