Port of models from Keeling and Rohani

[sdwfrost]

See http://www.modelinginfectiousdiseases.org/

[LloydChapman]

I'd like to implement the SEIR models from Keeling and Rohani and an SEIR version of the spatial kernel model in chapter 7, with an extension for households, in R, Matlab (Octave) and Julia.

[t-pollington]

Chapter 4. Section 2.2 Vectored transmission, program 4.4. It's a multi-host SIR model in R(using desolve) as I'm interested in vector-transmitted diseases. DONE FOR R VERSION: Find in shared/Multi-host SIR

[t-pollington]

Found an online version of the Keeling & Rohani book here http://acces.ens-lyon.fr/acces/thematiques/sante/epidemiologie/GlossairEpidem/livre_K-R.pdf

[theresasophia]

I am interested in implementing models for host heterogeneities from Chapter 3 in R

[emmaaccorsi]

I'm also interested in working on the models from Chapter 3 in R, in particular 3.1 and 3.2. Are you planning to implement all of Chapter 3?

[rek160]

I am interested in implementing models from Chapter 8 in Julia

[iholmdahl]

I'm interested in the metapopulation models for animals and humans from chapter 7

[theresasophia]

I'm also interested in working on the models from Chapter 3 in R, in particular 3.1 and 3.2. Are you planning to implement all of Chapter 3?

No, I am interested in the age-structured models, so I could do 3.3 and/or 3.4.

[emmaaccorsi]

I'm also interested in working on the models from Chapter 3 in R, in particular 3.1 and 3.2. Are you planning to implement all of Chapter 3?

No, I am interested in the age-structured models, so I could do 3.3 and/or 3.4.

Perfect!

[lvcooper]

I'm interested in working on multi-strain/multi-pathogen models from Chapter 4.1 in R.

[iholmdahl]

I'm interested in the metapopulation models for animals and humans from chapter 7

Actually, switching for now to seasonal forcing from chapter 5

[eqmooring]

I am interested in, at least in the first instance, writing up 7.1 and 7.2 (basic spatial models) in R.

[eqmooring]

I'd like to implement the SEIR models from Keeling and Rohani and an SEIR version of the spatial kernel model in chapter 7, with an extension for households, in R, Matlab (Octave) and Julia.

Sounds good. I will initially focus on earlier models in Chapter 7.

[LloydChapman]

I'd like to implement the SEIR models from Keeling and Rohani and an SEIR version of the spatial kernel model in chapter 7, with an extension for households, in R, Matlab (Octave) and Julia.

Sounds good. I will initially focus on earlier models in Chapter 7.

I've decided to change tack and focus on implementing an SEIR version of the spatial kernel model in 7.5 and extended versions. I have however implemented the basic SEIR model in Chapter 2 in R and Julia.

[EBucksJeff]

I'm going to start working on 3.5 in R, if anyone isn't already?

[aineniamh]

I'm working through implementing models from Chapter 2 in python using widgets.

[rek160]

I am interested in implementing models from Chapter 8 in Julia

Have done 8.1 and 8.2 in Julia and now doing them in R

[emmaaccorsi]

I'm also interested in working on the models from Chapter 3 in R, in particular 3.1 and 3.2. Are you planning to implement all of Chapter 3?

3.1 and 3.2 are complete in R.

[sdwfrost]

Can you put finished models on the server, e.g. in shared/kr08/3_1, shared/kr08/3_2 etc., so I can review and integrate into the cookbook?

[HelenaStage]

Interested in 4.3 in Python.

[Federica-Giardina]

Starting 6.1 and 6.2 in R if nobody is working on it

[emmaaccorsi]

Can you put finished models on the server, e.g. in shared/kr08/3_1, shared/kr08/3_2 etc., so I can review and integrate into the cookbook?

Yes, they should be uploaded there now. Thanks!

[c-lack]

I'm going to make 7.8 in JavaScript. It'll be on Observable though, so not on the server.

[t-pollington]

QUIRK IN LSODA() FOR R_DESOLVE

When using the init or parms arguments for lsoda() make sure they are named. In most of the examples they are explicitly named i.e. parms <- c(beta=0.1,gamma=0.05) which doesn't just give 0.1 & 0.05 as information to the ODE function but also gives the column labels "beta" and "gamma". Doing parms = c(beta,gamma) isn't sufficient as it won't inherit the variable labels. To fix this either: i) After doing parms = c(0.1,0.05) do names(parms) = c("beta","gamma") where the labels match the equation notation in sirODE() function. ii) In sirODE(times, init, parms){ Add some lines that define the labels wrt the parms argument of this function i.e. beta = parms[1] gamma = parms[2]

then you can continue with the default: dS <- -betaSI dI <- betaSI-gammaI dR <- gammaI

}

[emmaaccorsi]

I'm doing 3.1 and 3.2 in Julia.

[theresasophia]

We will implement 3.3 and 3.4 in Julia

[EBucksJeff]

3.5 done in R and in the shared folder.

[ersouthall]

I'm doing 7.6 (FMD Spatial model) in observable

[nayantaraw]

I am working on 5.1 and 7.2 from Keeling and Rohani in R.

[emmaaccorsi]

I'm doing 3.1 and 3.2 in Julia.

3.1 and 3.2 in Julia are complete and in the shared folder.

[rek160]

I am interested in implementing models from Chapter 8 in Julia

Have done 8.1 and 8.2 in Julia and now doing them in R

Also doing 8.1 in Observable

[iholmdahl]

I've done 5.1 and 5.4 in R and Julia, now doing in Observable

[cnd27]

Working with 6.3 in Julia

[eqmooring]

I am interested in, at least in the first instance, writing up 7.1 and 7.2 (basic spatial models) in R.

7.1 in R using deSolve plus an Intro file with documentation on using matrices for metapopulation calculations are in the shared/kr08 folder. I am now working on 7.1 in Julia.