PhD Courses

Last changed: 04 May 2021

Upcoming courses organized or co-organized by FoSW.

Spring 2021

Advanced statistics in practice

This course aims to help preparing students to analyze, interpret and report their data using the most up-to-date methods in R. Special attention will be given to discuss questions springing from the students own work and the biological interpretation of data. The course is intended to deepen the students’ understanding of all aspects of ecological inferences, not as a cook book of “how to”.

Course units

Course activities include initial readings, classroom discussions, lectures, hands-on and home exercises. Each unit corresponds to one credit and includes theme/workshop and is planned for one full day except the Meta-analysis unit that is planned for two days.

  1. Time series analysis: Jonas Knape and Örjan Östman, 1 February.
  2. GIS and spatial analysis: Alistair Auffret and Mohammad Bahram, 15 February.
  3. Meta-analysis: Julia Koricheva, 12-13 Apri.
  4. Getting more out of community data: Tomas Roslin and Giovanni Strona, 3 May.
  5. Dealing with complexities of GLMs: Matt Low 31 May.


Apply by sending an email indicating which specific units you are interested in to the course organizer: Mohammad Bahram ( no later than 29 November 2020.

How to write and publish a scientific paper

  • Wednesday 10 March from 10:00-12:00, and then every two weeks until 16 June.
  • Additional studies (not scheduled) consist of literature studies and written exercises.
  • Zoom.
  • Important: The students will be receiving constructive-feedback on their own manuscript, thus they must be at a writing stage in their research.
  • The number of participants is limited to 10.
  • Priority will be given to members of the Organism Biology and Focus on Soils & Waters research schools, but is also open to other PhD students.
  • Apply by sending an e-mail to the course leader Marisol Sanchez-Garcia ( – no later than 2 March 2021.
  • Research school cooperation, responsible RS: Organism Biology

High Temporal Resolution Water Quality Monitoring and Analysis

This course is run together with the 4th International Workshop on High Temporal Resolution Water Quality Monitoring and Analysis held at SLU 31 May - 2 June 2021. The general focus of the course is on exploring recent technological and scientific advances in water quality measurements allowing for high-resolution determination of chemicals in water with a range of instruments. The objective of the course are to discuss how these new technologies and data can further advance catchment science and contribute to water resources management.

Understanding and coding the R language

A PhD course and an opportunity to learn more about programming in R! Basic knowledge in the R programming language and tools for programming, processing data and analyses. Planned for May and autumn 2021. For more information, please please see the website of RS Ecology.

To communicate science

OmAqua - Organic Micropollutants in the Aquatic Environment: Measurements and Transport from Source to Tap

The course will focus on organic chemical pollutants in the aquatic environment, including their measurement and transport from source to tap. Online lectures will be held in late spring, and sampling and laboratory work in autumn this year.  

Minerals in soils and sediments and their X-ray identification and quantification

The course consists of lectures and exercises by Stephen Hillier from The James Hutton Institute in Aberdeen, Scotland. Steve is a highly qualified scientist in mineralogy in sediments and has held a guest professorship at our department at SLU. With his team at James Hutton he has won first (2008, 2018) and second (2006, 2012, 2014) place in The Reynolds Cup competition in quantitative mineralogy.

Autumn 2021

Aquatic sciences: theory, practical methods, management, threats

Ecosystem functioning: From theory to application

The concept of "ecosystem functioning" has over the last two decades stimulated research focussed on what ecosystems do, as opposed to what they are composed of, and is increasingly important in policy and management because of its strong linkages with ecosystem services. Focussing on ecosystem functioning in inland waters (lakes and streams) and terrestrial ecosystems (soils, riparian habitats, agricultural and forest landscapes), this course will cover basic definitions, the relationship between ecosystem functioning and ecosystem services, and several currently topical themes in ecosystem functioning research. These include the roles of functional traits and calculation of functional diversity (including practical exercises in R), multifunctionality, and an overview of biodiversity-ecosystem functioning research.

Throughout, a range of practical methods for quantifying ecosystem functioning will be covered, as will the application of these methods in research, biomonitoring and environmental assessment.

Soil systems: Analytical methods for integrating the chemical, biophysical interface in soils

  • 3 ECTS
  • Four literature meetings and a one-week workshop.
  • Please do not hesitate to contact Katharina Meurer ( if you have any questions regarding the course.

Multivariate statistics

Previous PhD Courses


Multivariate methods for ecologists

The course aims to illustrate the application of a number of multivariate methods on ecological data. Following the course, participants should be familiar with different multivariate techniques, and how they can be applied on various types of data. The course will focus on developing an understanding of the application of multivariate techniques, with only a minimum amount of effort placed on comprehending the underlying mathematical detail.

  • The course is given in two parts. The first part (2-6 November 2020) is compulsory and consists of lectures and exercises.
  • The second part (9-20 November) is optional and consists of supervised work with own data, at your home university.
  • Due to the Corona pandemic, the 2020 course will be entirely on-line.
  • Course organizer: Ulf Grandin (, Department of Aquatic Sciences and Assessment.
  • 3 or 4.5 ECTS
  • Course code:For 3 ECTS PNS0190 and for 4.5 ECTS PNS0074.

More details at the Department of Aquatic Sciences and Assessment.

Agricultural catchments in changing world

This course recognises the importance of agricultural catchments and their sensitivity to global change and provides a comprehensive synthesis of dominant processes shaping agricultural
landscapes: hydrological, biogeochemical, ecological, economic and societal. The course comprises theoretical lectures and practical assignments focused on environmental assessment and management, all adapted to maximise the potential of distant based learning.

