Update final function versions to main. (#111)

* 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>

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: epiCo
-Title: Provides statistical tools for the analysis of vector-borne diseases in Colombia
-Version: 0.2
+Title: provides statistical and visualization tools for the analysis of outbreaks of vector-borne diseases (VBDs) in Colombia
+Version: 0.3.0
 Authors@R: 
     c(person("Juan D.", "Umaña", , "jd.umana10@uniandes.edu.co", role = c("aut", "cre")),
       person("Juan", "Montenegro-Torres", , "jf.montenegro@uniandes.edu.co", role = c("aut")),
       person("Julian", "Otero", , "jd.otero10@uniandes.edu.co", role = c("aut")),
       person("Hugo", "Gruson", , "hugo.gruson+R@normasup.org", role = c("ctb")))
-Description: Provides statistical tools for the analysis of demographic trends, spatiotemporal behavior, outbreaks characterization, underreporting estimation, and short-term forecasting of vector-borne diseases in Colombia.
+Description: provides statistical and visualization tools for the analysis of demographic indicators, and spatio-temporal behavior and characterization of outbreaks of vector-borne diseases (VBDs) in Colombia
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
@@ -24,7 +24,9 @@ Imports:
     utils,
     stats,
     magrittr,
-    rlang
+    rlang,
+    igraph,
+    ggraph
 Suggests: 
     checkmate,
     covr,

NAMESPACE

@@ -8,10 +8,12 @@ export(endemic_channel)
 export(epi_calendar)
 export(ewma)
 export(geom_mean)
+export(geom_sd)
 export(incidence_rate)
 export(morans_index)
 export(neighborhoods)
 export(occupation_plot)
+export(occupation_plot_2)
 export(population_pyramid)
 importFrom(magrittr,"%>%")
 importFrom(rlang,.data)