AH1N1 cases in Finland: Difference between revisions

Latest revision as of 10:32, 26 August 2013

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Question

What was the number of AH1N1 cases in Finland during 2009-2010?

Answer

Data

cases:~100 000^[1]
deaths:~50^[1]

**Lab confirmed flu cases in the 2009-2010 period by week^[2]**
Year	Week	Period	Infl_A new cases	Infl_A cumulative cases	H1N1v new cases	H1N1v cumulative cases	Infl_B new cases	Infl_B cumulative cases
2009	20	11.05-17.05	2	10	0	2	13	33
2009	21	18.05-24.05	7	17	5	7	7	40
2009	22	25.05-31.05	5	22	3	10	4	44
2009	23	01.06-07.06	5	27	0	10	4	48
2009	24	08.06-14.06	16	43	7	17	0	48
2009	25	15.06-21.06	17	60	15	32	1	49
2009	26	22.06-28.06	12	72	10	42	4	53
2009	27	29.06-05.07	41	113	34	76	1	54
2009	28	06.07-12.07	42	155	39	115	1	55
2009	29	13.07-19.07	48	203	48	163	0	55
2009	30	20.07-26.07	34	237	32	195	0	55
2009	31	27.07-02.08	18	255	12	207	2	57
2009	32	03.08-09.08	15	270	13	220	2	59
2009	33	10.08-16.08	5	275	5	225	0	59
2009	34	17.08-23.08	15	290	12	237	1	60
2009	35	24.08-30.08	12	302	9	246	0	60
2009	36	31.08-06.09	25	327	21	267	3	63
2009	37	07.09-13.09	26	353	23	290	2	65
2009	38	14.09-20.09	17	370	14	304	2	67
2009	39	21.09-27.09	15	385	11	315	0	67
2009	40	28.09-04.10	8	393	7	322	0	67
2009	41	05.10-11.10	58	451	58	380	0	67
2009	42	12.10-18.10	124	575	122	502	1	68
2009	43	19.10-25.10	348	923	332	834	0	68
2009	44	26.10-01.11	749	1672	722	1556	3	71
2009	45	02.11-08.11	1922	3594	1687	3243	3	74
2009	46	09.11-15.11	2662	6256	2169	5412	9	83
2009	47	16.11-22.11	1914	8170	1354	6766	9	92
2009	48	23.11-29.11	851	9021	597	7363	2	94
2009	49	30.11-06.12	265	9286	204	7567	5	99
2009	50	07.12-13.12	86	9372	56	7623	2	101
2009	51	14.12-20.12	33	9405	16	7639	2	103
2009	52	21.12-27.12	17	9422	7	7646	4	107
2010	53	28.12-03.01	12	9434	7	7653	2	109
2010	1	04.01-10.01	10	9444	9	7662	0	109
2010	2	11.01-17.01	9	9453	3	7665	2	111
2010	3	18.01-24.01	1	9454	0	7665	0	111
2010	4	25.01-31.01	3	9457	2	7667	1	112
2010	5	01.02-07.02	1	9458	1	7668	0	112
2010	6	08.02-14.02	1	9459	0	7668	2	114
2010	7	15.02-21.02	0	9459	0	7668	1	115
2010	8	22.02-28.02	0	9459	0	7668	1	116
2010	9	01.03-07.03	2	9461	0	7668	1	117
2010	10	08.03-14.03	1	9462	1	7669	2	119

**Lab confirmed flu cases by age group^[2]**
Age group	A_Infl	H1N1v	B_Infl
0-4	1332	914	31
5-14	2989	2385	26
15-64	4880	4134	57
65+	261	236	5

Unit

#

Dependencies

Formula

Prevalence of swine flu in the unimmune population is assumed to be the same for all sub age groups of the age groups in data above. This is used to calculate the number of swine flu cases in the age groups of our population data.
It is also assumed that vaccinated subjects did not catch swine flu.

