Public policy and vaccination
library(httr)
library(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
library(RColorBrewer)
library(tidyr)
library(dplyr)
library(rvest)
## Loading required package: xml2
library("ggplot2");
disease_names=c("Diptheria",
"Hib","Measles","Mumps",'Pneumococcal',
"Whooping cough",
"Rotavirus","Rubella","Tetanus",
"Chicken pox",
"Polio",
"Hepatitis")
disease_num=c('009',
"012", "021","043","065",
"024",
"077","029",
"033","073",
"026",
"039")
names(disease_num)=disease_names
library(reshape2)
##
## Attaching package: 'reshape2'
## The following object is masked from 'package:tidyr':
##
## smiths
df<-melt(disease_num)
df$disease<-rownames(df)
url <- "http://www9.health.gov.au/cda/source/rpt_3_sel.cfm"
cocorahs <- html_session(url)
form.unfilled <- cocorahs %>% html_node("form") %>% html_form()
getstuff <- function(code){
print(code)
# Specify URL
# Grab Initial Form
# Form is filled in stages. Here, only do country and date
form.filled <- form.unfilled %>%
set_values(
CAUSE=code,REPORT_OPTION=1)
# submit the form and save as a new session
session <- submit_form(cocorahs, form.filled)
# look for a table in the nodes
table <- session %>% html_nodes("table")
print("in here")
# The table you want
df<-table[[1]] %>% html_table()
colnames(df)
colnames(df)<-c("Year","Jan","Feb","Mar","Apr","May","Jun","Jul","Aug","Sep","Oct","Nov","Dec","AnnualTotal")
dd=(spread(df[,c("Year",'AnnualTotal')],key = as.numeric(Year), value = AnnualTotal))
print(head(dd))
return(dd)
}
all_df=lapply(df$value,getstuff)%>% bind_rows()
## [1] 009
## Levels: 009 012 021 024 026 029 033 039 043 065 073 077
## Submitting with 'CAUSE'
## [1] "in here"
## 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
## 1 1 4 0 0 0 0 0 0 0 0 1 0 0 0
## 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018
## 1 0 0 0 0 0 0 4 0 3 2 2 8 8 7
## [1] 012
## Levels: 009 012 021 024 026 029 033 039 043 065 073 077
## Submitting with 'CAUSE'
## [1] "in here"
## 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
## 1 589 490 339 153 71 47 45 35 41 27 20 29 21 18
## 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018
## 1 17 21 17 25 19 23 13 16 20 21 16 17 16 11
## [1] 021
## Levels: 009 012 021 024 026 029 033 039 043 065 073 077
## Submitting with 'CAUSE'
## [1] "in here"
## 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
## 1 1479 1438 4680 4794 1182 478 831 285 240 108 131 31 92 44
## 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018
## 1 10 125 12 65 104 70 194 199 158 339 74 99 81 79
## [1] 043
## Levels: 009 012 021 024 026 029 033 039 043 065 073 077
## Submitting with 'CAUSE'
## [1] "in here"
## 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
## 1 57 64 78 90 157 132 188 174 183 209 113 70 77 102
## 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018
## 1 240 274 582 286 166 97 153 201 216 186 645 804 811 544
## [1] 065
## Levels: 009 012 021 024 026 029 033 039 043 065 073 077
## Submitting with 'CAUSE'
## [1] "in here"
## 1993 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012
## 1 1 1 1754 2415 2221 2356 1676 1445 1470 1628 1554 1639 1883 1824
## 2013 2014 2015 2016 2017 2018
## 1 1552 1564 1498 1664 2049 1473
## [1] 024
## Levels: 009 012 021 024 026 029 033 039 043 065 073 077
## Submitting with 'CAUSE'
## [1] "in here"
## 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
## 1 342 803 4516 5469 4199 4561 10799 5675 4359 5991 9513 5569 5098 8742
## 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
## 1 11151 9759 4857 14294 30186 34836 38755 24093 12368 11863 22540 20099
## 2017 2018
## 1 12194 7124
## [1] 077
## Levels: 009 012 021 024 026 029 033 039 043 065 073 077
## Submitting with 'CAUSE'
## [1] "in here"
## 2010 2011 2012 2013 2014 2015 2016 2017 2018
## 1 3919 3331 3798 3208 3022 4134 2731 7131 2048
## [1] 029
## Levels: 009 012 021 024 026 029 033 039 043 065 073 077
## Submitting with 'CAUSE'
## [1] "in here"
## 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
## 1 104 610 4034 3485 5541 2951 1399 730 371 321 263 252 54 