From 5deb9734033c9525fc3f44ee230c91c4801a0b5c Mon Sep 17 00:00:00 2001 From: Daniel Vedder <daniel.vedder@idiv.de> Date: Tue, 30 Jul 2024 11:31:16 +0200 Subject: [PATCH] Largely completed skylark ODD closes #19 --- docs/src/odd.md | 2 +- docs/src/skylark.md | 120 +++++++++++++++++++++++++++++++++++--------- 2 files changed, 98 insertions(+), 24 deletions(-) diff --git a/docs/src/odd.md b/docs/src/odd.md index bfc2a65..fb8b9d6 100644 --- a/docs/src/odd.md +++ b/docs/src/odd.md @@ -40,4 +40,4 @@ The model description follows the ODD (Overview, Design concepts, Details ## 7. Submodels -## Sources +## 8. References diff --git a/docs/src/skylark.md b/docs/src/skylark.md index 09ac908..bc2dcff 100644 --- a/docs/src/skylark.md +++ b/docs/src/skylark.md @@ -27,24 +27,24 @@ when disturbance (e.g. mowing, harvesting, tillage) takes place. The simulated individuals (a.k.a. agents) are mature [skylarks](species#Skylark). Each skylark is characterised by the following variables: -- **ID:** A unique identifier for this individual, which can be used to link it to its parents +- `ID` A unique identifier for this individual, which can be used to link it to its parents and its offspring. -- **sex:** Male or female. +- `sex` Male or female. -- **phase:** The individual's current stage in the annual/life cycle. May be one of: `migration`, +- `phase` The individual's current stage in the annual/life cycle. May be one of: `migration`, `nonbreeding`, `territorysearch`, `occupation`, `matesearch`, `nesting`, `breeding`. -- **position** The individual's position in the simulated landscape. +- `position` The individual's position in the simulated landscape. -- **mate** The ID of the individual with which this individual has mated this year, if any. +- `mate` The ID of the individual with which this individual has mated this year, if any. -- **territory** A list of coordinates of the positions in the landscape that this individual +- `territory` A list of coordinates of the positions in the landscape that this individual claims as its nesting and feeding territory. -- **nest** A coordinate giving the location of the currently active nest. +- `nest` A coordinate giving the location of the currently active nest. -- **clutch** The number of juvenile (i.e. not yet independent) skylarks that this individual is +- `clutch` The number of juvenile (i.e. not yet independent) skylarks that this individual is currently raising. @@ -73,7 +73,7 @@ breeding season is over. - `occupation`: The male moves at random about its territory until the breeding season is over. Then it changes its phase to `nonbreeding`. (*Note:* Skylark males actively help with feeding their chicks. However, feeding is only modelled indirectly here, through the process of habitat - selection when the male forms its territory.) + selection when the male forms its territory - see section 4.1.) - `nesting`: The female selects a suitable location within the male's territory for the nest. Building the nest and laying eggs takes a number of days, during which she does nothing else. @@ -96,52 +96,120 @@ If it is, she changes her phase to `nonbreeding`. ### 4.1 Basic principles -### 4.2 Emergence - +This model assumes that the two most important drivers of skylark distribution and abundance +are **habitat availability** and **juvenile mortality** (see literature below). The factors +and processes affecting these are therefore given the most attention in the model, while other +factors and processes are only included superficially, indirectly, or not at all. Specifically, +this means that the phases `territorysearch`, `nesting`, and `breeding` are the most relevant +and detailed parts of the model, as these determine the selection of habitat and the survival of +offspring. + +Furthermore, the model concentrates on predation and anthropogenic disturbance (through management +actions such as mowing) as the main causes of juvenile mortality. Other causes, such as hunger +or bad weather, are currently ignored as they are usually not significant. + +The focus on habitat availability and juvenile mortality opens up two avenues by which agricultural +management influences skylark populations. First, the farmers' choice of crops and date of sowing +determines the quality of the habitat when skylarks select a territory. (For example, unlike summer +grain, winter grain is already so high and dense in spring that it is generally avoided for nesting.) +Secondly, the frequency and timing of management actions (especially mowing) is a major cause of +brood loss. This means that there are direct causal links between agriculture and population trends. + +Concentrating on these two drivers allows the rest of the model to be kept simple, reducing both the +scientific complexity and computational costs. Thus, foraging movement (both during and after the +breeding season) can be ignored or represented as random movement, as it does not directly impact +either of the drivers. Likewise, chick growth and winter migration are represented very simply. -Patterns that can be used for validation with POM: +### 4.2 Emergence -- territory size +Multiple patterns emerge from the basic principles outlined above. The most important