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030_eurostat_analyses_deces_std_hebdo.R
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030_eurostat_analyses_deces_std_hebdo.R
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library(pyramid)
library(maps)
library(eurostat)
library(dplyr)
library(stringr)
library(leaflet)
library(questionr)
library(ggplot2)
library(lubridate)
library(sf)
library(rnaturalearth)
library(rnaturalearthdata)
library(readr)
library(lsr)
library(igraph)
library(rapportools)
library(broom)
library(purrr)
library(tidyr)
library(gridExtra)
library(formattable)
#---------------------------------------#
####analyse des donnees hebdomadaires####
#---------------------------------------#
b__es_deces_week_standardises_si_pop_2020_owid_vaccination <- a__f_loadRdsIfNeeded(var = b__es_deces_week_standardises_si_pop_2020_owid_vaccination,
rdsRelFilePath = "gen/rds/Eurostat_owid_deces_standard_pays_semaine.RDS")
#---------------------------------------#
#### analyse glissante ####
#---------------------------------------#
es_deces_standard_pays_semaine_autriche <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "AT") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_belgique <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "BE") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_bulgarie <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "BG") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_suisse <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "CH") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_rtcheque <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "CZ") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_danmark <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "DK") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_estonie <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "EE") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_espagne <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "ES") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_france <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "FR") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
# Pourquoi filtre-t-on sur numSemaineDepuis2013 > 52 ?
# REP : Parce que les données ne ressemblent à rien pour ce pays les 51 premières semaines
es_deces_standard_pays_semaine_croatie <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "HR") %>%
filter(numSemaineDepuis2013 > 52) %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_hongrie <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "HU") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_islande <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "IS") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_italie <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "IT") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_lichtenstein <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "LI") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_lituanie <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "LT") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_luxembourg <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "LU") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_lettonie <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "LV") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_montenegro <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "ME") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_malte <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "MT") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_norvege <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "NO") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_paysbas <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "NL") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_portugal <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "PT") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_pologne <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "PL") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_serbie <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "RS") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_suede <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "SE") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_slovenie <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "SI") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_slovaquie <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "SK") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_allemagne <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "DE") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_chypre <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "CY") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_albanie <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "AL") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_armenie <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "AM") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_grece <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "EL") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_finlande <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "FI") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
es_deces_standard_pays_semaine_roumanie <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo == "RO") %>%
filter(numSemaineDepuis2013<=base::max(numSemaineDepuis2013)-4)
#---------------------------------------------------#
#### Graphe superposé France / Suede / Portugal ####
#---------------------------------------------------#
# Moyenne mobile sur 52 semaines
es_moyenne_mobile <- running_mean(es_deces_standard_pays_semaine_france$deces_standardises_si_pop_2020,
52)
es_moyenne <- mean(es_moyenne_mobile)
es_moyenne_mobile <- data_frame(es_moyenne_mobile)
es_moyenne_mobile$numSemaineDepuis2013 <- 1:nrow(es_moyenne_mobile) + 51
es_deces_standard_pays_semaine_france <- es_deces_standard_pays_semaine_france %>%
left_join(es_moyenne_mobile, by = "numSemaineDepuis2013")
es_deces_standard_pays_semaine_france$moyenne <- es_moyenne
if (shallDeleteVars) rm(es_moyenne)
if (shallDeleteVars) rm(es_moyenne_mobile)
france<- es_deces_standard_pays_semaine_france %>%
ungroup() %>%
select(numSemaineDepuis2013,deces_standardises_si_pop_FR_2020) %>%
dplyr::rename(deces_france=deces_standardises_si_pop_FR_2020)
