Ecosyste.ms: Issues

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GitHub / canmod/macpan2 issues and pull requests

#165 - SHIVER model in library

Issue - State: open - Opened by stevencarlislewalker 9 months ago

#164 - Testing in an SIR model in model library

Issue - State: open - Opened by stevencarlislewalker 9 months ago

#163 - change log for 1.0.0

Issue - State: open - Opened by stevencarlislewalker 9 months ago

#162 - calibration stuff

Pull Request - State: closed - Opened by stevencarlislewalker 9 months ago

#160 - tmb_model.Rmd crashes/dumps core/segfaults

Issue - State: open - Opened by bbolker 9 months ago - 2 comments

#157 - tricky argument match problem with .phases

Issue - State: closed - Opened by bbolker 9 months ago - 3 comments

#157 - tricky argument match problem with .phases

Issue - State: open - Opened by bbolker 9 months ago - 2 comments

#156 - COVID wastewater model to match macpan1.5 implementation

Issue - State: open - Opened by stevencarlislewalker 10 months ago - 2 comments

#155 - Merge `refactorcpp` with `main`

Issue - State: closed - Opened by stevencarlislewalker 10 months ago - 8 comments

#152 - Design outline of a multi-engine interface for calibration

Issue - State: closed - Opened by stevencarlislewalker 10 months ago - 1 comment

#148 - stop diverging refactorcpp from main

Issue - State: closed - Opened by stevencarlislewalker 10 months ago - 6 comments
Labels: documentation, infrastructure, calibration

#147 - add an SIR model with vital dynamics to the model library

Issue - State: closed - Opened by papsti 11 months ago - 4 comments
Labels: model library

#146 - Informative message if two LedgerData objects use the same column name

Issue - State: open - Opened by stevencarlislewalker 11 months ago
Labels: documentation, model space operations

#145 - Calibration interface

Issue - State: open - Opened by stevencarlislewalker 11 months ago - 1 comment
Labels: calibration

#144 - Models in small and isolated locations with importation.

Issue - State: open - Opened by stevencarlislewalker 11 months ago
Labels: model space operations, model library

#143 - Alarm functions

Issue - State: open - Opened by stevencarlislewalker 11 months ago
Labels: model space operations, model library

#142 - Models of opinion dynamics

Issue - State: open - Opened by stevencarlislewalker 11 months ago
Labels: model space operations, model library

#141 - Models of vaccination following Dushoff/Park framework

Issue - State: open - Opened by stevencarlislewalker 11 months ago
Labels: model space operations, model library

#140 - Models of contact tracing

Issue - State: open - Opened by stevencarlislewalker 11 months ago
Labels: model space operations, model library

#139 - Linear chain expansion

Issue - State: open - Opened by stevencarlislewalker 11 months ago - 2 comments
Labels: model space operations

#137 - Informative error message when insufficient numbers of dots are used in vector names

Issue - State: closed - Opened by stevencarlislewalker 11 months ago - 1 comment
Labels: model definition files

#135 - add a basic Lotka-Volterra model to the model library

Issue - State: closed - Opened by papsti 11 months ago - 5 comments
Labels: documentation, model library

#134 - update model library with examples using new `mp_*()` spec

Issue - State: closed - Opened by papsti 11 months ago - 1 comment
Labels: documentation

#133 - have `macpan2` infer missing values in initial state vecs for internally calculated quantities?

Issue - State: closed - Opened by papsti 11 months ago - 1 comment
Labels: enhancement, engine adaptor

#132 - example for the `labelling_column_names` argument of `mp_index()`

Issue - State: open - Opened by papsti 11 months ago
Labels: documentation

#131 - clean up documentation of `mp_vector()` and `mp_set_numbers()`

Issue - State: open - Opened by papsti 11 months ago
Labels: documentation

#130 - Refactorcpp quickstart

Pull Request - State: closed - Opened by stevencarlislewalker 11 months ago

#129 - `mp_union` doesn't work on `Link` class

Issue - State: closed - Opened by papsti 11 months ago - 1 comment
Labels: bug

#128 - Append v2 of the quickstart with a structured model

Issue - State: closed - Opened by papsti 11 months ago - 1 comment

#127 - Draft v2 of the quickstart with a simple unstructured model

Issue - State: closed - Opened by papsti 11 months ago - 1 comment

#125 - Check whether we need `gcc` install instructions for Mac

Issue - State: closed - Opened by papsti 12 months ago - 8 comments
Labels: documentation

#124 - Issues installing v1.0.0 from `refactorcpp` branch

Issue - State: closed - Opened by papsti 12 months ago - 2 comments
Labels: bug

#123 - Add Matrix as an explicit dependency?

