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modify moran index function #26

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2 tasks done
juan-umana opened this issue Aug 16, 2023 · 0 comments
Closed
2 tasks done

modify moran index function #26

juan-umana opened this issue Aug 16, 2023 · 0 comments
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@Juanmontenegro99
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enhancement New feature or request test Create test

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juan-umana commented Aug 16, 2023 •
edited by Juanmontenegro99
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  • Modify morans_index function in the spatiotemporal.R module so the user inputs an incidence object and the incidence rate is estimated within the function using incidence_rate from utils.R
  • Update morans_index tests accordingly
@juan-umana juan-umana added enhancement New feature or request test Create test labels Aug 16, 2023
Juanmontenegro99 added a commit that referenced this issue Aug 27, 2023
@Juanmontenegro99
#26 modified function and test
52f24b0
Juanmontenegro99 added a commit that referenced this issue Aug 27, 2023
@Juanmontenegro99
Revert "#26 modified function and test"
4a6132e 
This reverts commit 52f24b0.
Juanmontenegro99 added a commit that referenced this issue Aug 27, 2023
@Juanmontenegro99
#26 modified function and test
644d039
@Juanmontenegro99 Juanmontenegro99 mentioned this issue Sep 5, 2023
Merged
juan-umana pushed a commit that referenced this issue Sep 5, 2023
@Juanmontenegro99
26 modify moran index function (#29)
e665caa 
* #26 modified function and test

* Revert "#26 modified function and test"

This reverts commit 52f24b0.

* #26 modified function and test

* Update lint

* Fix lint
juan-umana added a commit that referenced this issue Sep 19, 2023
@juan-umana @Juanmontenegro99
30 population pyramids age ranges (#31)
ab9fa1c 
* 24 fix incidence historic length handling (#28)

* #24 verify incidence and observations

* #24 Verify length of the incidence historic

* #24 adding warnings and final tests

* Fix warnings

* Fix unused variable

* 26 modify moran index function (#29)

* #26 modified function and test

* Revert "#26 modified function and test"

This reverts commit 52f24b0.

* #26 modified function and test

* Update lint

* Fix lint

* Update demographics.R

* Age ranges feature

Include the feature to customize the age ranges for the population pyramids and specific age rates

* Update

* Create detect_outbreaks_ewma.Rd

---------

Co-authored-by: Juan Montenegro Torres <60274234+Juanmontenegro99@users.noreply.github.com>
juan-umana added a commit that referenced this issue Sep 19, 2023
@juan-umana @Juanmontenegro99
8 demographics vignette (#32)
d0d9b13 
* Vignette creation

* Update demographics-vignette.Rmd

* Update demographics-vignette.Rmd

* Actualizar demographics-vignette.Rmd

* Actualizar demographics-vignette.Rmd

* Update demographics-vignette.Rmd

* Update demographics-vignette.Rmd

* Update demographics-vignette.Rmd

* Update of vignette format

* 30 population pyramids age ranges (#31)

* 24 fix incidence historic length handling (#28)

* #24 verify incidence and observations

* #24 Verify length of the incidence historic

* #24 adding warnings and final tests

* Fix warnings

* Fix unused variable

* 26 modify moran index function (#29)

* #26 modified function and test

* Revert "#26 modified function and test"

This reverts commit 52f24b0.

* #26 modified function and test

* Update lint

* Fix lint

* Update demographics.R

* Age ranges feature

Include the feature to customize the age ranges for the population pyramids and specific age rates

* Update

* Create detect_outbreaks_ewma.Rd

---------

Co-authored-by: Juan Montenegro Torres <60274234+Juanmontenegro99@users.noreply.github.com>

* Update demographic_vignette.Rmd

* Update demographic_vignette.Rmd

---------

Co-authored-by: Juan Montenegro Torres <60274234+Juanmontenegro99@users.noreply.github.com>
Juanmontenegro99 added a commit that referenced this issue Oct 13, 2023
@Juanmontenegro99 @juan-umana
@Bisaloo @jd-otero
Dev (#48)
3331d5a 
* Create test-endemic_channel

* Tests endemic channel (#25)

* #23 create endemic channel test

* #23 update endemic channel assertions

* Update documentation

* Update lint

* Uptade lint

* Update lint

* Update README.md (#27)

* 24 fix incidence historic length handling (#28)

* #24 verify incidence and observations

* #24 Verify length of the incidence historic

* #24 adding warnings and final tests

* Fix warnings

* Fix unused variable

* 26 modify moran index function (#29)

* #26 modified function and test

* Revert "#26 modified function and test"

This reverts commit 52f24b0.