Advanced Data Handling with R

The course aims at improving the effectiveness of the scientific code you write and will teach you how to write more ordered code and to deal with the automation of data handling tasks. This will allow you to save time and handle bigger data-sets. The course includes three main themes and learning targets, those are to: 1) write reproducible code, 2) confidently manipulate data and R-objects and 3) check for and fix errors in data and code.

Understanding and coding the R language, 2hp

A PhD course and an opportunity to learn more about programming in R! Basic knowledge in the R programming language and tools for programming, processing data and analyses.

To communicate science, 2 hp

How to plan and perform an effective communication using different methods and channels. Research school cooperation. Please contact course coordinator Elisabeth Müllner for more information.

PNS0070 Reviewing and Summarizing Science - Everything You Always Wanted to Know About Science* (*But Were Afraid to Ask), 2hp 

Overall the objectives of the course is to help the students to navigate scientific publications, and to understand the process of scientific communication.

The objectives of this course are:

  1. to learn how to find and to evaluate scientific key publications
  2. to understand the purpose of the peer review system and to learn writing a constructive scientific review
  3. to be able to summarize the key findings of a paper in 1-2 sentences
  4. to understand the value of conferences.

More info



Multivariate methods for ecologists, 4,5 hp. October 2019. More information is available here.

Watershed Ecology and Biogeochemistry. A PhD course in the Krycklan catchment September 19-25, 2019. 'Watershed Ecology and Biogeochemistry' addresses the foundational concepts and modern challenges within the broad field of watershed science. More information here.

PNG0079 Mini-course: UN Sustainable Development goals: relevance, achievements, conflicts and politics. Workshop 8th of February 2019, Uppsala, and optional ‘mini-course’, 1 ECTS.Syllabus. Find detailed information about the workshop 8th of February here

PNS0169 Traditional and molecular methods to assess biodiversity. Focus on DNA (meta)barcoding & Aquatic Organisms, 7hp.Detailed schedule is available here (pdf). Course page with syllabus.

PNS0171. Nitrogen cycling in terrestrial ecosystems, 4hp. 25-29th of March 2019

Understanding and coding the R programming language, 2 hp. April 1-5 (Mon-Fri) 2019. Course flyer. Course plan.


PNG0044 How to write and publish a scientific paper, 4.5 HEC

Ecological stability in times of rapid environmental change (3 credits). 15 – 19 October, 2018

Multivariate Methods for Ecologists (3 + 1.5 ECTS), 12 – 16 Feb 2018,  Optional 19 Feb – 2 March

Understanding & Coding the R Programming Language (2 ECTS), April 23 - 27th 2018, Course flyer & Course plan

Organic micropollutants in the aquatic environment – measurements and transport processes (5 ECTS), April 11 - May 16 2018, Course web page & More information about the course


Reviewing and Summarizing Science: A guide on how to navigate through and ocean of paper (2ECTS), 15 to 18 May 2017

Phosphorus cycling in terrestrial and aquatic ecosystems (3 ECTS), 12 to 16 June 2017

Watershed Ecology and Biogeochemistry (7.5 ECTS), September 14 - 20 2017


How to write and publish a scientific paper (4.5 HEC), 18 Aug 2016 - 26 Jan 2017

Soil systems: Analytical methods for integrating the chemical, biophysical interface in soils (3 ECTS), 5 Oct 2016 - 30 Nov 2016

Minerals in soils and sediments and their X-ray identification and quantification, 5.0 credits, 2016-04-11

Multivariate methods for ecologists 3 (+1.5 optional) ECTS, 2016-02-29


Organic micropollutants in the aquatic environment – measurements and transport processes 5 hp, 2015-04-13

Systems Analysis, Model Building and Simulation 6.0 (+1.5) ECTS, 2015-09-14

Carbon cycling: from molecular to global processes, 3 (+1.5 Optional) ECTS, 2015-09-30

Ecological stability vs resilience: straightening up concepts and making them useful for management 3.0 ECTS, 2015-10-26


Linear mixed models and experimental design with applications to agricultural field experiments 3 ECTS, 2014-01-27

Ecosystem Functioning: From Theory to Application Post graduate course, Biology and Environmental Assessment 3 ECTS, 2014-11-17

X-ray image processing and analyses 3.0 credits, 18 - 21 November 2014.


How to write and publish a scientific paper 3 ECT, 3 September - 12 November, 2013

Statistics in Practice, 2013-09-06

Research communication with the media: training and skills acquisition 2 HEC, 2013-10-01

Biogeochemical cycles at different scales 3 HEC, 2013-10-21


Research communication with the media: training and skills acquisition 1.5 HEC, 2012-03-06

Biogeochemical cycles at different scales 3 ECTS, 2012-03-12

The role of DOC and DON in plant-soil C and N cycling 5.0 HEC, 2012-03-20

Environmental Impact Assessment (EIA) for Natural Scientist 3 HEC, oct-nov 2012


Soil systems: Integrating the chemical & biophysical interface in soils, 2011-03-02

Ecosystem services in soil and water research 3-4 ECTS, May-June 2011


An introduction to R and MS Access (1.5 ECTS), February 2010

Constraints on decomposition, March 2010

PhD-course 'Soil Organic Matter Modeling'


PhD-course "Climate impacts on terrestrial and aquatic ecosystems"

PhD-course "Legumes: Plant - soil interactions and agricultural applications"

Biogeochemical cycles at different scales, april 2009


Soil and Water Chemistry Modelling 5 (+2 optional) ECTS, May 2008

PhD-course ''Modelling of chemical and hydrological processes using PHREEQC''

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