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Review issues #121

Merged
merged 127 commits into from
May 16, 2024
Merged

Review issues #121

merged 127 commits into from
May 16, 2024

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Juanmontenegro99
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This Pull Request presents all the changes suggested in the Package review #112

juan-umana and others added 30 commits March 6, 2024 10:18
@juan-umana @Bisaloo
Update DESCRIPTION
abac584 
Update email

Co-authored-by: Hugo Gruson <[email protected]>
@juan-umana @Bisaloo
Update DESCRIPTION
8c7f8ec 
Co-authored-by: Hugo Gruson <[email protected]>
@Juanmontenegro99
#114
f23774e
@Juanmontenegro99
Documentation geometric_mean and geometric_sd
28bdf29
@Juanmontenegro99
Update function names
4ad3db4
@Juanmontenegro99
update name functions
63a9ec4
@Juanmontenegro99 @juan-umana
Create lint-changed-files.yml (#117)
e897ec3 
Co-authored-by: Juan D. Umaña <[email protected]>
@Juanmontenegro99
documentation
71af1d2
@Juanmontenegro99
Update parameters #115
50d979c
@Juanmontenegro99
Update Readme #118
7b3588d
@Juanmontenegro99 @Bisaloo
Update README.md
4c41c34 
Co-authored-by: Hugo Gruson <[email protected]>
@juan-umana
Update according to #115
ff7f627
@juan-umana
Merge branch 'review-issues' of https://github.com/epiverse-trace/epiCo…
fd31749 
… into review-issues
@juan-umana @Bisaloo
Update R/utils.R
c5620b2 
Co-authored-by: Hugo Gruson <[email protected]>
@juan-umana @Bisaloo
Update R/endemic_channel.R
77c1bb0 
Co-authored-by: Hugo Gruson <[email protected]>
@juan-umana @Bisaloo
Update R/endemic_channel.R
9d46e7a 
Co-authored-by: Hugo Gruson <[email protected]>
@juan-umana @Bisaloo
Update R/endemic_channel.R
a4bdda4 
Co-authored-by: Hugo Gruson <[email protected]>
@Juanmontenegro99 @Bisaloo
Update R/endemic_channel.R
2ad9a93 
Co-authored-by: Hugo Gruson <[email protected]>
@Juanmontenegro99
Change return to stop
b9c091c
@juan-umana @Bisaloo
Update R/endemic_channel.R
605ebca 
Co-authored-by: Hugo Gruson <[email protected]>
@juan-umana @Bisaloo
Update R/demographics.R
845ea6c 
Co-authored-by: Hugo Gruson <[email protected]>
@juan-umana @Bisaloo
Update R/demographics.R
9b23d5a 
Co-authored-by: Hugo Gruson <[email protected]>
@juan-umana @Bisaloo
Update R/demographics.R
424b574 
Co-authored-by: Hugo Gruson <[email protected]>
@juan-umana @Bisaloo
Update R/demographics.R
ac9975f 
Co-authored-by: Hugo Gruson <[email protected]>
@juan-umana @Bisaloo
Update R/demographics.R
a624e83 
Co-authored-by: Hugo Gruson <[email protected]>
@Juanmontenegro99
Change name function
ea2186a
@juan-umana @Bisaloo
Update R/utils.R
78ed340 
Co-authored-by: Hugo Gruson <[email protected]>
@juan-umana @Bisaloo
Update R/utils.R
f3cd52a 
Co-authored-by: Hugo Gruson <[email protected]>
@juan-umana @Bisaloo
Update R/spatiotemporal.R
a845d80 
Co-authored-by: Hugo Gruson <[email protected]>
@juan-umana @Bisaloo
Update R/spatiotemporal.R
b659dbb 
Co-authored-by: Hugo Gruson <[email protected]>
@github-actions GitHub Actions
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This pull request:

  • Adds 0 new dependencies (direct and indirect)
  • Adds 0 new system dependencies
  • Removes 1 existing dependencies (direct and indirect)
  • Removes 1 existing system dependencies

(Note that results may be inacurrate if you branched from an outdated version of the target branch.)

@github-actions GitHub Actions
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This pull request:

  • Adds 0 new dependencies (direct and indirect)
  • Adds 0 new system dependencies
  • Removes 1 existing dependencies (direct and indirect)
  • Removes 1 existing system dependencies

(Note that results may be inacurrate if you branched from an outdated version of the target branch.)

@github-actions GitHub Actions
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This pull request:

  • Adds 0 new dependencies (direct and indirect)
  • Adds 0 new system dependencies
  • Removes 1 existing dependencies (direct and indirect)
  • Removes 1 existing system dependencies

(Note that results may be inacurrate if you branched from an outdated version of the target branch.)

@github-actions GitHub Actions
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This pull request:

  • Adds 0 new dependencies (direct and indirect)
  • Adds 0 new system dependencies
  • Removes 1 existing dependencies (direct and indirect)
  • Removes 1 existing system dependencies

(Note that results may be inacurrate if you branched from an outdated version of the target branch.)