suede<-es_deces_standard_pays_semaine_suede %>%
ungroup() %>%
select(numSemaineDepuis2013,deces_standardises_si_pop_FR_2020)%>%
dplyr::rename(deces_suede=deces_standardises_si_pop_FR_2020)
portugal<-es_deces_standard_pays_semaine_portugal %>%
ungroup() %>%
select(numSemaineDepuis2013,deces_standardises_si_pop_FR_2020)%>%
dplyr::rename(deces_portugal=deces_standardises_si_pop_FR_2020)
france_suede_portugal <- france %>% left_join(suede) %>% left_join(portugal)
g<-ggplot(data = france_suede_portugal) +
geom_area(aes(x = numSemaineDepuis2013,
y = deces_portugal),color="#006600",fill="#006600",size=1,alpha=1/4) +
geom_area(aes(x = numSemaineDepuis2013,
y = deces_suede),color="#0066CC",fill="#0066CC",size=1,alpha=1/2) +
geom_area(aes(x = numSemaineDepuis2013,
y = deces_france),
color="#CC0000",fill="#CC0000",size=1,alpha=1/2) +
geom_vline(xintercept = seq(from=0, to=600, by = 52),linetype = "dashed",color="steelblue")+
theme(axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.title.y = element_text(color="#000000", size=20 ),
plot.title = element_text(color="#003366", size=25 ),
axis.text.y = element_text(color="#000000", size=15 , angle =45))+
ylab("Décès hebdomadaires standardisés")+
geom_text(x=26, y=1000, label="2013",size=10)+
geom_text(x=79, y=1000, label="2014",size=10)+
geom_text(x=131, y=1000, label="2015",size=10)+
geom_text(x=183, y=1000, label="2016",size=10)+
geom_text(x=235, y=1000, label="2017",size=10)+
geom_text(x=287, y=1000, label="2018",size=10)+
geom_text(x=339, y=1000, label="2019",size=10)+
geom_text(x=391, y=1000, label="2020",size=10)+
geom_text(x=443, y=1000, label="2021",size=10)+
geom_text(x=495, y=1000, label="2022",size=10)+
geom_text(x=547, y=1000, label="2023",size=10)+
annotate(geom = "text", x = 50, y = 30000, label = "Portugal", color = "#006600",
angle = 0, size = 15)+
annotate(geom = "text", x = 50, y = 28000, label = "Suède", color = "#0066CC",
angle = 0, size = 15)+
annotate(geom = "text", x = 50, y = 26000, label = "France", color = "#CC0000",
angle = 0, size = 15)+
ggtitle(paste0("Décès hebdomadaires standardisés selon 2020 par pays"))+
scale_y_continuous(labels=function(x) format(x,big.mark=" ",scientific = FALSE))
g
repertoire <- paste0(K_DIR_GEN_IMG_EUROSTAT,"/Deces/Hebdo/Std/Deces_FR_SU_PO")
a__f_createDir(repertoire)
dev.print(device = png, file = paste0(repertoire, "/Deces_Hebdo_france_suede_portugal_couleur.png"), width = 1000)
g<-ggplot(data = france_suede_portugal) +
geom_area(aes(x = numSemaineDepuis2013,
y = deces_portugal),color="#999999",fill="#999999",size=1,alpha=1/4) +
geom_area(aes(x = numSemaineDepuis2013,
y = deces_suede),color="#666666",fill="#666666",size=1,alpha=1/2) +
geom_area(aes(x = numSemaineDepuis2013,
y = deces_france),
color="#000000",fill="#000000",size=1,alpha=1/2) +
geom_vline(xintercept = seq(from=0, to=600, by = 52),linetype = "dashed",color="steelblue")+
theme(axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.title.y = element_text(color="#000000", size=20 ),
plot.title = element_text(color="#003366", size=25 ),
axis.text.y = element_text(color="#000000", size=15 , angle =45))+
ylab("Décès hebdomadaires standardisés")+
geom_text(x=26, y=1000, label="2013",size=10)+
geom_text(x=79, y=1000, label="2014",size=10)+
geom_text(x=131, y=1000, label="2015",size=10)+
geom_text(x=183, y=1000, label="2016",size=10)+
geom_text(x=235, y=1000, label="2017",size=10)+
geom_text(x=287, y=1000, label="2018",size=10)+
geom_text(x=339, y=1000, label="2019",size=10)+
geom_text(x=391, y=1000, label="2020",size=10)+
geom_text(x=443, y=1000, label="2021",size=10)+
geom_text(x=495, y=1000, label="2022",size=10)+
geom_text(x=547, y=1000, label="2023",size=10)+
annotate(geom = "text", x = 50, y = 30000, label = "Portugal", color = "#999999",
angle = 0, size = 15)+
annotate(geom = "text", x = 50, y = 28000, label = "Suède", color = "#666666",
angle = 0, size = 15)+
annotate(geom = "text", x = 50, y = 26000, label = "France", color = "#000000",
angle = 0, size = 15)+
ggtitle(paste0("Décès hebdomadaires standardisés selon 2020 par pays"))+
scale_y_continuous(labels=function(x) format(x,big.mark=" ",scientific = FALSE))
g
dev.print(device = png, file = paste0(repertoire, "/Deces_Hebdo_france_suede_portugal.png"), width = 1000)
if (shallDeleteVars) rm(france)
if (shallDeleteVars) rm(suede)
if (shallDeleteVars) rm(portugal)
if (shallDeleteVars) rm(france_suede_portugal)
#---------------------------------------#
#### analyse juillet-juin ####
#---------------------------------------#
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_allemagne)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_autriche)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_belgique)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_chypre)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_croatie)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_danmark)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_espagne)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_estonie)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_finlande)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_france)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_grece)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_hongrie)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_islande)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_italie)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_malte)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_norvege)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_paysbas)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_pologne)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_portugal)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_rtcheque)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_serbie)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_suede)
a__f_cumul_and_plot_es_deces_hebdo_std_annee_juin(es_deces_standard_pays_semaine_suisse)
#--------------------------#
#### cumul Janvier/Déc ####
#--------------------------#
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_allemagne)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_autriche)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_belgique)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_chypre)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_croatie)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_danmark)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_espagne)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_estonie)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_finlande)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_france)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_grece)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_hongrie)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_islande)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_italie)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_malte)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_norvege)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_paysbas)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_pologne)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_portugal)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_rtcheque)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_serbie)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_suede)
a__f_cumul_and_plot_es_deces_hebdo_std(es_deces_standard_pays_semaine_suisse)
#-------------------------------------------------#
#### vaccinations grippe et deces France ####
#-------------------------------------------------#
repertoire <- paste0(K_DIR_GEN_IMG_EUROSTAT, "/Deces/Hebdo/Std/owid/Deces_Pays_Vaccin")
a__f_createDir(repertoire)
pngFileRelPath <- paste0(repertoire, "/France_vaccins_grippe_covid.png")
# Message
cat(paste0("Creation image (", pngFileRelPath,")\n"))
# Déterminer le plus grand numéro de semaine, puis le time (2021W27) associé pour l'afficher dans le titre
maxWeekTime <- es_deces_standard_pays_semaine_france %>%
ungroup %>%
filter(numSemaineDepuis2013 == max(numSemaineDepuis2013)) %>%
distinct() %>%
select(time)
maxWeekTime <- maxWeekTime[1, 1]
if (shallDeleteVars) rm(maxWeekTime)
# Moyenne mobile sur 8 semaines, des 15-24 ans
moyenne_mobile <- running_mean(es_deces_standard_pays_semaine_france$deces_standardises_si_pop_2020_ge60,
8)
# Moyenne de la Moyenne mobile
moyenne_mobile <- data_frame(moyenne_mobile)
moyenne_mobile$numSemaineDepuis2013 <- 1:nrow(moyenne_mobile) + 5
# Ajouter les colonnes de la moyenne mobile
es_deces_standard_pays_semaine_france <- es_deces_standard_pays_semaine_france %>%
left_join(moyenne_mobile, by = "numSemaineDepuis2013")
if (shallDeleteVars) rm(moyenne_mobile)
es_deces_standard_pays_semaine_france$moyenne_ge60 <- mean(es_deces_standard_pays_semaine_france$deces_standardises_si_pop_2020_ge60)
es_deces_standard_pays_semaine_france$binf_ge60 <- mean(es_deces_standard_pays_semaine_france$deces_standardises_si_pop_2020_ge60) - 2*sd(es_deces_standard_pays_semaine_france$deces_standardises_si_pop_2020_ge60)
es_deces_standard_pays_semaine_france$bsup_ge60 <- mean(es_deces_standard_pays_semaine_france$deces_standardises_si_pop_2020_ge60) + 2*sd(es_deces_standard_pays_semaine_france$deces_standardises_si_pop_2020_ge60)
essai <- es_deces_standard_pays_semaine_france %>% filter(numSemaineDepuis2013 > 192)%>% filter(numSemaineDepuis2013< 451)
grippe_lissage <- read.csv("data/csv/lissage_grippe.csv", sep=";")
essai<-essai %>% left_join(grippe_lissage, by = "numSemaineDepuis2013")
essai<-essai %>% mutate(vaccins_grippe=ifelse(is.na(vaccins_grippe),0,vaccins_grippe))
if (shallDeleteVars) rm(grippe_lissage)
g<-ggplot(data = essai) +
geom_area(aes(x = numSemaineDepuis2013,
y = deces_standardises_si_pop_2020_ge60),color="#000099",fill="#000099",size=1,alpha=1/4) +
geom_area(aes(x = numSemaineDepuis2013,
y = vaccins_grippe/130),color="#000000",fill="#000000",size=1,alpha=1/2) +
geom_area(aes(x = numSemaineDepuis2013,
y = (essai$Age60_69_dose1+essai$Age70_79_dose1+essai$`Age80+_dose1`)/130),
color="#666666",fill="#333333",size=1,alpha=1/2) +
geom_area(aes(x = numSemaineDepuis2013,
y = (essai$Age60_69_dose2+essai$Age70_79_dose2+essai$`Age80+_dose2`)/130),
color="#666666",fill="#666666",size=1,alpha=1/2) +
geom_vline(xintercept = seq(from=0, to=500, by = 52),linetype = "dashed",color="steelblue")+
geom_vline(xintercept = base::max(essai$numSemaineDepuis2013),color="black")+
geom_hline(yintercept = base::max(essai$bsup_ge60),linetype = "dashed",color="purple")+
geom_hline(yintercept = base::max(essai$binf_ge60),linetype = "dashed",color="purple")+
geom_hline(yintercept = base::max(essai$moyenne_ge60),color="purple")+
theme(axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.title.y = element_text(color="#000000", size=15 ),
plot.title = element_text(color="#003366", size=25 ))+
ylab("Décès hebdomadaires standardisés")+
geom_text(x=235, y=base::max(essai$deces_standardises_si_pop_2020_ge60), label="2017",size=6)+
geom_text(x=287, y=base::max(essai$deces_standardises_si_pop_2020_ge60), label="2018",size=6)+
geom_text(x=339, y=base::max(essai$deces_standardises_si_pop_2020_ge60), label="2019",size=6)+
geom_text(x=391, y=base::max(essai$deces_standardises_si_pop_2020_ge60), label="2020",size=6)+
geom_text(x=440, y=base::max(essai$deces_standardises_si_pop_2020_ge60), label="2021",size=6)+
annotate(geom = "text", x = 400, y = 4000, label = "vaccins antigrppaux", color = "black",
angle = 90, size = 5)+
annotate(geom = "text", x = 430, y = 4000, label = "vaccins anticovid", color = "black",
angle = 90, size = 5)+
ggtitle(paste0("Décès hebdomadaires standardisés des plus de 60 ans et vaccinations"))+
xlim(base::min(essai$numSemaineDepuis2013), base::max(essai$numSemaineDepuis2013)+20)+
theme(axis.text.y = element_text(face = "bold", color = "#000000",size = 12, angle = 45))+
annotate("rect",
xmin = base::max(essai$numSemaineDepuis2013)+2,
xmax = base::max(essai$numSemaineDepuis2013)+20,
ymin = 0,
ymax = base::max(essai$deces_standardises_si_pop_2020_ge60),
alpha = 1,
fill = "white")+
annotate(geom = "text", x = base::max(essai$numSemaineDepuis2013), y = 15000, label = "2", color = "black",
angle = 45, size = 5,fontface = "bold")+
annotate(geom = "text", x = base::max(essai$numSemaineDepuis2013), y = 7500, label = "1", color = "black",
angle = 45, size = 5,fontface = "bold")+
annotate(geom = "text", x = base::max(essai$numSemaineDepuis2013)+10, y = 7500, label = "nombre de doses en millions", color = "black",
angle = 90, size = 5)
print(g)
dev.print(device = png, file = pngFileRelPath, width = 1000)
if (shallDeleteVars) rm(essai)
#es_deces_standard_pays_semaine__analysables <- es_deces_standard_owid_vaccination_by_pays_semaine %>%
# filter(time >"2015-01-01")
#es_deces_standard_pays_semaine__surmortalite <- es_deces_standard_owid_vaccination_by_pays_semaine %>%
# filter(surmortalite == "surmortalite") %>%
# filter(time >= "2020W01") %>%
# filter(time <= "2020W40")
#---------------------------------------#
#### realisation de cartes dynamiques avec 1 carte par semaine####
#---------------------------------------#
# TODO : geodata is not defined !
#map_data_init <- inner_join(geodata, es_deces_standard_pays_semaine_plus_40)
#
#es_deces_week_France_numero_semaine <- es_deces_week_France_numero_semaine %>%
# mutate(saison=if_else(numSemaineDanslAnnee < 13 | numSemaineDanslAnnee > 51, "hiver", "autre"))
#es_deces_week_France_numero_semaine <- es_deces_week_France_numero_semaine %>%
# mutate(saison=if_else(numSemaineDanslAnnee > 12 & numSemaineDanslAnnee < 26, "printemps", saison))
#es_deces_week_France_numero_semaine <- es_deces_week_France_numero_semaine %>%
# mutate(saison=if_else(numSemaineDanslAnnee > 25 & numSemaineDanslAnnee < 39, "?t?", saison))
#es_deces_week_France_numero_semaine <- es_deces_week_France_numero_semaine %>%
# mutate(saison=if_else(numSemaineDanslAnnee > 38 & numSemaineDanslAnnee < 52, "automne", saison))
#
#
#
#classe1 <- map_data %>%
# filter(geo == "FR")
#
#classe1 <- classe1 %>%
# mutate (id="classe1", geo = "classe1", geometry=geocanada, deces_standard_tot_rec="[0, 1.203e+05)")
#classe2 <- classe1 %>%
# mutate (id="classe1", geo = "classe1", geometry=geocanada, deces_standard_tot_rec="[1.203e+05, 1.503e+05)")
#classe3 <- classe1 %>%
# mutate (id="classe1", geo = "classe1", geometry=geocanada, deces_standard_tot_rec="[1.503e+05, 1.763e+05)")
#classe4 <- classe1 %>%
# mutate (id="classe1", geo = "classe1", geometry=geocanada, deces_standard_tot_rec="[1.763e+05, 2.028e+05)")
#classe5 <- classe1 %>%
# mutate (id="classe1", geo = "classe1", geometry=geocanada, deces_standard_tot_rec="[2.028e+05, 2.328e+05)")
#classe6 <- classe1 %>%
# mutate (id="classe1", geo = "classe1", geometry=geocanada, deces_standard_tot_rec="[2.328e+05, 2.652e+05)")
#classe7 <- classe1 %>%
# mutate (id="classe1", geo = "classe1", geometry=geocanada, deces_standard_tot_rec="[2.652e+05, 3.023e+05)")
#classe8 <- classe1 %>%
# mutate (id="classe1", geo = "classe1", geometry=geocanada, deces_standard_tot_rec="[3.023e+05, 3.563e+05)")
#classe9 <- classe1 %>%
# mutate (id="classe1", geo = "classe1", geometry=geocanada, deces_standard_tot_rec="[3.563e+05, 4.677e+05)")
#
#for (i in 158:432) {
# map_data <- map_data_init %>%
# filter(es_deces_week_France_numero_semaine == i)
#
# semaine <- es_deces_week_France_numero_semaine %>%
# filter(es_deces_week_France_numero_semaine == i) %>%
# select(numSemaineDanslAnnee)
# annee <- es_deces_week_France_numero_semaine %>%
# filter(es_deces_week_France_numero_semaine == i) %>%
# select(annee)
# saison <- es_deces_week_France_numero_semaine %>%
# filter(es_deces_week_France_numero_semaine == i) %>%
# select(saison)
#
# map_data <- map_data %>%
# rbind(classe1, classe2, classe3, classe4, classe5, classe6, classe7, classe8, classe9)
#
# p <- ggplot(data=map_data) + geom_sf(aes(fill=deces_standard_tot_rec), color="dim grey", size=.1) +
# scale_fill_brewer(palette = "Oranges") +
# guides(fill = guide_legend(reverse=T, title = "Nombre de d?c?s")) +
# labs(title= paste0("Nombre de d?c?s de la semaine ", semaine[1, 1], " de l'ann?e ", annee[1, 1], " (saison ", saison[1, 1], ")"),
# caption="(C) EuroGeographics for the administrative boundaries
# Map produced in R with a help from Eurostat-package <github.com/ropengov/eurostat/>") +
# theme_light() + theme(legend.position=c(.1, .5)) +
# coord_sf(xlim=c(-22, 34), ylim=c(35, 70))
#
# ggsave(paste0("gen/images/carte", i, ".png"), plot=p, width = 11, height = 8)
#}
#-------------------------------------------------------------#
#### Graphe deces_hebdo_std_moyenne_mobile de chaque pays ####
#-------------------------------------------------------------#
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_albanie, 1000, 157)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_allemagne, 30000)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_autriche, 3000)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_belgique, 4000)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_bulgarie, 5000)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_chypre, 300, 157)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_croatie, 2000, 104)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_danmark, 2000)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_espagne, 25000)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_estonie, 500)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_finlande, 2000)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_france, 20000)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_grece, 5000, 157)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_hongrie, 5000)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_islande, 100)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_italie, 30000)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_lettonie, 1000)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_lichtenstein, 20)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_lituanie, 2000)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_luxembourg, 200)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_malte, 200)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_montenegro, 200)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_norvege, 1500)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_paysbas, 6000)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_pologne, 17000)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_portugal, 6000)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_roumanie, 10000, 157)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_rtcheque, 5000)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_serbie, 5000)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_slovaquie, 3000)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_slovenie, 1000)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_suede, 3000)
a__f_plot_es_deces_hebdo_std_moyenne_mobile(es_deces_standard_pays_semaine_suisse, 3000)
#---------------------------------------------------------------------------#
#### vaccinations et deces standard ####
#---------------------------------------------------------------------------#
# Aucune donnée pour les moins de 40 ans en Allemagne
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_allemagne)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_autriche)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_belgique)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_chypre)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_croatie)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_danmark)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_espagne)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_estonie)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_finlande)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_france)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_grece)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_hongrie)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_islande)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_italie)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_malte)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_norvege)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_paysbas)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_pologne)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_portugal)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_serbie)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_suede)
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_suisse)
#---------------------------------------------------------------------------#
#### vaccinations et deces standard avec interpolation linéaire ####
#---------------------------------------------------------------------------#
# Aucune donnée pour les moins de 40 ans en Allemagne
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_allemagne)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_autriche)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_belgique)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_chypre)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_croatie)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_danmark)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_espagne)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_estonie)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_finlande)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_france)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_grece)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_hongrie)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_islande)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_italie)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_malte)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_norvege)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_paysbas)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_pologne)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_portugal)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_rtcheque)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_serbie)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_suede)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_suisse)
#---------------------------------------#
#### vaccinations et deces compare ####
#---------------------------------------#
# Aucune donnée pour les moins de 40 ans en Allemagne
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_allemagne)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_autriche)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_belgique)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_chypre)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_croatie)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_danmark)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_espagne)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_estonie)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_finlande)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_france)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_grece)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_hongrie)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_islande)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_italie)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_luxembourg)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_malte)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_norvege)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_paysbas)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_pologne)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_portugal)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_serbie)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_suede)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_suisse)
#---------------------------------------------#
#### vaccinations et deces europe ####
#---------------------------------------------#
es_deces_standard_pays_semaine_europe <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
filter(geo %in% c('AT','BE','CY','HR','DK',
'ES','EE','FI','FR','EL','HU',
'IS','IT','LU','MT','NO','NL',
'PL','PT','SE')&numSemaineDepuis2013<=490) %>%
select(numSemaineDepuis2013,semaine,annee,time,
deces_tot_15_24,
deces_tot_25_49,
deces_tot_50_59,
deces_tot_60_69,
deces_tot_70_79,
deces_tot_plus_80,
deces_standardises_si_pop_2020_15_24,
deces_standardises_si_pop_2020_25_49,
deces_standardises_si_pop_2020_50_59,
deces_standardises_si_pop_2020_60_69,
deces_standardises_si_pop_2020_70_79,
deces_standardises_si_pop_2020_ge80,
predit_stand_15_24,
predit_stand_25_49,
predit_stand_50_59,
predit_stand_60_69,
predit_stand_70_79,
predit_stand_plus_80,
predit_15_24,
predit_25_49,
predit_50_59,
predit_60_69,
predit_70_79,
predit_plus_80,
pop_week_15_24,
pop_week_25_49,
pop_week_50_59,
pop_week_60_69,
pop_week_70_79,
pop_week_ge80,
Age15_17,
Age18_24,
Age25_49,
Age50_59,
Age60_69,
Age70_79,
`Age80+`,
Age15_17_dose1,
Age18_24_dose1,
Age25_49_dose1,
Age50_59_dose1,
Age60_69_dose1,
Age70_79_dose1,
`Age80+_dose1`,
Age15_17_dose2,
Age18_24_dose2,
Age25_49_dose2,
Age50_59_dose2,
Age60_69_dose2,
Age70_79_dose2,
`Age80+_dose2`,
Age15_17_dose3,
Age18_24_dose3,
Age25_49_dose3,
Age50_59_dose3,
Age60_69_dose3,
Age70_79_dose3,
`Age80+_dose3`,
Age15_17_dose4,
Age18_24_dose4,
Age25_49_dose4,
Age50_59_dose4,
Age60_69_dose4,
Age70_79_dose4,
`Age80+_dose4`,
Age15_17_dose5,
Age18_24_dose5,
Age25_49_dose5,
Age50_59_dose5,
Age60_69_dose5,
Age70_79_dose5,
`Age80+_dose5`,
diff_deces_tot_predit_15_24,
diff_deces_tot_predit_25_49,
diff_deces_tot_predit_50_59,
diff_deces_tot_predit_60_69,
diff_deces_tot_predit_70_79,
diff_deces_tot_predit_ge80,
diff_deces_tot_predit_stand_15_24,
diff_deces_tot_predit_stand_25_49,
diff_deces_tot_predit_stand_50_59,
diff_deces_tot_predit_stand_60_69,
diff_deces_tot_predit_stand_70_79,
diff_deces_tot_predit_stand_ge80)
es_deces_standard_pays_semaine_europe <-es_deces_standard_pays_semaine_europe %>%
group_by(numSemaineDepuis2013) %>%
summarise(semaine=base::min(semaine,na.rm=TRUE),
annee=base::min(semaine,na.rm=TRUE),
time=base::min(time),
deces_standardises_si_pop_2020_15_24=sum(deces_standardises_si_pop_2020_15_24),
deces_standardises_si_pop_2020_25_49=sum(deces_standardises_si_pop_2020_25_49),
deces_standardises_si_pop_2020_50_59=sum(deces_standardises_si_pop_2020_50_59),
deces_standardises_si_pop_2020_60_69=sum(deces_standardises_si_pop_2020_60_69),
deces_standardises_si_pop_2020_70_79=sum(deces_standardises_si_pop_2020_70_79),
deces_standardises_si_pop_2020_ge80=sum(deces_standardises_si_pop_2020_ge80),
predit_stand_15_24=sum(predit_stand_15_24),
predit_stand_25_49=sum(predit_stand_25_49),
predit_stand_50_59=sum(predit_stand_50_59),
predit_stand_60_69=sum(predit_stand_60_69),
predit_stand_70_79=sum(predit_stand_70_79),
predit_stand_plus_80=sum(predit_stand_plus_80),
deces_tot_15_24=sum(deces_tot_15_24),
deces_tot_25_49=sum(deces_tot_25_49),
deces_tot_50_59=sum(deces_tot_50_59),
deces_tot_60_69=sum(deces_tot_60_69),
deces_tot_70_79=sum(deces_tot_70_79),
deces_tot_plus_80=sum(deces_tot_plus_80),
predit_15_24=sum(predit_15_24),
predit_25_49=sum(predit_25_49),
predit_50_59=sum(predit_50_59),
predit_60_69=sum(predit_60_69),
predit_70_79=sum(predit_70_79),
predit_plus_80=sum(predit_plus_80),
pop_week_15_24=sum(pop_week_15_24),
pop_week_25_49=sum(pop_week_25_49),
pop_week_50_59=sum(pop_week_50_59),
pop_week_60_69=sum(pop_week_60_69),
pop_week_70_79=sum(pop_week_70_79),
pop_week_ge80=sum(pop_week_ge80),
Age15_17=sum(Age15_17),
Age18_24=sum(Age18_24),
Age25_49=sum(Age25_49),
Age50_59=sum(Age50_59),
Age60_69=sum(Age60_69),
Age70_79=sum(Age70_79),
`Age80+`=sum(`Age80+`),
Age15_17_dose1=sum(Age15_17_dose1),
Age18_24_dose1=sum(Age18_24_dose1),
Age25_49_dose1=sum(Age25_49_dose1),
Age50_59_dose1=sum(Age50_59_dose1),
Age60_69_dose1=sum(Age60_69_dose1),
Age70_79_dose1=sum(Age70_79_dose1),
`Age80+_dose1`=sum(`Age80+_dose1`),
Age15_17_dose2=sum(Age15_17_dose2),
Age18_24_dose2=sum(Age18_24_dose2),
Age25_49_dose2=sum(Age25_49_dose2),
Age50_59_dose2=sum(Age50_59_dose2),
Age60_69_dose2=sum(Age60_69_dose2),
Age70_79_dose2=sum(Age70_79_dose2),
`Age80+_dose2`=sum(`Age80+_dose2`),
Age15_17_dose3=sum(Age15_17_dose3),
Age18_24_dose3=sum(Age18_24_dose3),
Age25_49_dose3=sum(Age25_49_dose3),
Age50_59_dose3=sum(Age50_59_dose3),
Age60_69_dose3=sum(Age60_69_dose3),
Age70_79_dose3=sum(Age70_79_dose3),
`Age80+_dose3`=sum(`Age80+_dose3`),
Age15_17_dose4=sum(Age15_17_dose4),
Age18_24_dose4=sum(Age18_24_dose4),
Age25_49_dose4=sum(Age25_49_dose4),
Age50_59_dose4=sum(Age50_59_dose4),
Age60_69_dose4=sum(Age60_69_dose4),
Age70_79_dose4=sum(Age70_79_dose4),
`Age80+_dose4`=sum(`Age80+_dose4`),
Age15_17_dose5=sum(Age15_17_dose5),
Age18_24_dose5=sum(Age18_24_dose5),
Age25_49_dose5=sum(Age25_49_dose5),
Age50_59_dose5=sum(Age50_59_dose5),
Age60_69_dose5=sum(Age60_69_dose5),
Age70_79_dose5=sum(Age70_79_dose5),
`Age80+_dose5`=sum(`Age80+_dose5`),
diff_deces_tot_predit_15_24=sum(diff_deces_tot_predit_15_24),
diff_deces_tot_predit_25_49=sum(diff_deces_tot_predit_25_49),
diff_deces_tot_predit_50_59=sum(diff_deces_tot_predit_50_59),
diff_deces_tot_predit_60_69=sum(diff_deces_tot_predit_60_69),
diff_deces_tot_predit_70_79=sum(diff_deces_tot_predit_70_79),
diff_deces_tot_predit_ge80=sum(diff_deces_tot_predit_ge80),
diff_deces_tot_predit_stand_15_24=sum(diff_deces_tot_predit_stand_15_24),
diff_deces_tot_predit_stand_25_49=sum(diff_deces_tot_predit_stand_25_49),
diff_deces_tot_predit_stand_50_59=sum(diff_deces_tot_predit_stand_50_59),
diff_deces_tot_predit_stand_60_69=sum(diff_deces_tot_predit_stand_60_69),
diff_deces_tot_predit_stand_70_79=sum(diff_deces_tot_predit_stand_70_79),
diff_deces_tot_predit_stand_ge80=sum(diff_deces_tot_predit_stand_ge80))%>%
mutate(Response_measure ='NA')
a__f_plot_es_deces_hebdo_std_vaccination(es_deces_standard_pays_semaine_europe)
a__f_plot_es_deces_hebdo_compare_vaccination(es_deces_standard_pays_semaine_europe)
a__f_plot_es_deces_hebdo_std_interp_vaccination(es_deces_standard_pays_semaine_europe)
if (shallDeleteVars) rm(es_deces_standard_pays_semaine_europe)
#----------------------------------------------------#
#### génération des tableaux Spearman et Wilcoxon ####
#----------------------------------------------------#
#! Il faut avoir fait tourner les graphiques précédents !
#Création des fonctions de format
a__f_spearman_icon_formatter <- function() {
formatter("span",
style = x ~ style(color = ifelse(x, "green", "red")), x ~ icontext(ifelse(x, "ok", "remove"), "")
)
}
a__f_spearman_positive_formatter <- function() {
formatter("span",
style = ~ style(color = ifelse(`estimateur de Spearman` < 0, "darkgreen", "red"))
)
}
a__f_spearman_arrow_formatter <- function() {
formatter("span",
style = x ~ style(color = ifelse(x, "red", "green")), x ~ icontext(ifelse(x, "arrow-up", "arrow-down"), "")
)
}
for (pays in c('autriche','belgique','croatie','danmark','espagne',
'estonie','finlande','france','grece','hongrie',
'italie','malte','norvege','pologne','portugal',
'suede','europe')){
nom_table_spearman <- paste0("gen/rds/table_spearman_stand_",pays,".RDS")
table_spearman_en_cours <- readRDS(file = nom_table_spearman)
table_spearman_en_cours <- table_spearman_en_cours %>%
mutate(`p-value significative` = ifelse((`p-value de Spearman`)<0.05,TRUE,FALSE),
`sens de l'estimateur`= ifelse((`estimateur de Spearman`)>0,TRUE,FALSE) )
widget_format_table_spearman = format_table(table_spearman_en_cours,
list(`estimateur de Spearman` = a__f_spearman_positive_formatter(),
`p-value significative` = a__f_spearman_icon_formatter(),
`sens de l'estimateur` = a__f_spearman_arrow_formatter()))
nom_table_wilcoxon <- paste0("gen/rds/table_wilcoxon_stand_",pays,".RDS")
table_wilcoxon_en_cours <- readRDS(file = nom_table_wilcoxon)
table_wilcoxon_en_cours <- table_wilcoxon_en_cours %>%
mutate(`p-value significative` = ifelse((`p-value de Wilcoxon 2021-2020`)<0.05,TRUE,FALSE))
widget_format_table_wilcoxon = format_table(table_wilcoxon_en_cours,
list(`p-value significative` = a__f_spearman_icon_formatter()))
html_header="
<head>
<meta charset=\"utf-8\">
<meta name=\"viewport\" content=\"width=device-width, initial-scale=1\">
<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css\">
</head>
<body>
"
write(paste(html_header, widget_format_table_spearman, sep=""), paste0("gen/html/table_spearman_",pays,".html"))
write(paste(html_header, widget_format_table_wilcoxon, sep=""), paste0("gen/html/table_wilcoxon_",pays,".html"))
table_spearman_en_15_24 <- table_spearman_en_cours %>% filter(`tranche d'age` == "15-24")
}
if (shallDeleteVars) rm(html_header)
if (shallDeleteVars) rm(nom_table_spearman)
if (shallDeleteVars) rm(table_spearman_en_cours)
if (shallDeleteVars) rm(widget_format_table_spearman)
if (shallDeleteVars) rm(nom_table_wilcoxon)
if (shallDeleteVars) rm(table_wilcoxon_en_cours)
if (shallDeleteVars) rm(widget_format_table_wilcoxon)
#------------------------------------------------------------------------------------#
#### rechercher de DRIFTS entre les tranches d'âges par pays ####
#------------------------------------------------------------------------------------#
table_spearman_age <- data.frame()
for (pays in c('AT','BE','CY','HR','DK',
'ES','EE','FI','FR','EL','HU',
'IS','IT','LU','MT','NO',
'PL','PT','SE')){
table_pays <- b__es_deces_week_standardises_si_pop_2020_owid_vaccination %>%
ungroup() %>%
filter(geo == pays) %>% select(annee,
diff_deces_tot_predit_15_24,
diff_deces_tot_predit_25_49,
diff_deces_tot_predit_50_59,
diff_deces_tot_predit_60_69,
diff_deces_tot_predit_70_79,
diff_deces_tot_predit_ge80
)
table_2021 <- table_pays %>% filter(annee==2021)
table_2020 <- table_pays %>% filter(annee==2020)
table_2019 <- table_pays %>% filter(annee==2019)
res15_24_2021<-cor.test(table_2021$diff_deces_tot_predit_15_24,table_2021$diff_deces_tot_predit_70_79 ,method="spearman")
res25_49_2021<-cor.test(table_2021$diff_deces_tot_predit_25_49,table_2021$diff_deces_tot_predit_70_79 ,method="spearman")
res60_69_2021<-cor.test(table_2021$diff_deces_tot_predit_60_69,table_2021$diff_deces_tot_predit_70_79 ,method="spearman")
res50_59_2021<-cor.test(table_2021$diff_deces_tot_predit_50_59,table_2021$diff_deces_tot_predit_70_79 ,method="spearman")
resge80_2021<-cor.test(table_2021$diff_deces_tot_predit_ge80,table_2021$diff_deces_tot_predit_70_79 ,method="spearman")
res15_24_2020<-cor.test(table_2020$diff_deces_tot_predit_15_24,table_2020$diff_deces_tot_predit_70_79 ,method="spearman")
res25_49_2020<-cor.test(table_2020$diff_deces_tot_predit_25_49,table_2020$diff_deces_tot_predit_70_79 ,method="spearman")
res60_69_2020<-cor.test(table_2020$diff_deces_tot_predit_60_69,table_2020$diff_deces_tot_predit_70_79 ,method="spearman")
res50_59_2020<-cor.test(table_2020$diff_deces_tot_predit_50_59,table_2020$diff_deces_tot_predit_70_79 ,method="spearman")
resge80_2020<-cor.test(table_2020$diff_deces_tot_predit_ge80,table_2020$diff_deces_tot_predit_70_79 ,method="spearman")
res15_24_2019<-cor.test(table_2019$diff_deces_tot_predit_15_24,table_2019$diff_deces_tot_predit_70_79 ,method="spearman")
res25_49_2019<-cor.test(table_2019$diff_deces_tot_predit_25_49,table_2019$diff_deces_tot_predit_70_79 ,method="spearman")
res60_69_2019<-cor.test(table_2019$diff_deces_tot_predit_60_69,table_2019$diff_deces_tot_predit_70_79 ,method="spearman")
res50_59_2019<-cor.test(table_2019$diff_deces_tot_predit_50_59,table_2019$diff_deces_tot_predit_70_79 ,method="spearman")
resge80_2019<-cor.test(table_2019$diff_deces_tot_predit_ge80,table_2019$diff_deces_tot_predit_70_79 ,method="spearman")
pays_concerne<-c(pays,pays,pays,pays,pays)
tranches_dages<-c("15-24","25-49","60-69","50-59","ge80")
estimateur_2021<-c(res15_24_2021$estimate,res25_49_2021$estimate,res60_69_2021$estimate,res50_59_2021$estimate,resge80_2021$estimate)
pvalue_2021<-c(res15_24_2021$p.value,res25_49_2021$p.value,res60_69_2021$p.value,res50_59_2021$p.value,resge80_2021$p.value)
pos_pvalue_2021 <- c(ifelse(res15_24_2021$p.value<0.05,TRUE,FALSE),ifelse(res25_49_2021$p.value<0.05,TRUE,FALSE),ifelse(res60_69_2021$p.value<0.05,TRUE,FALSE),ifelse(res50_59_2021$p.value<0.05,TRUE,FALSE),ifelse(resge80_2021$p.value<0.05,TRUE,FALSE))
estimateur_2020<-c(res15_24_2020$estimate,res25_49_2020$estimate,res60_69_2020$estimate,res50_59_2020$estimate,resge80_2020$estimate)
pvalue_2020<-c(res15_24_2020$p.value,res25_49_2020$p.value,res60_69_2020$p.value,res50_59_2020$p.value,resge80_2020$p.value)
pos_pvalue_2020 <- c(ifelse(res15_24_2020$p.value<0.05,TRUE,FALSE),ifelse(res25_49_2020$p.value<0.05,TRUE,FALSE),ifelse(res60_69_2020$p.value<0.05,TRUE,FALSE),ifelse(res50_59_2020$p.value<0.05,TRUE,FALSE),ifelse(resge80_2020$p.value<0.05,TRUE,FALSE))
estimateur_2019<-c(res15_24_2019$estimate,res25_49_2019$estimate,res60_69_2019$estimate,res50_59_2019$estimate,resge80_2019$estimate)
pvalue_2019<-c(res15_24_2019$p.value,res25_49_2019$p.value,res60_69_2019$p.value,res50_59_2019$p.value,resge80_2019$p.value)
pos_pvalue_2019 <- c(ifelse(res15_24_2019$p.value<0.05,TRUE,FALSE),ifelse(res25_49_2019$p.value<0.05,TRUE,FALSE),ifelse(res60_69_2019$p.value<0.05,TRUE,FALSE),ifelse(res50_59_2019$p.value<0.05,TRUE,FALSE),ifelse(resge80_2019$p.value<0.05,TRUE,FALSE))
table_temp<-data.frame(list(pays_concerne,tranches_dages,estimateur_2021,pvalue_2021,pos_pvalue_2021,estimateur_2020,pvalue_2020,pos_pvalue_2020,estimateur_2019,pvalue_2019,pos_pvalue_2019))
colnames(table_temp)<-c("geo","tranche d'age","estimateur de Spearman 2021","p-value de Spearman 2021","significativité 2021","estimateur de Spearman 2020","p-value de Spearman 2020","significativité 2020","estimateur de Spearman 2019","p-value de Spearman 2019","significativité 2019")
if(length(table_spearman_age)==0){
table_spearman_age<-table_temp
}else{
table_spearman_age<-table_spearman_age %>%
rbind(table_temp)
}