R/contacts.R
In cbreto/panelPomp: Inference for Panel Partially Observed Markov Processes
Defines functions
contacts
Documented in
contacts
##' Contacts model
##'
##' A panel model for dynamic variation in sexual contacts, with
##' data from Vittinghof et al (1999). The model was developed by
##' Romero-Severson et al (2015) and discussed by \Breto et al (2020).
##'
##' @param params parameter vector.
##' @return
##' A \code{panelPomp} object.
##'
##' @author Edward L. Ionides
##'
##' @examples
##' \donttest{
##' contacts()
##' }
##' @export
##'
##' @references \breto2020
##'
##' \romeroseverson2015
##'
##' \vittinghoff1999
##' @family panelPomp examples
contacts <- function(params=c(mu_X=1.75,sigma_X=2.67,mu_D=3.81,
sigma_D=4.42,mu_R=0.04,sigma_R=0,alpha=0.90)){
contact_data <- read.table(
text = '"y1" "y2" "y3" "y4" "individual"
5 0 0 0 1
2 2 31 4 2
9 2 0 0 3
12 8 10 6 4
0 10 4 1 5
25 23 15 2 6
12 6 0 0 7
10 2 0 4 8
31 58 24 48 9
0 0 0 0 10
32 42 9 1 11
5 4 12 2 12
0 1 0 1 13
2 0 3 0 14
1 3 0 0 15
92 40 7 5 16
3 0 1 10 17
2 4 3 3 18
5 1 3 2 19
18 1 22 2 20
0 12 12 11 21
5 9 15 19 22
20 10 0 0 23
1 0 0 6 24
9 8 5 6 25
17 7 10 10 26
0 1 0 3 27
0 3 13 5 28
15 16 12 8 29
9 0 1 1 30
0 1 0 0 31
15 5 9 0 32
0 25 0 0 33
75 59 45 30 34
160 34 40 145 35
2 0 0 4 36
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150 30 49 22 42
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58 23 6 4 46
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33 17 2 0 58
0 2 15 8 59
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14 13 1 8 64
12 3 0 0 65
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2 4 2 2 71
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8 127 99 45 73
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1 1 20 7 76
3 1 0 0 77
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4 3 0 3 79
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1 0 0 2 81
23 10 1 2 82
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5 0 0 0 85
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14 1 0 0 88
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4 7 1 1 90
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3 4 1 2 92
5 40 1 52 93
15 0 6 0 94
0 2 6 0 95
23 10 4 3 96
7 25 51 3 97
16 30 5 1 98
10 2 0 0 99
0 1 0 4 100
10 22 11 3 101
2 0 0 0 102
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11 0 0 0 112
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6 10 2 72 114
6 3 6 4 115
3 1 5 2 116
8 8 7 12 117
1 1 0 0 118
0 0 0 0 119
236 101 26 32 120
0 2 1 18 121
0 0 0 0 122
91 0 0 0 123
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0 0 2 0 127
27 35 15 16 128
0 0 0 0 129
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1 6 2 2 137
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9 0 0 0 139
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50 3 0 0 143
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33 46 105 96 147
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6 1 1 1 160
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31 31 15 5 162
72 43 56 61 163
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5 6 6 11 168
12 0 0 0 169
22 58 5 4 170
1 23 14 0 171
25 2 9 4 172
0 0 0 1 173
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4 4 5 2 175
2 4 0 8 176
4 4 0 0 177
15 26 30 26 178
2 12 2 0 179
22 3 9 58 180
0 0 0 0 181
4 5 3 1 182
14 50 29 0 183
6 3 1 1 184
2 2 1 1 185
4 0 5 1 186
37 57 20 9 187
31 1 0 0 188
2 6 11 3 189
54 12 3 4 190
32 17 6 2 191
3 0 1 2 192
13 0 3 9 193
3 30 2 1 194
0 0 0 0 195
0 0 0 0 196
69 0 0 0 197
1 1 1 0 198
36 30 22 80 199
0 0 0 0 200
2 2 60 84 201
44 0 0 2 202
0 0 0 1 203
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2 1 0 4 205
5 11 18 17 206
33 45 6 15 207
34 18 60 54 208
0 0 0 0 209
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17 20 45 6 211