+ Show code - Hide code

# Observed swine flu cases expanded to all age groups

library(OpasnetBaseUtils)

Pop <- op_baseGetData("opasnet_base", "Op_en2949")[,-1]
Imm <- op_baseGetData("opasnet_base", "Op_en4943")[,-1]
names(Pop)[length(Pop)] <- "pop"
names(Imm)[length(Imm)] <- "imm"

Age <- as.factor(c("0-4 ","5-9","10-14","15-19","20-24","25-29","30-34","35-39","40-44","45-49","50-54","55-59",
"60-64","65-69","70-74","75-79","80+","All"))
cases <- c(914, rep(2385, 2), rep(4134, 10), rep(236, 4), 914+2385+4314+236)

sf <- data.frame(Age, cases)
sf <- merge(sf, Pop)
sf <- merge(sf, Imm)

sff <- data.frame(Age = sf$Age, Result=NA)
for (i in 1:nrow(sf)) {sff[i,2] <- sf$pop[i] * (1 - sf$imm[i]) * sf$cases[i] / sum(sf[sf$cases==sf$cases[i], "pop"] * 
(1 - sf[sf$cases==sf$cases[i], "imm"]))}
sff

#op_baseWrite("opasnet_base", sff)

Result

Keywords

References

↑ ^1.0 ^1.1 fi:Vuoden 2009 influenssapandemia
↑ ^2.0 ^2.1 Infectious disease registry (TTR) maintained by THL [1]

Related files

[wp-1] 1.0 ^1.1 fi:Vuoden 2009 influenssapandemia

[TTR-2] 2.0 ^2.1 Infectious disease registry (TTR) maintained by THL [1]

[1]

[2]

AH1N1 cases in Finland: Difference between revisions

Latest revision as of 10:32, 26 August 2013

Contents

Question

Answer

Data

Unit

Dependencies

Formula

Result

See also

Keywords

References

Related files

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@@ Line 1: / Line 1: @@
 {{variable|moderator=Teemu R|stub=Yes}}
+[[Category:Code under inspection]]
-== Scope ==
+== Question ==
 What was the number of AH1N1 cases in Finland during 2009-2010?
-== Definition ==
+== Answer ==
 === Data ===
@@ Line 502: / Line 503: @@
 *[[A(H1N1)v immunity in the Finnish population]]
+*[[Population of Finland]]
+=== Formula ===
+*Prevalence of swine flu in the unimmune population is assumed to be the same for all sub age groups of the age groups in data above. This is used to calculate the number of swine flu cases in the age groups of our [[Population of Finland| population data]].
+*It is also assumed that vaccinated subjects did not catch swine flu.
+<rcode>
+# Observed swine flu cases expanded to all age groups
+library(OpasnetBaseUtils)
+Pop <- op_baseGetData("opasnet_base", "Op_en2949")[,-1]
+Imm <- op_baseGetData("opasnet_base", "Op_en4943")[,-1]
+names(Pop)[length(Pop)] <- "pop"
+names(Imm)[length(Imm)] <- "imm"
+Age <- as.factor(c("0-4 ","5-9","10-14","15-19","20-24","25-29","30-34","35-39","40-44","45-49","50-54","55-59",
+"60-64","65-69","70-74","75-79","80+","All"))
+cases <- c(914, rep(2385, 2), rep(4134, 10), rep(236, 4), 914+2385+4314+236)
+sf <- data.frame(Age, cases)
+sf <- merge(sf, Pop)
+sf <- merge(sf, Imm)
+sff <- data.frame(Age = sf$Age, Result=NA)
+for (i in 1:nrow(sf)) {sff[i,2] <- sf$pop[i] * (1 - sf$imm[i]) * sf$cases[i] / sum(sf[sf$cases==sf$cases[i], "pop"] *
+(1 - sf[sf$cases==sf$cases[i], "imm"]))}
+sff
+#op_baseWrite("opasnet_base", sff)
+</rcode>
 == Result ==