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The productivity and its performance is one of the core topics of economics studies. The growth of productivity is an indicator of competitiveness, as well as a possible way to achieve economic growth and wellbeing. After joining the EU, the agriculture of the Baltic countries faced increasing competition of the EU Single Market, while having relatively lower productivity indicators. Since 2004, significant structural changes have taken place in the agriculture of the Baltic countries, and it is a topical question whether these changes and overall trends in the agricultural sectors of the Baltic countries have facilitated to increase productivity. Therefore, the objective of the study is to evaluate the productivity growth of the main production factors and the total factor productivity growth in the agriculture of the Baltic countries between 2004 and 2015, in relation to the changes in the use of the production factors. The paper focuses on the value added as output, and land, labour and capital as individual inputs to obtain partial productivity measures. The evaluation of TFP is based on the Index number approach, where TFP growth is a ratio of the Output index to the Input index. The calculations and analyses show that since 2004 both the agricultural output and value added have increased in the agriculture of the Baltic countries, and also productivity performance has improved.