* #26 modified function and test

* Update lint

* Fix lint

* 8 demographics vignette (#32)

* Vignette creation

* Update demographics-vignette.Rmd

* Update demographics-vignette.Rmd

* Actualizar demographics-vignette.Rmd

* Actualizar demographics-vignette.Rmd

* Update demographics-vignette.Rmd

* Update demographics-vignette.Rmd

* Update demographics-vignette.Rmd

* Update of vignette format

* 30 population pyramids age ranges (#31)

* 24 fix incidence historic length handling (#28)

* #24 verify incidence and observations

* #24 Verify length of the incidence historic

* #24 adding warnings and final tests

* Fix warnings

* Fix unused variable

* 26 modify moran index function (#29)

* #26 modified function and test

* Revert "#26 modified function and test"

This reverts commit 52f24b0.

* #26 modified function and test

* Update lint

* Fix lint

* Update demographics.R

* Age ranges feature

Include the feature to customize the age ranges for the population pyramids and specific age rates

* Update

* Create detect_outbreaks_ewma.Rd

---------

Co-authored-by: Juan Montenegro Torres <60274234+Juanmontenegro99@users.noreply.github.com>

* Update demographic_vignette.Rmd

* Update demographic_vignette.Rmd

---------

Co-authored-by: Juan Montenegro Torres <60274234+Juanmontenegro99@users.noreply.github.com>

* Create endemic_channel.Rmd

* Create endemic_channel_figure.png

Figure for the endemic channel vignette

* Update logo

New epiCo logo

* Update README

* Update endemic_channel.Rmd

* Style updates

* Restore dependency on R 3.2.0
because of anyNA()

* Spatiotemporal vignette (#37)

* Create spatiotemporal_vignette.Rmd

* Fix vignettes

* Fix lint errors

* Fix styler

* Temporal fix lint

* upload data

* Update tests and fix age range parameter (#35)

* Update tests and fix age range parameter

* Create project and fix concatenation_linter

* Update vignettes with the new data

* #40

* fix warnings lint

* Fix lint warnings

* fix warnings

* Delete unnecessary files

* Fix lint warnings

* Delete commented code

---------

Co-authored-by: Juan Montenegro Torres <60274234+Juanmontenegro99@users.noreply.github.com>

* 41 fix path bug (#42)

Relocate data and fix #41.

* update moran's example

* Fix bug in morans_index map

Now morans_index function returns a list with the data and the leaflet map that can be displayed later

* Bug age risk (#44)

* Add error handling age_risk

Function now checks that if `gender` info is provided it has the same number of elements as `age`

* Fix age_risk bug

The plot argument in the helping function `graphics::hist` has to be FALSE to avoid attempts of displaying data

* Fix age_risk bug

The function now can handle the case when users have a populatio_pyramid dissagreggated by gender but still want to estimate an age_risk distribution where genders are aggregated

* Style fix

* Delete unnecessary files

* Update test-demographics.R (#47)

* Handle warnings

* Documentation and style changes

* style and documentation changes

* fix lint warnings

---------

Co-authored-by: juan-umana <jd.umana10@uniandes.edu.co>
Co-authored-by: Juan D. Umaña <juan.umanacaro@gmail.com>
Co-authored-by: Juanmontenegro99 <jf.montenegro@uniandes.edu.co>
Co-authored-by: Hugo Gruson <Bisaloo@users.noreply.github.com>
Co-authored-by: Julian Otero <56242573+jd-otero@users.noreply.github.com>
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