30
## 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018
## 1 29 59 35 35 27 44 58 35 25 16 17 15 10 7
## [1] 033
## Levels: 009 012 021 024 026 029 033 039 043 065 073 077
## Submitting with 'CAUSE'
## [1] "in here"
## 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
## 1 11 13 10 13 7 3 7 8 2 8 2 4 4 6
## 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018
## 1 2 3 3 4 3 2 3 7 4 3 2 7 4 2
## [1] 073
## Levels: 009 012 021 024 026 029 033 039 043 065 073 077
## Submitting with 'CAUSE'
## [1] "in here"
## 1993 1994 1995 1996 1997 2003 2006 2007 2008 2009 2010 2011 2012 2013
## 1 5 27 1 11 5 1 1622 1664 1807 1796 1793 2100 1989 2134
## 2014 2015 2016 2017 2018
## 1 2111 2488 3025 3170 2708
## [1] 026
## Levels: 009 012 021 024 026 029 033 039 043 065 073 077
## Submitting with 'CAUSE'
## [1] "in here"
## 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018
## 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0
## [1] 039
## Levels: 009 012 021 024 026 029 033 039 043 065 073 077
## Submitting with 'CAUSE'
## [1] "in here"
## 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005
## 1 2 242 264 260 214 263 242 285 377 389 403 338 277 245
## 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018
## 1 289 281 253 238 209 180 175 164 162 136 154 132 76
mat<-as.matrix(all_df)
matnorm<-mat/rowSums(mat,na.rm=T)
datnorm<-as.data.frame(matnorm)
head(all_df)
## 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
## 1 1 4 0 0 0 0 0 0 0 0 1 0 0 0
## 2 589 490 339 153 71 47 45 35 41 27 20 29 21 18
## 3 1479 1438 4680 4794 1182 478 831 285 240 108 131 31 92 44
## 4 57 64 78 90 157 132 188 174 183 209 113 70 77 102
## 5 NA NA 1 NA NA NA NA NA NA 1 1754 2415 2221 2356
## 6 342 803 4516 5469 4199 4561 10799 5675 4359 5991 9513 5569 5098 8742
## 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
## 1 0 0 0 0 0 0 4 0 3 2 2 8
## 2 17 21 17 25 19 23 13 16 20 21 16 17
## 3 10 125 12 65 104 70 194 199 158 339 74 99
## 4 240 274 582 286 166 97 153 201 216 186 645 804
## 5 1676 1445 1470 1628 1554 1639 1883 1824 1552 1564 1498 1664
## 6 11151 9759 4857 14294 30186 34836 38755 24093 12368 11863 22540 20099
## 2017 2018
## 1 8 7
## 2 16 11
## 3 81 79
## 4 811 544
## 5 2049 1473
## 6 12194 7124
all_reqd=cbind(df,datnorm)
mat=data.matrix(all_reqd[,-c(1,2)])
colnames(all_reqd)
## [1] "value" "disease" "1991" "1992" "1993" "1994" "1995"
## [8] "1996" "1997" "1998" "1999" "2000" "2001" "2002"
## [15] "2003" "2004" "2005" "2006" "2007" "2008" "2009"
## [22] "2010" "2011" "2012" "2013" "2014" "2015" "2016"
## [29] "2017" "2018"
f<-melt(all_reqd[,-c(1)])
## Using disease as id variables
head(f)
## disease variable value
## 1 Diptheria 1991 0.025000000
## 2 Hib 1991 0.270555811
## 3 Measles 1991 0.084892664
## 4 Mumps 1991 0.008262067
## 5 Pneumococcal 1991 NA
## 6 Whooping cough 1991 0.001037134
cols <- c(colorRampPalette(c("#e7f0fa", "#c9e2f6", "#95cbee", "#0099dc", "#4ab04a", "#ffd73e"))(20),
colorRampPalette(c("#eec73a", "#e29421", "#e29421", "#f05336","#ce472e"), bias=2)(80))
a<-ggplot(f, aes((variable), disease, fill=value)) +
geom_tile(colour="white", size=0.25) +
#remove extra space
scale_y_discrete(expand=c(0,0))+
labs(y="Disease",x="Year",title="Notifications of vaccinated diseases in Australia")+
#remove extra space
#custom breaks on x-axis
scale_x_discrete(expand=c(0,0))+
#maintains aspect ratio.
coord_fixed()+
#set a base size for all fonts
theme_grey(base_size=8)+
#theme options
theme(
#bold font for both axis text
axis.text=element_text(face="bold"),
#set thickness of axis ticks
axis.ticks=element_line(size=0.4),
#remove plot background
plot.background=element_blank(),
#remove plot border
panel.border=element_blank())+
scale_fill_gradientn(colours=cols, limits=c(0, 0.3),
breaks=seq(0.003, 0.276, by=0.01),
#values=c(0,0.01, 0.02, 0.03,0.04,0.05,0.06,0.07,0.08, 0.09,0.1,0.12,0.15,0.175,0.2,0.25,0.3),
na.value=rgb(192,192,192 ,max=255))+
theme(axis.text.x = element_text(angle = 90, hjust = 1))
a
ggsave("vaccination_notification.png",a)
## Saving 12 x 15 in image