Issue - State: closed - Opened by papsti about 1 year ago - 3 comments

#122 - Update README.md

Pull Request - State: closed - Opened by papsti about 1 year ago

#121 - Breaking change somewhere between v0.0.3 and f4089a6

Issue - State: open - Opened by papsti about 1 year ago - 12 comments
Labels: bug, engine adaptor constructors

#120 - look into incorporating `AutomaticR0`?

Issue - State: open - Opened by papsti about 1 year ago - 2 comments

#119 - Adreport flag

Pull Request - State: closed - Opened by stevencarlislewalker about 1 year ago

#118 - Add `oor` remotes path to DESCRIPTION

Pull Request - State: closed - Opened by papsti about 1 year ago - 4 comments

#117 - Adreport flag

Pull Request - State: closed - Opened by stevencarlislewalker about 1 year ago - 1 comment

#116 - Refactorcpp

Pull Request - State: closed - Opened by stevencarlislewalker about 1 year ago - 5 comments
Labels: documentation, engine, engine adaptor, model definition files, engine adaptor constructors, model space operations

#115 - reference phac in readme

Pull Request - State: closed - Opened by stevencarlislewalker about 1 year ago - 1 comment

#114 - integrate `adaptivetau` for stochastic model simulation

Issue - State: open - Opened by papsti about 1 year ago - 1 comment

#113 - add `replace` methods complementary to `add`

Issue - State: open - Opened by papsti about 1 year ago - 3 comments

#112 - documentation for changes-in-place + add/insert methods

Issue - State: open - Opened by papsti about 1 year ago
Labels: documentation, engine adaptor, engine adaptor constructors

#111 - reviewing calibration vignette

Pull Request - State: open - Opened by papsti about 1 year ago - 2 comments

#110 - specify entries in derivations.json in the same way as model$insert$expressions

Issue - State: open - Opened by stevencarlislewalker about 1 year ago
Labels: model definition files, engine adaptor constructors

#109 - ADREPORT performance cost and related issues

Issue - State: open - Opened by bbolker about 1 year ago - 8 comments
Labels: engine, performance

#108 - how to change number of time steps (etc.) on the fly?

Issue - State: closed - Opened by bbolker about 1 year ago - 4 comments

#107 - Better messages when rbind_time (and pals) are used in the objective function

Issue - State: open - Opened by d31v1vi5 about 1 year ago - 6 comments
Labels: bug, engine, engine adaptor, calibration

#106 - add_calibrate() function?

Issue - State: closed - Opened by bbolker about 1 year ago - 2 comments
Labels: calibration

#105 - discoverability of known operators/functions

Issue - State: open - Opened by bbolker about 1 year ago
Labels: documentation

#104 - Use last.par.best when accessing parameters

Issue - State: open - Opened by stevencarlislewalker about 1 year ago
Labels: calibration

#103 - Mistakes in definitions of flows not caught during model initialization.

Issue - State: open - Opened by d31v1vi5 about 1 year ago
Labels: engine adaptor, model definition files, engine adaptor constructors

#102 - Thoughts on calibration quickstart

Issue - State: open - Opened by stevencarlislewalker about 1 year ago - 2 comments
Labels: documentation

#101 - Suggestion: Add more verbose error message when settings file and variables file do not match.

Issue - State: open - Opened by d31v1vi5 about 1 year ago - 1 comment
Labels: model definition files, engine adaptor constructors

#100 - Allow matrices and named expressions to be overwritten

Issue - State: open - Opened by bbolker over 1 year ago - 1 comment
Labels: documentation, engine adaptor

#99 - Duplicated person entries in DESCRIPTION

Issue - State: closed - Opened by jaganmn over 1 year ago - 1 comment

#98 - shout louder when convergence isn't achieved

Issue - State: open - Opened by bbolker over 1 year ago - 2 comments
Labels: calibration

#97 - Make sure NAs in initial matrices always get properly coerced to numeric type

Issue - State: open - Opened by stevencarlislewalker over 1 year ago
Labels: engine adaptor, engine adaptor constructors

#96 - explain/document last-step difference between macpan2 and deSolve

Issue - State: open - Opened by bbolker over 1 year ago - 1 comment

#95 - Missing column descriptions for `flow.csv` in the Quickstart example.