@juan-umana
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Commits resulting from the #112 epiCo full review are squashed and merged in this PR

@github-actions GitHub Actions
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This pull request:

  • Adds 0 new dependencies (direct and indirect)
  • Adds 0 new system dependencies
  • Removes 1 existing dependencies (direct and indirect)
  • Removes 1 existing system dependencies

(Note that results may be inacurrate if you branched from an outdated version of the target branch.)

@juan-umana juan-umana merged commit ce219ed into dev May 16, 2024
3 of 8 checks passed
@juan-umana juan-umana deleted the review-issues branch May 16, 2024 21:43
Juanmontenegro99 added a commit that referenced this pull request Jun 6, 2024
@Juanmontenegro99 @juan-umana @Bisaloo
Review issues (#121)
b118d3c 
* Update DESCRIPTION

Update email

Co-authored-by: Hugo Gruson <[email protected]>

* Update DESCRIPTION

Co-authored-by: Hugo Gruson <[email protected]>

* #114

* Documentation geometric_mean and geometric_sd

* Update function names

* update name functions

* Create lint-changed-files.yml (#117)

Co-authored-by: Juan D. Umaña <[email protected]>

* documentation

* Update parameters #115

* Update Readme #118

* Update README.md

Co-authored-by: Hugo Gruson <[email protected]>

* Update according to #115

* Update R/utils.R

Co-authored-by: Hugo Gruson <[email protected]>

* Update R/endemic_channel.R

Co-authored-by: Hugo Gruson <[email protected]>

* Update R/endemic_channel.R

Co-authored-by: Hugo Gruson <[email protected]>

* Update R/endemic_channel.R

Co-authored-by: Hugo Gruson <[email protected]>

* Update R/endemic_channel.R

Co-authored-by: Hugo Gruson <[email protected]>

* Change return to stop

* Update R/endemic_channel.R

Co-authored-by: Hugo Gruson <[email protected]>

* Update R/demographics.R

Co-authored-by: Hugo Gruson <[email protected]>

* Update R/demographics.R

Co-authored-by: Hugo Gruson <[email protected]>

* Update R/demographics.R

Co-authored-by: Hugo Gruson <[email protected]>

* Update R/demographics.R

Co-authored-by: Hugo Gruson <[email protected]>

* Update R/demographics.R

Co-authored-by: Hugo Gruson <[email protected]>

* Change name function

* Update R/utils.R

Co-authored-by: Hugo Gruson <[email protected]>

* Update R/utils.R

Co-authored-by: Hugo Gruson <[email protected]>

* Update R/spatiotemporal.R

Co-authored-by: Hugo Gruson <[email protected]>

* Update R/spatiotemporal.R

Co-authored-by: Hugo Gruson <[email protected]>

* Documentation

* Update R/ewma.R

Co-authored-by: Hugo Gruson <[email protected]>

* Update R/ewma.R

Co-authored-by: Hugo Gruson <[email protected]>

* Make functions index

* Update vignette title

* Delete emwa analysis

* Update DESCRIPTION

* Update examples

* Documentation

* Update examples

* Documentation

* Update module examples

* Documentation

* Standarise description

* workflows

* Revert "workflows"

This reverts commit 75b9a35.

* workflows

* package documentation

* Create dev-utils.R

* Update bug_report.md

* Update .lintr

* update tests

* Reconciliation

* Fix nolint error

* Fix warnings in demmographics

* solve warnings

* Update license year

* add new line

* Fix lint warnings

* lint fix warnings

* Population_pyramid suggestions

* Documentation

* describe_ethnicity suggestion

* describe_occupation suggestion 1-2

* Fix bug age_risk

* decrease lines in age_risk and documentation

* standarize outputs

* Avoid namespacing

* Update orcid

* update render-readme workflow

* Create new workflows

* Delete favicon

* Return render workflow version

* Delete update-copyright-year.yml

* render_readme previous version

* add observed case legend

* Update spatiotemporal_vignette.Rmd

* change neighborhoods output

* update tests

* population_pyramid validations

* lowercase columns names

* update validations population_pyramid

* Update documentation

* age_risk geral's suggestions

* age_risk geral's suggestions

* describe_occupation geral's suggestions

* occupation_plot geral's suggestions

* update tests

* Update references index

* improve test coverage

* Update documentation

* Change moran.plot() to localmoran()

* Update valid years documentation

* Update divipola_table characters

* Update distance_matrix characters

* Update divipola_table.rda

* Revert "Update divipola_table.rda"

This reverts commit 4cca1ee.

* Revert "Update divipola_table characters"

This reverts commit 329002d.

* Change divipola codes to character

* Divipola codes to characters

* Fix tests with divipola code as characters

* Fix with divipola codes as character

* Fix functions with divipola codes as characters

* Fix functions with divipola codes as characters

* Delete unused data

* Update divipola codes to character

* Fix function with divipola as character

* Update README.md

* Update demographic_vignette.Rmd

* Update endemic_channel.Rmd

* Update spatiotemporal_vignette.Rmd

* Fix function with divipola as character

* Documentation

* Update neighborhood function description

* Update demographics.R

* update distance case

* Update advisors' websites

* Style changes

* Update URL

* Update _pkgdown.yml

* Create pkgdown\favicon files

---------

Co-authored-by: Juan D. Umaña <[email protected]>
Co-authored-by: Hugo Gruson <[email protected]>
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@Juanmontenegro99 @juan-umana