Commit: 9c4265eca0143c2485d7fa8cf0b2deaa0644d4ae - myprojects-hg-reborn (hg)

Commit MetaInfo

• Revision: 9c4265eca0143c2485d7fa8cf0b2deaa0644d4ae (tree)
• Zeit: 2022-01-02 22:27:43
• Autor: Lorenzo Isella <lorenzo.isella@gmai...>
• Commiter: Lorenzo Isella

Log Message

I revised the plots and the statistics.

Ändern Zusammenfassung

• modified: R-codes/covid_process.R

Diff

diff -r b2eb0ca7a922 -r 9c4265eca014 R-codes/covid_process.R
--- a/R-codes/covid_process.R	Thu Dec 30 23:48:37 2021 +0100
+++ b/R-codes/covid_process.R	Sun Jan 02 14:27:43 2022 +0100
@@ -19,6 +19,8 @@
 
 weekly_aver <- rollify(mean, window = 7)
 
+system("rm *csv")
+system("rm *pdf")
 
 system("wget https://raw.githubusercontent.com/pcm-dpc/COVID-19/master/dati-andamento-nazionale/dpc-covid19-ita-andamento-nazionale.csv")
 
@@ -27,19 +29,21 @@
 
 
 df <- df_ini %>%
-    clean_names() %>%
+    clean_data() %>%
     mutate(data=as_date(data)) %>%
     mutate(deceduti_giornalieri=diff_col2(deceduti)) %>%
-    mutate(deceduti_settimanali=weekly_aver(deceduti_giornalieri)) %>%
     mutate(anno=year(data)) %>%
     mutate(anno=as.factor(anno)) %>%
     mutate(giorno=yday(data)) %>%
     mutate(data_no_anno=as_date(giorno)-1) %>%
+    mutate(positivi_progressione=cumsum(nuovi_positivi)) %>% 
+    ## group_by(anno) %>% 
+    mutate(deceduti_settimanali=weekly_aver(deceduti_giornalieri)) %>%
     mutate(ingressi_settimanali_terapia_intensiva=weekly_aver(ingressi_terapia_intensiva)) %>%
     mutate(terapia_intensiva_settimanale=weekly_aver(terapia_intensiva)) %>%
     mutate(ricoverati_settimanale=weekly_aver(ricoverati_con_sintomi)) %>%
-    mutate(ospedalizzati_settimanale=weekly_aver(totale_ospedalizzati))
-
+    mutate(ospedalizzati_settimanale=weekly_aver(totale_ospedalizzati)) ## %>%
+    ## ungroup
     
 
 gpl <- ggplot(df, aes(x=data, y=deceduti_settimanali       )) +
@@ -68,7 +72,7 @@
                  guide = guide_axis(n.dodge = 2) ,
                  expand=c(0.03,0.03)) +
     scale_color_scico_d(NULL, palette="hawaii" ,
-                       labels=c("2020", "2021")
+                       labels=c("2020", "2021", "2022")
                       )+
 
     labs(title=NULL)+
@@ -81,13 +85,15 @@
 
 
 gpl2bis <- ggplot(df, aes(x=data_no_anno, y=deceduti_giornalieri, color=anno       )) +
-    geom_line(size=1., alpha=1)+
+    geom_line(size=.7, alpha=1)+
+    geom_point(size=1., alpha=1)+
+    
     my_ggplot_theme2("top")+
     scale_x_date(breaks="1 months", date_labels = "%b",
                  guide = guide_axis(n.dodge = 2) ,
                  expand=c(0.03,0.03)) +
     scale_color_scico_d(NULL, palette="hawaii" ,
-                       labels=c("2020", "2021")
+                       labels=c("2020", "2021", "2022")
                       )+
 
     labs(title=NULL)+
@@ -100,53 +106,62 @@
 
 
 
