sick-bees issueshttps://git.ufz.de/ecoepi/sick-bees/-/issues2021-08-25T09:56:40+02:00https://git.ufz.de/ecoepi/sick-bees/-/issues/30Consider decontaminating infection2021-08-25T09:56:40+02:00Adam ReicholdConsider decontaminating infectionAs described in [Eristalis flower flies can be mechanical vectors...](https://www.nature.com/articles/s41598-021-95323-w)
> When vectors ingest parasites at a floral resource, they also remove them from existing floral hotspots; mechani...As described in [Eristalis flower flies can be mechanical vectors...](https://www.nature.com/articles/s41598-021-95323-w)
> When vectors ingest parasites at a floral resource, they also remove them from existing floral hotspots; mechanical vectors redistribute parasites across the landscape by increasing the number of hotspots, but at the expense of decreasing the average parasite load per hotspot.
we could generally consider infection to have a decontaminating effect on the flower either by modelling contamination as a discrete or even continuous degree instead of a binary state or by introducing a decontamination probability associated with infection events.https://git.ufz.de/ecoepi/sick-bees/-/issues/29Look into correlation between insect body size and amount of contamination2021-08-25T09:56:40+02:00Adam ReicholdLook into correlation between insect body size and amount of contaminationAs described in [Eristalis flower flies can be mechanical vectors...](https://www.nature.com/articles/s41598-021-95323-w)
> Susceptible pollinators are more likely to acquire fecal-orally transmitted parasites from large volumes of infe...As described in [Eristalis flower flies can be mechanical vectors...](https://www.nature.com/articles/s41598-021-95323-w)
> Susceptible pollinators are more likely to acquire fecal-orally transmitted parasites from large volumes of infected feces when foraging, as large fecal events take longer to evaporate, thus allowing parasites to survive for a greater period of time outside of a host.
we could make the decontamination rate depend not just on the flower patch species, but also on the insect species (which should be trivial to implement as this parameter is used only when creating the decontamination event), to understand which effects the correlation between insect body size and the amount of contamination could have on the transmission dynamics.https://git.ufz.de/ecoepi/sick-bees/-/issues/28Investigate mechanical vector scenario2021-08-25T09:44:03+02:00Adam ReicholdInvestigate mechanical vector scenarioAs described in [Eristalis flower flies can be mechanical vectors...](https://www.nature.com/articles/s41598-021-95323-w) and similar to the incompetent host scenario we look at for our niche overlap experiments, we could consider an inf...As described in [Eristalis flower flies can be mechanical vectors...](https://www.nature.com/articles/s41598-021-95323-w) and similar to the incompetent host scenario we look at for our niche overlap experiments, we could consider an infection mode where there will only be a fixed number of contamination events before recovery to capture the idea that the pathogen passes through the host without replicating so that only a fixed amount of pathogen can be shed.https://git.ufz.de/ecoepi/sick-bees/-/issues/27Consider Windschaften effect2021-05-18T08:56:47+02:00Adam ReicholdConsider Windschaften effectThe competitive effect of the attractiveness of a resource patch described in https://link.springer.com/article/10.1007/s10980-004-0678-0 could probably be integrated into this model by sorting patches by distance instead of randomly whe...The competitive effect of the attractiveness of a resource patch described in https://link.springer.com/article/10.1007/s10980-004-0678-0 could probably be integrated into this model by sorting patches by distance instead of randomly when performing sequential acceptance.https://git.ufz.de/ecoepi/sick-bees/-/issues/25Complete missing parts of ODD2021-08-25T09:41:27+02:00Adam ReicholdComplete missing parts of ODD- [x] The ODD section on parameters is just code.
- [ ] The ODD section on design concepts is not prose but a collection of bullet points.
- [ ] Not all the submodels are documented.- [x] The ODD section on parameters is just code.
- [ ] The ODD section on design concepts is not prose but a collection of bullet points.
- [ ] Not all the submodels are documented.Adam ReicholdAdam Reicholdhttps://git.ufz.de/ecoepi/sick-bees/-/issues/22Make source code optional part of ODD2021-03-02T13:19:59+01:00Adam ReicholdMake source code optional part of ODDThe fallback position would be a build-time flag to choose between code blocks and a prose description of these code blocks. The ideal result would probably be a document in which the code blocks can be shown/hidden interactively.The fallback position would be a build-time flag to choose between code blocks and a prose description of these code blocks. The ideal result would probably be a document in which the code blocks can be shown/hidden interactively.https://git.ufz.de/ecoepi/sick-bees/-/issues/17Investigate effect of particularly attractive flower patches on pathogen tran...2020-12-09T12:44:58+01:00Adam ReicholdInvestigate effect of particularly attractive flower patches on pathogen transmissionIn the [discussion](https://git.ufz.de/ecoepi/sick-bees/-/merge_requests/83#note_77562) of artificial correlation due to ordering in spatial indexes, we concluded that it would be nice to consider similar correlations or rather concentra...In the [discussion](https://git.ufz.de/ecoepi/sick-bees/-/merge_requests/83#note_77562) of artificial correlation due to ordering in spatial indexes, we concluded that it would be nice to consider similar correlations or rather concentrations induced via the preferences instead of accidental mechanisms to better understand the effect of particularly attractive flower patches on pathogen spread, i.e. if this could really reduce pathogen prevalence.https://git.ufz.de/ecoepi/sick-bees/-/issues/15Investigate further impairment mechanisms due to disease2020-11-17T13:26:26+01:00Adam ReicholdInvestigate further impairment mechanisms due to disease- [ ] Reduced memory capacity and effectiveness
- [ ] Reduced vision range and effectiveness
- [ ] Reduced movement speed
- [ ] Compare reduced vision effectiveness with reduced flower patch density
- [ ] Death- [ ] Reduced memory capacity and effectiveness
- [ ] Reduced vision range and effectiveness
- [ ] Reduced movement speed
- [ ] Compare reduced vision effectiveness with reduced flower patch density
- [ ] Deathhttps://git.ufz.de/ecoepi/sick-bees/-/issues/13Systematically investigate the effect or within-colony transmission2020-09-03T17:39:19+02:00Adam ReicholdSystematically investigate the effect or within-colony transmissionhttps://git.ufz.de/ecoepi/sick-bees/-/issues/11Consider mass flowering crop scenario2020-08-04T09:56:33+02:00Adam ReicholdConsider mass flowering crop scenarioThe mass flowering crop scenario, i.e. a single flower patch species will double the productivity and hence half the number of flower patches seems to be basically twice as bad as the narrow diet scenario. This seems reasonable as both i...The mass flowering crop scenario, i.e. a single flower patch species will double the productivity and hence half the number of flower patches seems to be basically twice as bad as the narrow diet scenario. This seems reasonable as both insect species have half the flower patches available to them instead of only the first one.
