Add explanations of point confidence intervals in figures.

Consider adding confidence ribbons to plots.

Not out but worth watching out for.

Colizza dog paper
Colizza bat paper

Olival. Richness does predict zoonotic potential.

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.

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

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

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

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.

Check when printed.

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

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.

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?

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

THE figure FOR #3 is hard to read.

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

Check throughout

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

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

Latex subfig labels are serif while cowplot are sanserif.

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.

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.

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

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

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?

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

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

Possible that having just the one interaction biases analysis.

Only Chapter 3 is up to date.

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.

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

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

Probably some more references.

This is currently a bit weak.

Add incfreased T-cells e.g. fenton2010applying

Add acquired immune response. etc.

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.

See Henry's paper for an example.

Probably applies to chapter 2 and 4 as well.

Do chapter 3 analysis with species with only 1 virus.

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"

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.

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

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

Colours in fig 5.5 need to match 5.4 and 5.6

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.

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

6e6c98a

Check that it's all fine.

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

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

Check all image captions.
Should be standalone.