Ejemplo reproducible comparando a Argentina con otros países latinoamericanos

[kenarab]

#install.packages("devtools")
#devtools::install_github("ROpenStats/COVID19analytics")

library(COVID19analytics)
#> Warning: replacing previous import 'ggplot2::Layout' by 'lgr::Layout' when
#> loading 'COVID19analytics'
#> Warning: replacing previous import 'readr::col_factor' by 'scales::col_factor'
#> when loading 'COVID19analytics'
#> Warning: replacing previous import 'magrittr::equals' by 'testthat::equals' when
#> loading 'COVID19analytics'
#> Warning: replacing previous import 'magrittr::not' by 'testthat::not' when
#> loading 'COVID19analytics'
#> Warning: replacing previous import 'magrittr::is_less_than' by
#> 'testthat::is_less_than' when loading 'COVID19analytics'
#> Warning: replacing previous import 'dplyr::matches' by 'testthat::matches' when
#> loading 'COVID19analytics'
#> Warning: replacing previous import 'testthat::matches' by 'tidyr::matches' when
#> loading 'COVID19analytics'
#> Warning: replacing previous import 'magrittr::extract' by 'tidyr::extract' when
#> loading 'COVID19analytics'
library(ggplot2)

env.data.dir <- getEnv("data_dir")

processor <- COVID19DataProcessor$new(provider.id = "JohnsHopkingsUniversity", missing.values.model.id = "imputation")
dummy <- processor$setupData()
#> INFO  [19:21:51.967]  {stage: processor-setup}
#> INFO  [19:21:51.999] Checking required downloaded  {downloaded.max.date: 2020-06-21, daily.update.time: 21:00:00, current.datetime: 2020-06-22 1.., download.flag: FALSE}
#> INFO  [19:21:52.114] Checking required downloaded  {downloaded.max.date: 2020-06-21, daily.update.time: 21:00:00, current.datetime: 2020-06-22 1.., download.flag: FALSE}
#> INFO  [19:21:52.135] Checking required downloaded  {downloaded.max.date: 2020-06-21, daily.update.time: 21:00:00, current.datetime: 2020-06-22 1.., download.flag: FALSE}
#> INFO  [19:21:52.263]  {stage: data loaded}
#> INFO  [19:21:52.263]  {stage: data-setup}
dummy <- processor$transform()
#> INFO  [19:21:52.266] Executing transform 
#> INFO  [19:21:52.266] Executing consolidate 
#> INFO  [19:21:54.135]  {stage: consolidated}
#> INFO  [19:21:54.135] Executing standarize 
#> INFO  [19:21:54.645] gathering DataModel 
#> INFO  [19:21:54.646]  {stage: datamodel-setup}
dummy <- processor$curate()
#> INFO  [19:21:54.650]  {stage: loading-aggregated-data-model}
#> Warning in countrycode(x, origin = "country.name", destination = "continent"): Some values were not matched unambiguously: MS Zaandam
#> INFO  [19:21:57.103]  {stage: calculating-rates}
#> INFO  [19:21:57.293]  {stage: making-data-comparison}
#> INFO  [19:22:03.474]  {stage: applying-missing-values-method}
#> INFO  [19:22:03.475]  {stage: Starting first imputation}
#> INFO  [19:22:03.483]  {stage: calculating-rates}
#> INFO  [19:22:03.707]  {stage: making-data-comparison-2}
#> INFO  [19:22:09.877]  {stage: calculating-top-countries}
#> INFO  [19:22:09.901]  {stage: curated}
selected.countries  <- c("Argentina", "Brazil", "Peru", "Chile", "Colombia", "Cuba", "Uruguay")
rg <- ReportGeneratorEnhanced$new(processor)
ggplot <-rg$ggplotCountriesLines(included.countries = selected.countries, countries.text = "Selected countries",
                        field = "rate.inc.daily", log.scale = TRUE)
ggplot
#> Warning: Removed 42 row(s) containing missing values (geom_path).

ggsave(file.path(env.data.dir, paste("comparison-inc.rate",".png", sep ="")), ggplot,
       width = 7, height = 5, dpi = 300)
#> Warning: Removed 42 row(s) containing missing values (geom_path).

ggplot <-rg$ggplotCountriesLines(included.countries = selected.countries, countries.text = "Selected countries",
                                 field = "confirmed.inc", log.scale = TRUE)
ggplot
#> Warning: Removed 42 row(s) containing missing values (geom_path).

ggsave(file.path(env.data.dir, paste("comparison-inc",".png", sep ="")), ggplot,
       width = 7, height = 5, dpi = 300)
#> Warning: Removed 42 row(s) containing missing values (geom_path).

^{Created on 2020-06-22 by the reprex package (v0.3.0)}