![prevalence](/uploads/17ce435cda1b55c595ab6f9ef01aa778/prevalence.png)https://git.ufz.de/ecoepi/sick-bees/-/issues/8Investigate water foraging of bumble bees2020-07-20T18:33:33+02:00Adam ReicholdInvestigate water foraging of bumble beeshttps://git.ufz.de/ecoepi/sick-bees/-/issues/7Increase detail of various biological processes2020-07-20T14:47:08+02:00Adam ReicholdIncrease detail of various biological processes- [ ] Specific diurnal rhythms and temperature-controlled level of activity
- [ ] Seasonal increase of workers in bumble bee colonies
- [ ] Specific seasonality of pollinator activity especially emergence from overwintering
- [ ] Specifi...- [ ] Specific diurnal rhythms and temperature-controlled level of activity
- [ ] Seasonal increase of workers in bumble bee colonies
- [ ] Specific seasonality of pollinator activity especially emergence from overwintering
- [ ] Specific seasonality of plant flowering including mass flowering crops
- [ ] Floral consistency, i.e. only one species of flower per foraging trip
- [ ] Explicitly model sex, mating and oogenesis include sexual foraging differences
- [ ] Impose weather as short-term effect on pollinator activityhttps://git.ufz.de/ecoepi/sick-bees/-/issues/6Adjust foraging rate for capacity utilisation2020-11-17T13:48:42+01:00Adam ReicholdAdjust foraging rate for capacity utilisationhttps://git.ufz.de/ecoepi/sick-bees/-/issues/5Adjust sampling efficiency of simulated observer w.r.t. individual size2020-08-25T14:48:40+02:00Adam ReicholdAdjust sampling efficiency of simulated observer w.r.t. individual sizehttps://git.ufz.de/ecoepi/sick-bees/-/issues/4Add honey bees as background activity2020-07-20T14:38:28+02:00Adam ReicholdAdd honey bees as background activityAs honey bees a generalist foragers, numerically dominant and highly dispersive, model them as a background activity. This could spatially and temporally explicit, but should be an aggregate effect on e.g. the depletion of plant resources.As honey bees a generalist foragers, numerically dominant and highly dispersive, model them as a background activity. This could spatially and temporally explicit, but should be an aggregate effect on e.g. the depletion of plant resources.https://git.ufz.de/ecoepi/sick-bees/-/issues/3More detailed description of nesting processes2020-07-20T14:46:03+02:00Adam ReicholdMore detailed description of nesting processes- [ ] Solitary bees make multiple foraging trips per brood cell
- [ ] Some solitary bees need to collect nest building materials
- [ ] Different species of solitary bees and hoverflies need different kinds of nesting sites
- [ ] Solitary bees make multiple foraging trips per brood cell
- [ ] Some solitary bees need to collect nest building materials
- [ ] Different species of solitary bees and hoverflies need different kinds of nesting sites
https://git.ufz.de/ecoepi/sick-bees/-/issues/2Implement distinct exploration modes for solitary and bumble bees2021-03-30T16:19:24+02:00Adam ReicholdImplement distinct exploration modes for solitary and bumble bees- [ ] Solitary bees use a two-scale approach with direct movement towards clusters and random exploration therein
- [ ] Bumble bees follow fixed routes of major and minor plants with small random variations, i.e. traplining- [ ] Solitary bees use a two-scale approach with direct movement towards clusters and random exploration therein
- [ ] Bumble bees follow fixed routes of major and minor plants with small random variations, i.e. traplininghttps://git.ufz.de/ecoepi/sick-bees/-/issues/1Select insect and plant species expected at experimental sites2020-07-28T20:40:50+02:00Adam ReicholdSelect insect and plant species expected at experimental sites- [ ] Determine which insect and plant species are expected at which experimental sites
- [ ] Find empirical studies for as many per-species parameters as possible- [ ] Determine which insect and plant species are expected at which experimental sites
- [ ] Find empirical studies for as many per-species parameters as possible