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Add code for traveling time estimations #69

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juan-umana opened this issue Oct 31, 2023 · 1 comment
Open

Add code for traveling time estimations #69

juan-umana opened this issue Oct 31, 2023 · 1 comment
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@jd-otero @Juanmontenegro99
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documentation Improvements or additions to documentation

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@juan-umana
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Add code and ask for review for distance matrix data
@juan-umana juan-umana added the documentation Improvements or additions to documentation label Oct 31, 2023
@Juanmontenegro99 Juanmontenegro99 self-assigned this Feb 7, 2024
Juanmontenegro99 added a commit that referenced this issue Feb 8, 2024
@Juanmontenegro99
Update distance_matrix #69
945ae1c
@Juanmontenegro99 Juanmontenegro99 mentioned this issue Feb 23, 2024
Merged
Juanmontenegro99 added a commit that referenced this issue Feb 23, 2024
@Juanmontenegro99 @juan-umana
Update final function versions to main. (#111)
952539c 
* Review plots and prints in the demographics funcitons (#93)

* Fix x-axis in population_pyramid plot

* Fix x-axis in age_risk plot

* Fix total population bug in pop_pyramid

* Fix x-axis in age_risk plot total False

* Fix morans_index legend

* Fix \n bug in describe_ethnicity

* Fix lint warnings

* 96 endemic channels calculation of the standard deviation (#102)

* Warning geom_mean

geom_mean handle zero values but is important to notify the user that the input includes them

* Fix geom_mean

Improve exceptions handling and fixing error in habib's implementation

* Fix geom_mean

Fix optimization method in geom_mean

* Create geom_sd

Creation of a function to return the standard deviation of a vector according to the method used to determine the geometric mean

* Change geom_mean epsilon

Change of scale of epsilon value to reduce standard deviation of the series. However optimal epsilon value ramains to be researched.

* Fix stats::sd usage

* Change standard deviation approach

As stated in #96 standard deviation should account for transformation of data

* Update utils.R

* Styling fix

* Udpate/create documentation

* export geom_sd

* Update utils.R

* Solve issue #96

* Change stop's for stopifnot's

* Delete print of delta

* Update test-utils.R

* Update demographics.R

* 101 index moran map (#103)

* Update and add legends in morans_index map

* Update colors in map

* Style and documentation

* Solve #101

* Fix conflicts

* 97 population projections (#106)

* Review plots and prints in the demographics funcitons (#93)

* Fix x-axis in population_pyramid plot

* Fix x-axis in age_risk plot

* Fix total population bug in pop_pyramid

* Fix x-axis in age_risk plot total False

* Fix morans_index legend

* Fix \n bug in describe_ethnicity

* Fix lint warnings

* update population projections post COVID-19

* Fix vignette bug

* correct columns names

* Fix population_pyramid function

* Style corrections

* Fix incidence_rate bug

* Fix age_risk bug

* Update tests for the new dimensions

* Update tests for the new dimensions

* Fix global functions definition

* 100 describe ethnicity (#104)

* #100 Fix lint

* Change to message and fix order

* update test and output function

* 96 endemic channels calculation of the standard deviation (#107)

* Warning geom_mean

geom_mean handle zero values but is important to notify the user that the input includes them

* Fix geom_mean

Improve exceptions handling and fixing error in habib's implementation

* Fix geom_mean

Fix optimization method in geom_mean

* Create geom_sd

Creation of a function to return the standard deviation of a vector according to the method used to determine the geometric mean

* Change geom_mean epsilon

Change of scale of epsilon value to reduce standard deviation of the series. However optimal epsilon value ramains to be researched.

* Fix stats::sd usage

* Change standard deviation approach

As stated in #96 standard deviation should account for transformation of data

* Update utils.R

* Styling fix

* Udpate/create documentation

* export geom_sd

* Update utils.R

* Solve issue #96

* Change stop's for stopifnot's

* Delete print of delta

* Update test-utils.R

* Update demographics.R

* Fix dimension bug

* Styler

* Update distance_matrix.rda

* Revert "Update distance_matrix.rda"

This reverts commit 7deba6f.

* Update distance_matrix #69

* 99 describe occupation (#110)

* Update occupational_plot

* Separe describe_occupation and plot

* Style

* Enhancement in occupational plot

* Change describe_occupation function

* add gender and plot options to describe_occupation

* Fix Occupational plot and create circular plot

* First draft of circular plotting of occupations

* Unify describe_occupation and occupation_plot

* Update test fpr describe_occupation

* Update vignette for new describe_occupation function

* Update documentation

* Style

* update plot parameter occupation_plot

* Style

* update tests

* Style

* Fix igraph bug

* fix distance_matrix bug

* Add new library

* Update tests for describe_occupation

* Fix global parameters and descriptions

* Revert "Fix global parameters and descriptions"

This reverts commit 0f0d84d.

* Update function descirptions

* global variables occupation_plot

* global variable occupation_plot_2

* Add warning to occupation_plot_2

* Documentation

* Style

* Fix note in check

Replace double use of %>% by double use of subset function

---------

Co-authored-by: juan-umana <juan.umanacaro@gmail.com>

* 108 vignette visualization (#109)

* Update tables visualization

* Update table visualization

* Update paper

* Update paper

* Update functions description

* Delete unused comments

* Extends interpretation of morans_index

* Update function descriptions and grammar

* Update function descriptions and grammar

* Style

* Fix bug

* Documentation

* 85+ clarification

* Update DESCRIPTION

* Update README.md

---------

Co-authored-by: juan-umana <juan.umanacaro@gmail.com>

---------

Co-authored-by: Juan D. Umaña <juan.umanacaro@gmail.com>
@Bisaloo
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Bisaloo commented Nov 6, 2024

We discussed this at the development meeting yesterday.

Adding this code would allow users to apply this functionality to other countries than Colombia, and future-proof the package to ensure distances for Colombia can be updated in the future.

We discussed it would probably make sense to package this as a separate package. epiCo would then:

  • use this new package as a dependency and call the code under the hood
  • keep the bundled data for Colombia but direct users to the new package if they want to get the distances for other countries

One potential issue @juan-umana mentioned is that it's difficult to get the required input data for some regions. I believe this can be resolved by leaving this task to the user. The new package would say "if you give me this data, I will output a travel time matrix".

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