timcdlucas / phdthesis Goto Github PK

There's more lit on group size that I should discuss and discuss why group size and population structure are not the same.

tag +social in jabref

As discussed with Colizza.
If invasion can occure in single pop, you don't need space.

Check when printed.

I added more detail to who did what in MEE paper.

6e6c98a

Check that it's all fine.

vogwill2009dispersal: our findings suggest that dispersal and natural enemies can interact to drive spatially synchronous population fluctuations that decrease stability

zhao2008population gives a value. But it's not a theory paper.

Depending on the mechanism by which structure affects richness, global change might predict increased richness in the majority of species. Or more new pathogens. Or more virulent paths.

Useful for intro to +ch2.

See discussion of ch3.

See Henry's paper for an example.

Probably applies to chapter 2 and 4 as well.

Bioecological Drivers of Rabies Virus Circulation in a Neotropical Bat Community

Cross species: "Positive animals were recorded in 14 out of the 30 species analysed"
monospecific colonies favoured infection?

"the high number of apparently healthy and seropositive bats indicates that, at least in a large number of cases, the clinical expression of the virus, if any, is undetectable"

Check all image captions.
Should be standalone.

This is currently a bit weak.

Add incfreased T-cells e.g. fenton2010applying

Add acquired immune response. etc.

WHY do I think there was no effect.

\subsubsection{Dispersal does not affect pathogen richness}

Irrespective of the network topology used, at very high dispersal rates a population will be well mixed.

\subsubsection{Network connectedness does not affect pathogen richness}

This is in direct contrast to \cite{campos2006pathogen}.
However, the model in \cite{campos2006pathogen} is a contact network, so increasing the connectedness increases the chance of succesful transmission events for the first few transmission generations.
This lends support to the idea that I found no affect of connectedness due to the dominance of local dynamics.

Is not enough.

Reinclude line explain why distrRange is worse than random. Wasn't working with rinline.

On average (mean
weighted by Akaiki weights) there is a negative relationship between gene flow and
viral richness (β = − 0.27, variance = 0.06) despite the apparent positive relationship
in Figure 3.

Add the actual bivariate result for this.

https://cran.r-project.org/web/packages/caper/caper.pdf

"The model is fitted using a data frame reduced to complete row cases to eliminate missing values.
In order to ensure that the models fitted using different subsets of the data are comparable, the
whole data frame data is reduced to complete cases."

Need to check I'm not dropping rows.

beta = 0.2: χ 2 = 9.44, df = 2, p = 0.01.

But order of p(invasion) does not increase or decrease with beta.

Maybse post hock tests and discuss.
Or run more sims here.

Would be good to see whether diversity is robust to different detection methods.

Need to use a proper virus taxonomy.
With a definition of virus species

Add explanations of point confidence intervals in figures.

Consider adding confidence ribbons to plots.

FSst anaylsis gives negative coefficient for mass. Needs discussing.

fstmtDNA <- fstallozyme <- function(fst){
  Nm <- 0.5 * (1 / fst - 1)
}

At the moment this is just a guess. I haven't really seen fst mtDNA equations. Bit confused.

Definitely want 1 species R0. Possible some idea of two species. Possibly Vespignani R*

Do all mammals for Chapter 3 general intro (previous studies). State that I am looking at mammals. Later state that my analysis is on bats (and mention that it's all bats that I could find data for.)

I had a brief look and didn't find many others.

Do I want to include group size?

Plotted natalensis distr and it was two tiny specks. Don't understand.

I don't like the bibliography having ampersands. Work out how to change.

Active debate in disease ecology centers on which measure is preferable for species with various social systems or for different scales of measurement, and on the consequences for modeling disease transmission 16, 17, 18, 19, 20 and 21;

A clarification of transmission terms in host-microparasite models: numbers, densities and areas
How does transmission of infection depend on population size?
A generalized model of parasitoid, venereal and vector-based transmission processes
Modelling transmission: mass action and beyond

Miniopterus natalensis: can't match 0.241 value to anything in paper (not mean of pairwise.)
This is from miller2003strong

There's another Miniopterus natalensis record, so ignore.

Only Chapter 3 is up to date.

In each simulation the population was seeded with 10 sets of 200 infected indi-
viduals of disease 1. There groups were seeded into randomly selected colonies with
replacement.

Don't think randomly selected anymore.

Check throughout

Totally depends on how strong I make the area interaction. Kind of false test.

Check that removing the interaction term in N. Subspecies doesn't make structure unimportant.

Possible that having just the one interaction biases analysis.

Not out but worth watching out for.

Colizza dog paper
Colizza bat paper

Olival. Richness does predict zoonotic potential.

More work I did that I lost. Probably can find.

Colours in fig 5.5 need to match 5.4 and 5.6

Figure 5.7 has very small text. Maybe better to cowplot.

Latex subfig labels are serif while cowplot are sanserif.

THE figure FOR #3 is hard to read.

Bin data and plot subsp ~ effort with colour as 1 vs >1 virus.

Do chapter 3 analysis with species with only 1 virus.

Currently simply calculating variance of coefficients. But I think a lot of models are identical (i.e. without bootstrapped var.) How should I deal with this?

+ch3 tree should include all species in both analyses. But it doesn't

Both nSpecies and fst analyses have species not in the bat clocks rocks phylogeny.

For now I am only using species in the phylogeny for nSpecies and will manually add species for fst. The species are all in genera that are represented in the three, so I will make these polytomys I guess.

to directly estimate infection durations in wild populations. But it seems that these
infections might be long lasting ().

Probably some more references.

Check particularly p values but also other values for 10^-50 type silly numbers.