* Bigger sim (#68)

* prevent printing wall of nulls

* fix plotting to avoid hardcoding range of prediction

* adjust truncation selection to fix missing samples

* expand simulation size

* update figure to use bland altman as it is more informative

* docs

* include labels

* add another plot to help with the explanations

* tweak figure

* update figures

* add new parameters

* fix bug where csv is parsed incorrectly

* adjust simulation duration and schedule to work with new params

* add some notes about the prior distribution they used

* describe prior

* remove repl code

* remove unneccesary return

* remove cruft

* constrain optimisation to get more plausible value

* fix nelder mead initial condition bug

* lint

* add distributions to specify prior

* lint

* add sanity check

* lint test to make easier to read

* remove some cruft

* specify the simulation seed in the config file

* make exports explicit

* simplify llhd calculation

* remove unused function

* simplify precondition

* guard against numerical error

* use eithers instead of throwing an error

* get a reasonable time series view going

* Simulation study no scheduled observations (#70)

* lint

* provide option to toggle scheduled observations

* Minimiser (#71)

* switch to powell minimisation

* remove remaining usage of hmatrix-gsl

* remove cruft

* condition against extinction in the time series simulation study

* enforce the condition that birth rate exceeds removal rate

* Ape sim (#72)

* condition against extinction in the time series simulation study

* enforce the condition that birth rate exceeds removal rate

* include a script to simulate with ape

* write cli for simulation

* include plotting in simulation script

* remove old helper script

* add some documentation

* Mcmc (#73)

* sketch out mcmc app and demo

* include a script to format the data for mcmc

* run mcmc and look at output

* include rho sampling in cli

* extend mcmc and ape viewer to work with rho

* make it easier to toggle rho sampling

* include a check to handle the case of less than a cherry in the tree

* add posterior marginal plots to ape simulation example

* remove demo file

* avoid external references in viewer file

* include missing cleanup files

* make it easier to toggle rho sample

* Maybe precision bug (#74)

* expose concerning lack of precision

* validate input data

* lint

* improve reporting if data is invalid

* make sure a sufficiently large number of digits are used in the json

* Timing it again (#75)

* include results from re-running the timing experiments

* include extra data from experiment

* All outbreaks (#76)

* include extracted values

* transcribe sequence counts

* include extracted values

* doc

* include total cases in table

* get the australian outbreak example working

* condition the simulations on at least a cherry

* doc

* remove uneeded dep

* record the final prevalence in the output

* doc

* Mcmc prevalence (#77)

* record the final prevalence in the mcmc

* include visualisation of final prevalence

* tweak figure

* ensure all traceplots are included

* linter

* include missing library

* linter

* Agg ex (#78)

* switch to using make

* silence library imports

* doc

* scaffold for new example

* doc and extend cleaning

* plot marginals and restructure slightly

* include marginal plot

* lint

* include a splom

* remove some burn-in

* include r-naught plot

* include prevalence estimate

* look up actual values from the jhu

* include capability to work with aggregated or scheduled data

* run analysis of aggregated data too

* extend ape-sim to export aggregated data too

* extend simulation duration to generate better figure

* produce additional plots from ape-sim and save to rds

* get simple aggregated example working neatly

* Ci calibration again (#79)

* sketch program

* get whole pipeline working

* lint

* include a dummy file to manage plotting

* build basic viewer index

* include parameter estimate figures

* include the size and number of simulations

* boost mcmc sample size

* ensure consistent times in command string

* include a plot to show the effectie sample sizes

* fix mcmc runner so it takes a cla and loops the correct number of times

* improve make file

* report coverage table

* lint

* include tables of parameter coverage

* lint

* include latest results

* Double count (#80)

* avoid double counting in the summary tables

* improve one of the figures

* lint

* Pdfs flag (#81)

* include flag to make pdfs of images

* update simulation results

* Ape sim 2 again (#82)

* scale up simulation

* report more summary statistics and diagnostics

* add figure files

* Thinning (#83)

* lint

* pass thinning factor through as cla

* add helper function for subsetting lists

* include thinning and burnin for mcmc

* enable burnin in config creation

* implement consistency demonstration figures

* Big ci result (#84)

* big ci results

* include summary data for re-generating figures

* Splom again (#85)

* lint

* style splom

* include extra figures and summary files

* Timing again again (#86)

* display figures in sensible size

* settings that produce minimally good result

* update timing results

* add missing index.html