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Add test suite#93

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jamesmbaazam wants to merge 100 commits intodevepiverse-trace/serofoi:devfrom dev-testsuiteepiverse-trace/serofoi:dev-testsuiteCopy head branch name to clipboard

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Commits

Commits on Aug 8, 2022

• Initial commit

  tracelac

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  fee9be3

Commits on Aug 9, 2022

• Adding package skeleton

  

  GeraldineGomez

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  d157dce

Commits on Sep 12, 2022

• plot for logo

  

  Zulma M. Cucunubá

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  Zulma M. Cucunubá

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  1665553

Commits on Sep 15, 2022

• basic model

  

  Zulma M. Cucunubá

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  Zulma M. Cucunubá

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• redme

  

  Zulma M. Cucunubá

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  Zulma M. Cucunubá

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• comments

  

  Zulma M. Cucunubá

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  Zulma M. Cucunubá

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• typo

  

  Zulma M. Cucunubá

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  Zulma M. Cucunubá

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  c82f4ef

• typo

  

  Zulma M. Cucunubá

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  Zulma M. Cucunubá

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  5684116

• Merge pull request #1 from TRACE-LAC/dev-feature-basicmodel

  Show description for babb4f8
  tracelac

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  babb4f8

Commits on Sep 20, 2022

• Update README.md

  zmcucunuba

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  de08085

Commits on Sep 21, 2022

• arreglo carpetas R/stanmodels

  

  Zulma M. Cucunubá

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  Zulma M. Cucunubá

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  21f6a6b

Commits on Oct 21, 2022

• Funciones finales pendientes a modificación

  megamezl

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  226ad64

Commits on Oct 30, 2022

• Delete Funciones eliminadas.docx

  megamezl

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• Delete Explicación del código del paquete SEROFOI.docx

  megamezl

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• Documentación en inglés y español

  megamezl

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• Merge branch 'dev-feature-strmodel' of github.com:TRACE-LAC/serofoi into dev-feature-strmodel

  megamezl

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  43320fe

Commits on Oct 31, 2022

• Documentación lista

  megamezl

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• modify package structure

  GeraldineGomez

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  8aee8eb

• modify package structure

  GeraldineGomez

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  4749504

Commits on Nov 3, 2022

• modify names and folder test

  GeraldineGomez

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  a74b3d3

Commits on Nov 9, 2022

• Creation of general modules and revision of functions

  megamezl

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  4621e97

• Merge branch 'dev-feature-strmodel-miguel' of github.com:TRACE-LAC/serofoi into dev-feature-strmodel-miguel

  megamezl

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  3293b70

Commits on Nov 10, 2022

• refactoring visualization functions and define some general pck structure

  GeraldineGomez

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  5522dba

• update readme file

  GeraldineGomez

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  d67b2d4

• update readme file

  GeraldineGomez

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  69b41d0

Commits on Nov 11, 2022

• general settings

  GeraldineGomez

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  6f6d804

Commits on Nov 21, 2022

• update dependecies, documentation and name functions (#2)

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  3 peopleauthored
  da33fd8

Commits on Dec 21, 2022

• Merge branch 'dev' into dev-feature-strmodel-miguel

  GeraldineGomez

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  26be6ca

Commits on Jan 7, 2023

• variable renaming, module names, programming syntax, and starting function separation by model.

  megamezl

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Commits on Jan 9, 2023

• renaming variables, inputs and outputs

  megamezl

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  df169bd

Commits on Jan 11, 2023

• Separation of model 0 with function run_model_0

  megamezl

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Commits on Jan 12, 2023

• funciones que deben estar listas

  megamezl

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Commits on Jan 14, 2023

• feat: Add function run_model to module R/modeling.R. This function returns an object with the result from running the specified model. The model is specified through the variable model_name. Right …

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  ntorresd

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  40f8dfe

Commits on Jan 19, 2023

• refrac: The visualization.R module function plot_model is refracted. The functions plot_seroprev, plot_foi and plot_rhats return the sero prevalence, the force of infection and the rhats-convergenc…

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  ntorresd

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  5d4e9ce

• refrac: The function run_model suffered several changes: 1) Since model_object now includes model_data, this last is not required as an argument anymore. 2) We created the save_or_read_model functi…

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  ntorresd

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  c26b567

• chore: minor changes.

  ntorresd

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  aa0de0b

Commits on Jan 20, 2023

• delete .RDS files corresponding to the compilation of the models.

  ntorresd

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• minor edits

  zmcucunuba

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• gitignore RDS comp files

  zmcucunuba

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• chore: Rename tests folder to test/ and modelling module to modelling.R. Remove old tests folders and test scripts.

  ntorresd

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  19dc3c3

Commits on Jan 24, 2023

• Merge branch 'main' into dev

  ntorresd

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  edc5c2b

• Merge pull request #3 from TRACE-LAC/dev

  Show description for c22e41d
  ntorresd

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  c22e41d

• remove R/stanmodels folder becuase it is redundant with inst/extdata/stanmodels.

  ntorresd

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  69398c4

• correct minor bugs and typos.

  ntorresd

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  15353d8

Commits on Jan 25, 2023

• Restructure package modules in preparation for compilation (#8)

  Show description for b571c3e
  

  ntorresd

  and

  megamezl

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  b571c3e

• Prepare data_test for package compilation (#9)