-gpl3 <- ggplot(df, aes(x=data_no_anno, y=ingressi_settimanali_terapia_intensiva, color=anno       )) +
-    geom_line(size=1., alpha=1)+
+gpl3 <- ggplot(df, aes(x=data_no_anno, y=ingressi_terapia_intensiva,
+                       color=anno       )) +
+    geom_line(size=.7, alpha=1)+
+    geom_point(size=1, alpha=1)+
+
     my_ggplot_theme2("top")+
     scale_x_date(breaks="1 months", date_labels = "%b",
                  guide = guide_axis(n.dodge = 2) ,
                  expand=c(0.03,0.03)) +
     scale_color_scico_d(NULL, palette="hawaii" ,
-                       labels=c("2020", "2021")
+                       labels=c("2020", "2021", "2022")
                       )+
 
     labs(title=NULL)+
     xlab(NULL)+
-    ylab("Media Mobile Settimanale\nIngressi Terapia Intensiva")
+    ylab("Ingressi Terapia Intensiva")
 
 
-ggsave("ingressi_terapia_intensiva_ma_settimanali.pdf",gpl3, width=7*golden_ratio,height=7 , device = cairo_pdf )
+ggsave("ingressi_terapia_intensiva.pdf",gpl3, width=7*golden_ratio,height=7 , device = cairo_pdf )
 
 
 
-gpl4 <- ggplot(df, aes(x=data_no_anno, y=terapia_intensiva_settimanale, color=anno       )) +
-    geom_line(size=1., alpha=1)+
+gpl4 <- ggplot(df, aes(x=data_no_anno, y=terapia_intensiva, color=anno       )) +
+    geom_line(size=.7, alpha=1)+
+    geom_point(## aes(x=data_no_anno,y=terapia_intensiva,
+               ##     color=anno ),
+               size=1, alpha=1)+
+
     my_ggplot_theme2("top")+
     scale_x_date(breaks="1 months", date_labels = "%b",
                  guide = guide_axis(n.dodge = 2) ,
                  expand=c(0.03,0.03)) +
     scale_color_scico_d(NULL, palette="hawaii" ,
-                       labels=c("2020", "2021")
+                       labels=c("2020", "2021", "2022")
                       )+
 
     labs(title=NULL)+
     xlab(NULL)+
-    ylab("Media Mobile Settimanale\nPazienti in Terapia Intensiva")
+    ylab("Pazienti in Terapia Intensiva")
 
 
-ggsave("occupazione_terapia_intensiva_ma_settimanali.pdf",gpl4, width=7*golden_ratio,height=7 , device = cairo_pdf )
+ggsave("occupazione_terapia_intensiva_settimanali.pdf",gpl4, width=7*golden_ratio,height=7 , device = cairo_pdf )
 
 
 
 
 gpl5 <- ggplot(df, aes(x=data_no_anno, y=isolamento_domiciliare, color=anno       )) +
-    geom_line(size=1., alpha=1)+
+    geom_point(size=1., alpha=1)+
+
+    geom_line(size=.7, alpha=1)+
     my_ggplot_theme2("top")+
     scale_x_date(breaks="1 months", date_labels = "%b",
                  guide = guide_axis(n.dodge = 2) ,
                  expand=c(0.03,0.03)) +
     scale_color_scico_d(NULL, palette="hawaii" ,
-                       labels=c("2020", "2021")
+                       labels=c("2020", "2021", "2022")
                       )+
 
     labs(title=NULL)+
@@ -158,55 +173,112 @@
 
 
 
-gpl6 <- ggplot(df, aes(x=data_no_anno, y=ricoverati_settimanale, color=anno       )) +
-    geom_line(size=1., alpha=1)+
+## gpl6 <- ggplot(df, aes(x=data_no_anno, y=ricoverati_settimanale, color=anno       )) +
+##     geom_line(size=1., alpha=1)+
+##     my_ggplot_theme2("top")+
+##     scale_x_date(breaks="1 months", date_labels = "%b",
+##                  guide = guide_axis(n.dodge = 2) ,
+##                  expand=c(0.03,0.03)) +
+##     scale_color_scico_d(NULL, palette="hawaii" ,
+##                        labels=c("2020", "2021", "2022")
+##                       )+
+
+##     labs(title=NULL)+
+##     xlab(NULL)+
+##     ylab("Ricoverati")
+
+
+## ggsave("ricoverati.pdf",gpl6, width=7*golden_ratio,height=7 , device = cairo_pdf )
+
+
+
+
+gpl7 <- ggplot(df, aes(x=data_no_anno, y=totale_ospedalizzati, color=anno       )) +
+    geom_line(size=.7, alpha=1)+
+    geom_point(size=1, alpha=1)+
+
     my_ggplot_theme2("top")+
     scale_x_date(breaks="1 months", date_labels = "%b",
                  guide = guide_axis(n.dodge = 2) ,
                  expand=c(0.03,0.03)) +
     scale_color_scico_d(NULL, palette="hawaii" ,
-                       labels=c("2020", "2021")
+                       labels=c("2020", "2021", "2022")
                       )+
 