are listed here: -- *TODO* +- **Territory size and population density:** The model assumes that skylarks occupy only as much + area as they need to satisfy their nesting and foraging requirements, and that population size is + limited by the amount of available habitat. This means that territories in high-quality habitat + are smaller than in low-quality habitat. Scaling up, this leads to a pattern whereby population + densities are highest in open landscapes with a diversity of crops, grassland, semi-natural habitat, + and lower in landscapes with low habitat diversity or many woody features. + +- **Ecological traps:** Jenny (1990) describes a strong ecological trap effect whereby skylarks avoid + winter grain crops, preferentially nesting in more open grassland sites. However, the mowing + frequency associated with modern agriculture means that nest loss in grassland is almost assured, + since there is insufficient time between two mowing dates to raise a brood. This means that landscape + composition leads skylarks to breed in habitats that have a high mortality, resulting in population + declines. ### 4.3 Adaptation -- habitat choice +In the model, skylarks primarily adapt to their surroundings by choosing suitable territories. +These are chosen by evaluating the quality of surrounding habitats for breeding and foraging, +and occupying as much area as needed to satisfy requirements (see section 7.1). ### 4.4 Objectives +Skylarks' main objective in the model is to have sufficient habitat available to raise a brood. +Habitat quality is calculated as a function of habitat type, vegetation height, vegetation cover, +and distance to vertical structures (see section 7.1). + ### 4.5 Learning +The model includes no learning by individuals. + ### 4.6 Prediction -### 4.7 Sensing +The model includes no predictions by individuals. -- habitat quality (type, height, cover) +### 4.7 Sensing -- proximity of conspecifics +Skylarks can perceive the landscape structure in a given radius around them (habitat type, +vegetation height and cover). They can also see nearby conspecifics and are aware of the territories +claimed by other individuals. When mating, they recognise whether another individual already has a +mate, and mated individuals share information about their territory and brood status. ### 4.8 Interaction -- mating +The model includes two direct forms of interaction. First, during mating, females move around the +landscape looking for males who have a territory but no mate yet. Once they have found one, the +two individuals set each other as their mate. Secondly, after the breeding seasons, individuals +move around the landscape, keeping close to other individuals in their vicinity (flocking behaviour). -- flocking +There are also indirect interactions, in that there is a competition for habitat (territory that has +been claimed by one male cannot be occupied by another) and males (males that have mated with one +female will not mate with another in the same season). ### 4.9 Stochasticity +Stochasticity is used when modelling mortality and movement. Predation mortality is modelled as an +age- and habitat-dependent probability, while migration mortality is a simple probability. Dispersal +movement (when searching for a territory or a mate) is modelled as a random walk, as it is assumed +that skylarks are not significantly impeded in their long-range movement by habitats that are +unsuitable for foraging or nesting. Foraging movement by the male and by non-breeding individuals is +also random, as it is desirable to show movement (to help model analysis) but unimportant to model +this exactly. + ### 4.10 Collectives +After the breeding season, skylarks move around in loose agglomerations (flocking behaviour). However, +this has no relevant ecological effect. + ### 4.11 Observation +*TODO* + ## 5. Initialisation +At the beginning of a model run, pairs of skylarks are created on grassland and agricultural land, +keeping a distance of 60m to vertical structures and allowing each pair approximately 3ha of +suitable habitat (an average territory size in agricultural landscapes). + +For details, see the [source code](https://git.idiv.de/persefone/persefone-model/-/blob/master/src/nature/species/skylark.jl?ref_type=heads) and the associated [documentation](nature#populations.jl). + ## 6. Input data -The general input to Persefone (i.e. maps and weather data) is described [here](gis). +The general input to Persefone (i.e. land use maps and weather data) is described [here](gis). The following extract from the [source code](https://git.idiv.de/persefone/persefone-model/-/blob/master/src/nature/species/skylark.jl?ref_type=heads) -lists the species parameters and their values as used by the Skylark model: +lists the species parameters and values used by the Skylark model, based on the literature cited below: ```julia @species Skylark begin @@ -176,9 +244,15 @@ end ## 7. Submodels +### 7.1 Territory formation + +*TODO* + +### 7.2 Juvenile mortality +*TODO* -## Sources +## 8. References - Bauer, H.-G., Bezzel, E., & Fiedler, W. (Eds.). (2012). Das Kompendium der Vögel Mitteleuropas: Ein umfassendes Handbuch zu Biologie, Gefährdung -- GitLab