Issue - State: closed - Opened by d31v1vi5 over 1 year ago - 4 comments

#94 - calibration to hospital occupancy and waste in calibration_ww.R not working as expected

Issue - State: open - Opened by mayaearn over 1 year ago - 19 comments
Labels: calibration

#93 - Better clamping

Issue - State: open - Opened by stevencarlislewalker over 1 year ago
Labels: engine

#92 - set unused flow initial values to NA in quickstart example?

Issue - State: closed - Opened by bbolker over 1 year ago - 4 comments
Labels: documentation, engine adaptor constructors

#91 - Flow Types Vignette

Issue - State: open - Opened by stevencarlislewalker over 1 year ago - 3 comments
Labels: documentation, model definition files

#90 - missing end of sentence/¶ in 'composing models' vignette

Issue - State: closed - Opened by bbolker over 1 year ago

#89 - Optimize simulator object size

Issue - State: open - Opened by stevencarlislewalker over 1 year ago - 5 comments
Labels: engine adaptor, performance

#88 - fixed number of rows from rbf

Pull Request - State: closed - Opened by Kevinozoid over 1 year ago - 1 comment

#87 - Show models is generating a warning

Issue - State: closed - Opened by stevencarlislewalker over 1 year ago - 1 comment
Labels: bug, documentation

#86 - mention starter_model in quickstart

Issue - State: open - Opened by bbolker over 1 year ago - 5 comments

#85 - convolution examples

Issue - State: closed - Opened by stevencarlislewalker over 1 year ago - 1 comment
Labels: documentation, engine

#84 - Implement Asher Ebola model as a starter_model

Issue - State: open - Opened by stevencarlislewalker over 1 year ago
Labels: documentation, model definition files, model library

#83 - optimize many-time-steps case

Issue - State: closed - Opened by stevencarlislewalker over 1 year ago - 2 comments
Labels: engine, engine adaptor, performance

#82 - Adder classes for adding observed trajectories

Issue - State: open - Opened by stevencarlislewalker over 1 year ago
Labels: calibration

#81 - optim default should be BFGS because we always have gradients thanks to TMB

Issue - State: open - Opened by stevencarlislewalker over 1 year ago - 2 comments
Labels: calibration

#80 - R 3.5.0 isn't really supported

Issue - State: closed - Opened by jaganmn over 1 year ago - 1 comment

#79 - improving show_models(), exporting

Pull Request - State: closed - Opened by bbolker over 1 year ago

#76 - differential equation hacks

Issue - State: open - Opened by bbolker over 1 year ago - 7 comments
Labels: engine adaptor constructors

#75 - Report specific problematic expression when an engine error comes back

Issue - State: closed - Opened by stevencarlislewalker over 1 year ago
Labels: engine, engine adaptor

#74 - logistic and logit engine functions

Issue - State: open - Opened by stevencarlislewalker over 1 year ago
Labels: engine

#73 - comments in model definition files

Issue - State: open - Opened by bbolker over 1 year ago - 1 comment
Labels: enhancement, question, model definition files

#72 - unary minus not recognized in r-side symbolic manipulation

Issue - State: closed - Opened by stevencarlislewalker over 1 year ago
Labels: bug

#71 - segfault when optimization parameters enter into the init_mats as emtpy_matrix

Issue - State: open - Opened by stevencarlislewalker over 1 year ago - 1 comment
Labels: bug, engine

#70 - comments/TODO in make_model_index.R

Pull Request - State: closed - Opened by bbolker over 1 year ago

#69 - Generate simulator for producing the components of the next generation matrix from a set of model definition files

Issue - State: open - Opened by stevencarlislewalker over 1 year ago
Labels: engine, engine adaptor, model definition files, engine adaptor constructors

#68 - optimize simulator constructor

Issue - State: closed - Opened by stevencarlislewalker over 1 year ago - 2 comments
Labels: engine adaptor, engine adaptor constructors, performance

#67 - Dimnames for automatically created matrices

Issue - State: open - Opened by stevencarlislewalker over 1 year ago
Labels: engine adaptor