     labs(title=NULL)+
     xlab(NULL)+
-    ylab("Ricoverati Media Mobile Settimanale")
+    ylab("Totale Ospedalizzati")
 
 
-ggsave("ricoverati_media_mobile.pdf",gpl6, width=7*golden_ratio,height=7 , device = cairo_pdf )
+ggsave("ospedalizzati.pdf",gpl7, width=7*golden_ratio,height=7 , device = cairo_pdf )
 
 
 
 
-gpl7 <- ggplot(df, aes(x=data_no_anno, y=ospedalizzati_settimanale, color=anno       )) +
-    geom_line(size=1., alpha=1)+
+
+
+gpl8 <- ggplot(df, aes(x=data_no_anno, y=totale_positivi, color=anno       )) +
+    geom_line(size=.7, alpha=1)+
+    geom_point(size=1., alpha=1)+
+
     my_ggplot_theme2("top")+
     scale_x_date(breaks="1 months", date_labels = "%b",
                  guide = guide_axis(n.dodge = 2) ,
                  expand=c(0.03,0.03)) +
     scale_color_scico_d(NULL, palette="hawaii" ,
-                       labels=c("2020", "2021")
+                       labels=c("2020", "2021", "2022")
                       )+
 
     labs(title=NULL)+
     xlab(NULL)+
-    ylab("Totale Ospedalizzati Media Mobile Settimanale")
+    ylab("Totale Positivi")
 
 
-ggsave("ospedalizzati_media_mobile.pdf",gpl7, width=7*golden_ratio,height=7 , device = cairo_pdf )
-
-
-system("wget https://raw.githubusercontent.com/pcm-dpc/COVID-19/master/dati-regioni/dpc-covid19-ita-regioni.csv")
-
-
-df_regio_ini <- read_csv("dpc-covid19-ita-regioni.csv")
+ggsave("totale_positivi.pdf",gpl8, width=7*golden_ratio,height=7 , device = cairo_pdf )
 
 
 
-system("wget https://raw.githubusercontent.com/pcm-dpc/COVID-19/master/dati-province/dpc-covid19-ita-province.csv")
+
+gpl9 <- ggplot(df, aes(x=data, y=positivi_progressione## , color=anno
+                       )) +
+    geom_line(size=.7, alpha=1)+
+    geom_point(size=1., alpha=1)+
+
+    my_ggplot_theme2("top")+
+    scale_x_date(breaks="1 months", date_labels = "%b\n%y",
+                 guide = guide_axis(n.dodge = 2) ,
+                 expand=c(0.03,0.03)) +
+    ## scale_color_scico_d(NULL, palette="hawaii" ,
+    ##                    labels=c("2020", "2021", "2022")
+    ##                   )+
+
+    labs(title=NULL)+
+    xlab(NULL)+
+    ylab("Incidenza cumulativa")
 
 
-df_pro_ini <- read_csv("dpc-covid19-ita-province.csv")
+ggsave("incidenza.pdf",gpl9, width=7*golden_ratio,height=7 , device = cairo_pdf )
+
+
+
+
+
+
+
+
+
+
+## system("wget https://raw.githubusercontent.com/pcm-dpc/COVID-19/master/dati-regioni/dpc-covid19-ita-regioni.csv")
+
+
+## df_regio_ini <- read_csv("dpc-covid19-ita-regioni.csv")
+
+
+
+## system("wget https://raw.githubusercontent.com/pcm-dpc/COVID-19/master/dati-province/dpc-covid19-ita-province.csv")
+
+
+## df_pro_ini <- read_csv("dpc-covid19-ita-province.csv")
 
 
 print("So far so good")