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library(COVID19AR) #> Loading required package: dplyr #> #> Attaching package: 'dplyr' #> The following objects are masked from 'package:stats': #> #> filter, lag #> The following objects are masked from 'package:base': #> #> intersect, setdiff, setequal, union #> Loading required package: knitr #> Loading required package: magrittr #> Loading required package: lgr #> Warning: replacing previous import 'ggplot2::Layout' by 'lgr::Layout' when #> loading 'COVID19AR' #> Warning: replacing previous import 'readr::col_factor' by 'scales::col_factor' #> when loading 'COVID19AR' #> Warning: replacing previous import 'magrittr::equals' by 'testthat::equals' when #> loading 'COVID19AR' #> Warning: replacing previous import 'magrittr::not' by 'testthat::not' when #> loading 'COVID19AR' #> Warning: replacing previous import 'magrittr::is_less_than' by #> 'testthat::is_less_than' when loading 'COVID19AR' #> Warning: replacing previous import 'dplyr::matches' by 'testthat::matches' when #> loading 'COVID19AR' library(ggplot2) #> #> Attaching package: 'ggplot2' #> The following object is masked from 'package:lgr': #> #> Layout #library(dplyr) #library(RColorBrewer) knitr::opts_chunk$set(fig.width = 4, fig.height = 6, dpi = 300, warning = FALSE) covid19.curator <- COVID19ARCurator$new() self <- covid19.curator dummy <- covid19.curator$loadData() #> INFO [11:20:20.164] Exists dest path? {dest.path: ~/.R/COVID19AR/Covid19Casos.csv, exists.dest.path: TRUE} dummy <- covid19.curator$curateData() #> INFO [11:20:20.931] Normalize #> INFO [11:20:21.146] checkSoundness #> INFO [11:20:21.263] Mutating data covid19.ar.provincia.summary <- covid19.curator$makeSummary(group.vars = c("residencia_provincia_nombre")) covid19.ar.provincia.summary.selected <- covid19.ar.provincia.summary %>% filter(confirmados >= 100) covid19.ar.summary <- covid19.curator$makeSummary(group.vars = c("residencia_provincia_nombre", "sepi_apertura")) #> INFO [11:20:42.203] Processing {current.group: residencia_provincia_nombre = Buenos Aires} #> INFO [11:20:44.308] Processing {current.group: residencia_provincia_nombre = CABA} #> INFO [11:20:46.407] Processing {current.group: residencia_provincia_nombre = Catamarca} #> INFO [11:20:47.608] Processing {current.group: residencia_provincia_nombre = Chaco} #> INFO [11:20:48.966] Processing {current.group: residencia_provincia_nombre = Chubut} #> INFO [11:20:50.203] Processing {current.group: residencia_provincia_nombre = Córdoba} #> INFO [11:20:51.692] Processing {current.group: residencia_provincia_nombre = Corrientes} #> INFO [11:20:52.982] Processing {current.group: residencia_provincia_nombre = Entre Ríos} #> INFO [11:20:54.319] Processing {current.group: residencia_provincia_nombre = Formosa} #> INFO [11:20:55.798] Processing {current.group: residencia_provincia_nombre = Jujuy} #> INFO [11:20:56.984] Processing {current.group: residencia_provincia_nombre = La Pampa} #> INFO [11:20:58.204] Processing {current.group: residencia_provincia_nombre = La Rioja} #> INFO [11:20:59.412] Processing {current.group: residencia_provincia_nombre = Mendoza} #> INFO [11:21:00.789] Processing {current.group: residencia_provincia_nombre = Misiones} #> INFO [11:21:01.846] Processing {current.group: residencia_provincia_nombre = Neuquén} #> INFO [11:21:03.054] Processing {current.group: residencia_provincia_nombre = Río Negro} #> INFO [11:21:04.316] Processing {current.group: residencia_provincia_nombre = Salta} #> INFO [11:21:05.406] Processing {current.group: residencia_provincia_nombre = San Juan} #> INFO [11:21:06.543] Processing {current.group: residencia_provincia_nombre = San Luis} #> INFO [11:21:07.661] Processing {current.group: residencia_provincia_nombre = Santa Cruz} #> INFO [11:21:08.843] Processing {current.group: residencia_provincia_nombre = Santa Fe} #> INFO [11:21:10.445] Processing {current.group: residencia_provincia_nombre = Santiago del Estero} #> INFO [11:21:11.606] Processing {current.group: residencia_provincia_nombre = SIN ESPECIFICAR} #> INFO [11:21:12.901] Processing {current.group: residencia_provincia_nombre = Tierra del Fuego} #> INFO [11:21:14.326] Processing {current.group: residencia_provincia_nombre = Tucumán} data2plot <- covid19.ar.summary %>% filter(residencia_provincia_nombre %in% covid19.ar.provincia.summary.selected$residencia_provincia_nombre) %>% filter(confirmados > 0 ) %>% filter(positividad.porc <=0.6 | confirmados >= 20) sepi.fechas <- covid19.curator$data %>% group_by(sepi_apertura) %>% summarize(ultima_fecha_sepi = max(fecha_apertura), .groups = "keep") data2plot %<>% inner_join(sepi.fechas, by = "sepi_apertura") dates <- sort(unique(data2plot$ultima_fecha_sepi)) total.dates <- length(dates) report.date <- max(dates) covplot <- data2plot %>% ggplot(aes(x = ultima_fecha_sepi, y = confirmados, color = "confirmados")) + geom_line() + facet_wrap(~residencia_provincia_nombre, ncol = 2, scales = "free_y") + labs(title = "Evolución de casos confirmados y tests\n en provincias > 100 confirmados") covplot <- covplot + geom_line(aes(x = ultima_fecha_sepi, y = tests, color = "tests")) + facet_wrap(~residencia_provincia_nombre, ncol = 2, scales = "free_y") covplot <- setupTheme(covplot, report.date = report.date, x.values = dates, x.type = "dates", total.colors = 2, data.provider.abv = "@msalnacion", base.size = 6) covplot <- covplot + scale_y_log10() #> Scale for 'y' is already present. Adding another scale for 'y', which will #> replace the existing scale. covplot
ggsave(file.path(data.dir, paste("provincias-confirmados-tests",".png", sep ="")), covplot, width = 7, height = 5, dpi = 300) #> Error in file.path(data.dir, paste("provincias-confirmados-tests", ".png", : object 'data.dir' not found covplot <- data2plot %>% ggplot(aes(x = ultima_fecha_sepi, y = positividad.porc, color = "positividad.porc")) + geom_line() + facet_wrap(~residencia_provincia_nombre, ncol = 2, scales = "free_y") + labs(title = "Porcentajes de positividad, uso de UCI, respirador y letalidad\n en provincias > 100 confirmados") covplot <- covplot + geom_line(aes(x = ultima_fecha_sepi, y = cuidado.intensivo.porc, color = "cuidado.intensivo.porc")) + facet_wrap(~residencia_provincia_nombre, ncol = 2, scales = "free_y") covplot <- covplot + geom_line(aes(x = ultima_fecha_sepi, y = respirador.porc, color = "respirador.porc"))+ facet_wrap(~residencia_provincia_nombre, ncol = 2, scales = "free_y") covplot <- covplot + geom_line(aes(x = ultima_fecha_sepi, y = letalidad.min.porc, color = "letalidad.min.porc")) + facet_wrap(~residencia_provincia_nombre, ncol = 2, scales = "free_y") covplot <- setupTheme(covplot, report.date = report.date, x.values = dates, x.type = "dates", total.colors = 4, data.provider.abv = "@msalnacion", base.size = 6) covplot
ggsave(file.path(data.dir, paste("provincias-positividad",".png", sep ="")), covplot, width = 7, height = 5, dpi = 300) #> Error in file.path(data.dir, paste("provincias-positividad", ".png", sep = "")): object 'data.dir' not found
Created on 2020-06-12 by the reprex package (v0.3.0)
The text was updated successfully, but these errors were encountered:
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Created on 2020-06-12 by the reprex package (v0.3.0)
The text was updated successfully, but these errors were encountered: