factoring addtotals2

Graphs.R

@@ -8,23 +8,10 @@ verbose=3
 #latest numbers
 JHH[JHH$Date==max(JHH$Date)&JHH$PSCR %in% c('World','New York,US',"Kazakhstan",'Belgium','US','Netherlands','Europe','Germany','Africa','Iran','Russia','Brazil'),c('confirmed','new_confirmed','active_imputed','deaths','PSCR')]%>% mutate(newrate=round(new_confirmed/active_imputed*100,2))%>% arrange(newrate)
 #overtaking
+map(c('Belgium','Netherlands','Sweden','Germany',"United Kingdom",'Europe','Russia','New York,US'),function(x) overtakenInDays(JHH,x))
+map(c('Belgium','Netherlands','Sweden','Germany',"United Kingdom",'Russia','Europe','New York,US'),function(x) overtakingInDays(JHH,x))
 
-overtakenin(JHH,"Belgium")[1:10]
-overtakenin(JHH,"Netherlands")[1:10]
-overtakenin(JHH,"United Kingdom")[1:10]
-overtakenin(JHH,"Europe")[1:10]
-overtakingin(JHH,"North America")[1:10]
-overtakingin(JHH,'Brazil')
-overtakenin(JHH,'Russia')
-overtakenin(JHH,'New York,US')
-
-overtakingin(JHH,'Germany')
-overtakingin(JHH,'Belgium')
-overtakingin(JHH,'Sweden')
-overtakingin(JHH,'Indonesia')
-overtakingin(JHH,'Peru')
-overtakingin(JHH,'India')
-
+map(c("North America",'Brazil','Indonesia','Peru','India','Russia'),function(x) overtakingInDays(JHH,x))
 #compare my countries
 graph3Dard_fia(ECDC,c("Kazakhstan","Belgium","Netherlands","France"))
 #make all graphs

data/population.csv

@@ -1,5 +1,6 @@
 Country Name,Country Code,2018,
 Holy See,,801,
+Vatican,,801,
 Tuvalu,TUV,11508,
 Nauru,NRU,12704,
 Palau,PLW,17907,

definitions.R

@@ -689,14 +689,13 @@ addTotals3<- function(lpti=ECDC,totregions="", ID='Region'){
     filter(! (!!ID %in% totregions)) 
   World<- unique(lpti1[[ID]])
   varnames=c("confirmed","recovered", "deaths","population")
-  #,'recovered_imputed',"active_imputed") # we impute AFTER this function so no need. 
   for (regio in totregions[!is.na(totregions)]) 
     lpti<- rbind(lpti, 
                 lpti1%>% total(regio ,ID=ID, varnames= varnames,newrow=regio))
 }
 
 
-addTotals2<- function(lpdf=JHH,ID='PSCR'){
+addTotals2<- function(lpdf=JHH,totregions="",ID='PSCR'){
   lpti<- lpdf %>%
     #just to be sure, that if i do it twice i dont get double counts. 
     #And omit USA as country, as we have the individual states already. 
@@ -736,26 +735,26 @@ days2overtake<- function(lpti=JHH,countries=c('Belgium','China','Russia','Nether
   round(mconf/mnew,1)
 }
 
-overtakenin<- function(lpti,country){
+overtakenInDays<- function(lpti,country,nr=7){
   lastdata<- lpti[lpti$Date==max(lpti$Date),c('PSCR','confirmed','new_confirmed')]
   mydata<- subset(lastdata,PSCR==country)
   countries<- subset(lastdata,
                      confirmed<= mydata$confirmed &
                        new_confirmed>=mydata$new_confirmed,
                      select=PSCR)
   oc<- days2overtake(lpti,countries$PSCR)[,country]
-  oc[order(oc,na.last=FALSE)]
+  head(oc[order(oc,na.last=FALSE)],nr)
 
 }
-overtakingin<- function(lpti,country){
+overtakingInDays<- function(lpti,country,nr=7){
   lastdata<- lpti[lpti$Date==max(lpti$Date),c('PSCR','confirmed','new_confirmed')]
   mydata<- subset(lastdata,PSCR==country)
   countries<- subset(lastdata,
                      confirmed>= mydata$confirmed &
                        new_confirmed<=mydata$new_confirmed,
                      select=PSCR)
   oc<- days2overtake(lpti,countries$PSCR)[,country]
-  oc[order(oc,na.last=FALSE)]
+  head(oc[order(oc,na.last=FALSE)],nr)
 }
 
 

loadData.R

@@ -6,9 +6,10 @@ source("definitions.R")# make sure we have our definitions.
 JHH<- makeJHH(force=TRUE) #load data
 JHH0<- JHH
 
-regios<- c(provincializeJHH(),regios)
+regios<- c(list(World=c('World', unique(JHH[['PSCR']]))),provincializeJHH(),regios) #regiosP?
 
 verbose=2
+
 JHH <-  JHH0 %>%
   addPopulation() %>% addTotals2 %>% addRegions( Regiolist= regios)%>% 
   imputeRecovered()%>% extravars() %>% addDoublingDaysAllCountries %>%
@@ -20,7 +21,7 @@ writewithcounters(JHH,name="Covid19JHH") #no factors!
 
 #same with ECDC
 ECDC0 <- makeECDC()
-ECDC <- ECDC0 %>% imputeRecovered()%>%  extravars() %>% 
+ECDC <- ECDC0 %>% addTotals3%>% imputeRecovered()%>%  extravars() %>% 
             addDoublingDaysAllCountries %>% addSimVars(minval=100)
 writewithcounters(ECDC,name= "Covid19ECDC")
 

wip.R

@@ -31,6 +31,36 @@ checkdouble(c('USA','Netherlands'),JHHRegios)
 isdouble(c('Belgium','Netherlands'),regios)
 length(JHHRegios)
 
+addCountryTotals<- function(lpdf=JHH){
+  varnames=c("confirmed","recovered", "deaths","population")
+  existingTotals<- c("China","Australia","Canada",'US')
+  #just to be sure, that if i do it twice i dont get double counts. 
+  #And omit US as country and US states. 
+  lpti<- lpdf %>%
+    filter(!( PSCR %in% existingTotals )) #
+  rbind(lpdf, 
+        lpti%>% totals(c("China","Australia", "Canada",'US'),
+                       ID="Country.Region", varnames= varnames))
+
+}
+addRegionTotals<- function(lpdf=JHH,totRegions=""){
+  existingTotals<- c("South America", "Asia", "Africa", "Europe","China","Australia","Canada",'US','North America',"World")
+  #just to be sure, that if i do it twice i dont get double counts. 
+  #And omit US as country and US states. 
+    lpti<- lpdf %>%
+    filter(!(Country.Region =="US" | PSCR%in% existingTotals )) #we have US and USA
+  if (totRegions[1]=="") totRegions<- c(regios)
+  if (verbose>=3) {
+    print('world totals include the following countries: ')
+    print(paste(World,collapse=","))}
+  varnames=c("confirmed","recovered", "deaths","population")
+  for(myRegion in totRegions){
+    lpdf<- rbind(lpdf, 
+            lpti%>%total(regios[[myRegion]],ID=ID,newrow=myRegion[1], varnames= varnames))
+  }
+}
+tail(JHH0%>%  addPopulation()%>% addCountryTotals %>% addRegionTotals%>% filter(Date==max(Date)),10)
+
 #check colors
 graph3Dard_fia (JHH,regios$continents)