Mortality in Europe: Difference between revisions

Latest revision as of 12:12, 12 January 2015

This page is a knowledge crystal of subtype variable. The page identifier is Op_en4635
Moderator:Virpi Kollanus (see all)
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Upload data {{#opasnet_base_link:Op_en4635}}

Question

What is the annual mortality rate in Europe per country and ICD10 category?

Indices

Country (Geo)
Cause of death (Icd10)
Age
Sex
Year
Unit of measurement (Unit) RT means standardised mortality rate.

Answer

Example graphs from the data. [1]

+ Show code - Hide code

library(OpasnetUtils)
library(ggplot2)

d <- opbase.data("Op_en4635", subset = "d", include = list(Icd10 = c("W65-W74", "X60-X84_Y870", "X85-Y09_Y871")))
d$Year <- as.factor(d$Year)
d$Result <- as.numeric(as.character(d$Result))

ggplot(subset(d, Icd10 == "W65-W74"), aes(y = Result, x = Geo, colour = Year))+ geom_point() + labs(title="Drowning per 100000 py")
ggplot(subset(d, Icd10 == "X60-X84_Y870"), aes(y = Result, x = Geo, colour = Year))+ geom_point() + labs(title="Self-harm per 100000 py")
ggplot(subset(d, Icd10 == "X85-Y09_Y871"), aes(y = Result, x = Geo, colour = Year))+ geom_point() + labs(title="Assault per 100000 py")

Rationale

Data

The main data comes from Eurostat from where the file "Causes of death - standardised death rate per 100 000 inhabitants - annual Data (hlth_cd_asdr)" was downloaded on 12th Jan 2015 and stored in Opasnet base.

Other data:

WHO Mortality Database

Unit

Standardised incidence (1/100000py)
Deaths/year

Calculations

This code was used to manage the data before using the OpasnetBaseImport.

Show details

library(reshape2)
library(OpasnetUtils)

d <- read.table("//cesium/jtue$/_Downloads/hlth_cd_asdr.tsv", sep = "\t")
d1 <- strsplit(as.character(d$V1), split = ",")
d1 <- as.data.frame(t(array(unlist(d1), dim = c(length(d1[[1]]), length(d1)))))
colnames(d1) <- c("Unit", "Sex", "Age", "Icd10", "Geo")
colnames(d) <- c("Remove", 2010:1994)
d <- cbind(d1, d)
d$Remove <- NULL
d <- d[2:nrow(d) , ]
d <- melt(d, measure.vars = 6:ncol(d), variable.name = "Year", value.name = "Result")
d$Result <- gsub("[a-z]", "", d$Result)
d$Result[grepl(":", d$Result)] <- NA
d$Result <- as.numeric(d$Result)
d <- dropall(d)
write.csv(d, file = "//cesium/jtue$/_Documents/MortInEurope.csv", row.names = FALSE)

References

@@ Line 1: / Line 1: @@
-{{variable|moderator=|stub=Yes}}
+{{variable|moderator= Virpi Kollanus|stub=Yes}}
- '''Boxes with dashed borders''' contain brief guidance text
- for completing the entries for new variables.
-== Scope ==
+== Question ==
- This includes a verbal definition of the spatial, temporal, and other limits
+What is the annual mortality rate in Europe per country and ICD10 category?
- (system boundaries) of the variable. The scope is defined according to the use
- purpose of the assessment(s) that the variable belongs to.
-== Definition ==
+'''Indices
+*Country (Geo)
+*Cause of death (Icd10)
+*Age
+*Sex
+*Year
+*Unit of measurement (Unit) RT means standardised mortality rate.
+== Answer ==
+Example graphs from the data. [http://en.opasnet.org/en-opwiki/index.php?title=Special:RTools&id=FGBT3vMEcUavCJLu]
+<rcode graphics=1>
+library(OpasnetUtils)
+library(ggplot2)
+d <- opbase.data("Op_en4635", subset = "d", include = list(Icd10 = c("W65-W74", "X60-X84_Y870", "X85-Y09_Y871")))
+d$Year <- as.factor(d$Year)
+d$Result <- as.numeric(as.character(d$Result))
+ggplot(subset(d, Icd10 == "W65-W74"), aes(y = Result, x = Geo, colour = Year))+ geom_point() + labs(title="Drowning per 100000 py")
+ggplot(subset(d, Icd10 == "X60-X84_Y870"), aes(y = Result, x = Geo, colour = Year))+ geom_point() + labs(title="Self-harm per 100000 py")
+ggplot(subset(d, Icd10 == "X85-Y09_Y871"), aes(y = Result, x = Geo, colour = Year))+ geom_point() + labs(title="Assault per 100000 py")
+</rcode>
+== Rationale ==
 === Data ===
- Description of the data used for obtaining the value of the variable
+The main data comes from [http://ec.europa.eu/eurostat/data/database Eurostat] from where the file "Causes of death - standardised death rate per 100 000 inhabitants - annual Data (hlth_cd_asdr)" was downloaded on 12th Jan 2015 and stored in Opasnet base.
- (e.g. measurement data; mathematical method and its parameters). <br>
- Please include references (preferably using the ''<nowiki><ref> </ref></nowiki>'' tags)
- and links to original data, as appropriate.
-=== Dependencies ===
+'''Other data:
- List of upstream variables.
+[http://www.who.int/healthinfo/morttables/en/index.html WHO Mortality Database]
- The variables can be listed used descriptive (free-format) names or unambiguous identifiers
- (e.g. [[Analytica]] IDs).
 === Unit ===
- Unit in which the result is expressed.
+* Standardised incidence (1/100000py)
+* Deaths/year
+=== Calculations ===
-=== Formula ===
+This code was used to manage the data before using the OpasnetBaseImport.
- Algebra or other explicit methods if possible
+{{hidden|
- (e.g. [[Analytica]] code between the ''<nowiki><anacode> </anacode></nowiki>'' tags).
+<pre>
+library(reshape2)
+library(OpasnetUtils)
-== Result ==
+d <- read.table("//cesium/jtue$/_Downloads/hlth_cd_asdr.tsv", sep = "\t")
+d1 <- strsplit(as.character(d$V1), split = ",")
+d1 <- as.data.frame(t(array(unlist(d1), dim = c(length(d1[[1]]), length(d1)))))
+colnames(d1) <- c("Unit", "Sex", "Age", "Icd10", "Geo")
+colnames(d) <- c("Remove", 2010:1994)
+d <- cbind(d1, d)
+d$Remove <- NULL
+d <- d[2:nrow(d) , ]
+d <- melt(d, measure.vars = 6:ncol(d), variable.name = "Year", value.name = "Result")
+d$Result <- gsub("[a-z]", "", d$Result)
+d$Result[grepl(":", d$Result)] <- NA
+d$Result <- as.numeric(d$Result)
+d <- dropall(d)
+write.csv(d, file = "//cesium/jtue$/_Documents/MortInEurope.csv", row.names = FALSE)
- If possible, a numerical expression or distribution.
+</pre>
+}}
 ==See also==
- Links to relevant information that does not belong to ''Definition''.
 ==References==
- ...will appear here automatically, if cited above using the ''<nowiki><ref> </ref></nowiki>'' tags.
- Additional references can also be listed here.
 <references/>
+[[Category:Data]]