Skip to content
Snippets Groups Projects

Repository graph

You can move around the graph by using the arrow keys.
Select Git revision
  • master default protected
1 result
Created with Raphaël 2.2.018Nov30Mar2442Feb12Nov23Feb17Dec13Oct9628Sep241921Jul24Jun19171026May15421Apr20Merge branch 'cecilia_h-master-patch-76215' into 'master'mastermasterModified README.md to update the citation of the (now published) paperSmall modifications to format figures for publicationsModifications made during the revision of the paper (round 1)Update gitignoreSome scripts were missing (_Functions_MCMC.R and _Species_Fitting.R) to properly use the code. They're back.This repository contains code used in the following paper.Test code cleaned for Plos CB submissionWithin-host model fitted to needle vs mosquito infections, dead vs survive outcomesMerge branch 'master' of https://git.wur.nl/bosch123/riftvalley_withinhostModel from Petrie et al. 2013 Reducing Uncertainty in Within-Host Parameter Estimates of Influenza Infection by Measuring Both Infectious and Total Viral Loadupdating gitignore file (.Rhistory)First try at optimizing sd for the mcmc sampling. Results saved in Output. Nice acceptance rates but not always converging in the right place. Extreme acceptance rate (0 and 1) for some parameters. 15 optimization rounds of MCMC with 1000 iterations each lasted 25mins.Update bibliographyA bit more details on what was done in other papers with dual-measures (RNA and TCID)Model modification to differenciate between the observation process (RNA measures only M segments) and the entirety of non infectious particles. Need to decide whether empty particles are counted as non infectious, depends if they play a role in our self-limited infection modelsfix issue: do.call needs a list of parameters, each must have a name to be correctly passed to simulate_basic_model. Need to make sure that allpars is made of named vectors only.Fix file treeRemoved wrapper adding confusion and lacking transparencyFixing file treeHackathonMCMC algo written from scratch (Functions_MCMC)Upload Example Home cooked MCMCCode to test basic model (agreed on 21/09 meeting, see manuscript_draft "Target cell-limited model" )Script Rift_WithinHost_Temperature.R exploring correlations between viral loads and temperature dataDocument stating modelling hypothesis and research questions needing discussionTemporary new directory "start_fresh" where I proceed to clean the code to start with a clean state.Segment analysis : corrected confidence interval function (sample_from_CI) + compute CI of contribution of covariance (~ non randomness of packaging efficiency)Segment analysis: likelihood ratio test to justify the use of species-specific parameters. Contribution of covariances to complete particles.Segment analysis : going further on analysing the results, comparing fits of different datasets + quantifying the contribution of covariancesUpdated segments scripts to convert covariance to correlation, and compute confidence intervals on the fits by drawing 1000 combinations of parameters (normal distribution).Segment script modified to automatize the possibility to fix/estimate given parameters and perform likelihood ratio tests.Segment script modified to test 3 nested models:Segments script updated to include correlation between segmentsAdded RITRA data and scripts to create fitR models with different likelihoods and test their performance on simulated datadata path changed to match script. Comment added in codeUpdate Data/RVF_invitro_segmentcounts.csvUpload script to analyse segment count dataDelete Rift_Segments_Main.RUpload script to analyse segment counts