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  ntorresd

  and

  megamezl

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  13a5719

• remove unnecessary file data_bu.RDS

  ntorresd

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  94d7ed2

Commits on Mar 22, 2023

• remove unused man file

  ntorresd

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  752b07e

• Merge dev to main (#37)

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  8 peopleauthored
  835aef7

• Remove test folder. Correct minor mistake in vignettes.

  ntorresd

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  45b665b

Commits on Mar 28, 2023

• Merge dev -> main. (#38)

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  8 peopleauthored
  5676c2e

Commits on Mar 29, 2023

• doc: changed removed function plot_seromodels_grid for cowplot::plot_grid

  ntorresd

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• Dev (#39)

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  8 peopleauthored
  be8240f

Commits on Apr 4, 2023

• Dev: update vignettes content and test website publication. (#43)

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  8 peopleauthored
  7b89f4d

• Update _pkgdown.yml

  ntorresd

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  25ac900

• Dev (#44)

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  8 peopleauthored
  fc161ce

Commits on Apr 5, 2023

• doc: minor correction to references

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  ntorresd

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  bc0ebf6

Commits on Apr 6, 2023

• Remove files generated by pkgdown (#45)

  Show description for 3b4ffea
  Bisaloo

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  3b4ffea

Commits on Apr 13, 2023

• doc: update vignettes urls in the README as well as the installation repository

  ntorresd

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  6b24a88

• Merge pull request #46 from epiverse-trace/fix-vignettes-urls

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  zmcucunuba

  authored
  95ae01b

Commits on May 2, 2023

• Rename serofoi logo and use svg file (#51)

  Bisaloo

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  3cdfbfe

Commits on May 24, 2023

• Set up google analytics on documentation website (#55)

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  Bisaloo

  authored
  26633e2

Commits on Jun 7, 2023

• Minor correction to package maintainer. Add orcid and email to author information (ntorresd). (#58)

  ntorresd

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Commits on Jun 20, 2023

• Added commas to description file (#68)

  ben18785

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Commits on Jun 21, 2023

• small tweaks to documentation titles so that we identify them well as … (#75)

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  zmcucunuba

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  f1d83af

• update: lifecycle stage in README files (#76)

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  GeraldineGomez

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  3286fae

Commits on Jun 29, 2023

• Dev fix pr 1 (#80)

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  10 peopleauthored
  d7f66d7

Commits on Aug 14, 2023

• remove serodata .Rdata and .Rd files

  ntorresd

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  776bcfa

• remove R/serodata.R

  ntorresd

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• doc: update functions documentation replacing for in examples

  ntorresd

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  dc54d73

• doc: update serofoi logo

  ntorresd

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  3120493

• doc: update README and vignettes

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  ntorresd

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  1cd0084

• fix: minor correction to test_modelling

  ntorresd

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Commits on Aug 15, 2023

• feat: add function get_foi_central_estimates() to the modelling module.

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  ntorresd

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  a02b92b

• fix: minor corrections to tests according to commit a02b92b

  ntorresd

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• fix: change to in model_comparison

  ntorresd

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• doc: add documentation file for

  ntorresd

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  ec1edcb

• doc: minor correction to documentation

  ntorresd

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  b075340

• refac: updates

  ntorresd

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• refac: reduce the output of

  ntorresd

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  ec4335c

• fix(tests): change storing format of model object files from .json to .RDS and updates test_visualization accordingly

  ntorresd

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  034e63e

Commits on Aug 22, 2023

• Remove serodata from pre-loaded datasets of the package (#107)

  Show description for 6d07d15
  ntorresd

  authored
  6d07d15

Commits on Aug 23, 2023

• Merge branch 'dev' into refac-fit_seromodel

  ntorresd

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  6443a8c

Commits on Aug 24, 2023

• Merge pull request #109 from epiverse-trace/refac-fit_seromodel

  Show description for 5154176
  jpavlich

  authored
  5154176

Commits on Sep 7, 2023

• Fixes #115 (#116)

  jpavlich

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  308c0bd

Commits on Sep 11, 2023

• Add functions to simulate datasets to the seroprevalence_data module. (#59)

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  ntorresd

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  jamesmbaazam

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  4e918af

• Deleted testepidemics.R (closes #84)

  jamesmbaazam

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• deleted docker folder in tests directory (Closes #86)

  jamesmbaazam

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  bbc6d48

• Renamed extdata folder to testdata (Closes #87)

  jamesmbaazam

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  77dd46e

• Deleted testing_utils.R script (Closes #88)

  jamesmbaazam

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• Remove redundant steps

  jamesmbaazam

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  a9aa835

• Added initial tests for get_table_rhats()

  jamesmbaazam

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  8aaa27a

• Added initial phase of tests for run_seromodel()

  jamesmbaazam

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  d0a92ec

• Removed explicit namespacing of testthat and changed extdata to testdata

  jamesmbaazam

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  d550893

• moved issue-based tests to model-based test

  jamesmbaazam

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  1f1082b

• Removed an extra comma in function call

  jamesmbaazam

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• Added a nolint tag to preventing linting of a necessary long line

  jamesmbaazam

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• Removed skipping of os

  jamesmbaazam

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• Removed calling of libraries in tests because they are already in Suggests

  jamesmbaazam

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• Data generated as part of tests

  jamesmbaazam

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