0 0 11 6 212
6 0 0 0 213
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9 0 0 0 217
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0 0 0 0 222
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0 2 3 3 227
5 4 3 2 228
3 1 0 0 229
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0 1 4 2 231
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4 0 12 4 234
46 80 71 33 235
5 0 1 1 236
2 10 0 3 237
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6 0 0 0 239
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30 9 4 8 241
16 5 54 76 242
12 5 0 0 243
6 3 2 2 244
3 2 3 1 245
7 14 13 3 246
50 134 4 51 247
0 0 0 0 248
19 0 0 0 249
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15 10 3 1 251
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13 38 17 23 254
0 7 1 0 255
8 1 3 1 256
33 5 29 41 257
10 1 2 4 258
18 54 30 20 259
0 0 0 0 260
43 43 3 0 261
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7 2 0 7 264
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3 4 3 1 268
33 26 16 17 269
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27 26 21 5 276
12 2 2 0 277
1 12 4 3 278
16 2 0 0 279
27 0 0 0 280
15 14 10 9 281
2 2 5 5 282
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15 8 19 1 284
9 2 2 0 285
10 30 12 15 286
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47 47 17 2 289
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64 21 10 5 293
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3 9 6 10 297
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21 6 14 4 635
86 0 0 0 636
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3 1 1 0 638
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60 39 13 6 641
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25 6 19 30 653
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0 0 0 0 659
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1 3 3 2 662
1 2 0 4 663
2 0 0 0 664
1 3 0 0 665
10 0 8 8 666
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62 0 0 0 733
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3 1 2 3 755
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6 6 13 2 757
2 1 2 2 758
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54 40 13 0 760
2 0 0 1 761
76 119 84 12 762
20 24 4 24 763
0 0 0 0 764
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0 0 0 4 768
7 0 0 0 769
0 4 0 0 770
4 1 0 0 771
2 2 0 0 772
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24 16 25 18 774
1 7 3 4 775
268 3 15 5 776
48 0 0 0 777
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12 10 18 3 780
0 0 0 0 781
0 2 0 0 782
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1 0 0 4 784
12 11 6 11 785
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33 29 28 24 787
15 0 19 13 788
3 2 0 0 789
0 12 39 24 790
3 8 0 1 791
6 3 14 7 792
0 0 1 1 793
53 24 34 105 794
1 5 2 0 795
0 5 4 8 796
10 6 6 3 797
51 10 5 3 798
6 10 3 22 799
0 0 0 0 800
4 31 13 1 801
4 6 5 8 802
0 0 0 0 803
13 18 12 18 804
0 4 10 7 805
25 16 6 1 806
0 0 12 0 807
3 0 1 4 808
0 0 0 0 809
10 0 0 0 810
1 0 0 0 811
277 16 10 48 812
43 12 4 5 813
0 0 0 0 814
4 2 4 0 815
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1 2 0 10 817
0 11 0 12 818
2 7 3 6 819
3 3 0 0 820
17 1 1 1 821
0 0 0 0 822
6 7 5 59 823
67 16 28 2 824
0 0 0 0 825
0 2 0 2 826
0 0 25 12 827
10 6 3 6 828
4 0 4 0 829
214 0 2 0 830
3 2 0 1 831
3 2 4 1 832
1 0 0 1 833
7 4 3 7 834
4 4 42 18 835
8 5 10 37 836
2 0 25 0 837
3 3 1 8 838
0 0 0 3 839
120 221 5 98 840
0 2 20 2 841
10 43 80 32 842
8 5 0 0 843
2 1 6 6 844
8 1 3 3 845
1 0 0 0 846
208 0 0 0 847
13 8 5 23 848
1 15 3 0 849
19 6 7 4 850
3 1 2 2 851
0 1 0 0 852
1 2 0 0 853
3 0 4 5 854
9 38 17 12 855
0 0 2 2 856
8 13 33 22 857
0 0 4 6 858
1 0 1 0 859
0 0 1 3 860
10 5 1 0 861
13 0 0 0 862
7 2 0 2 863
15 121 4 0 864
5 14 14 2 865
6 0 0 0 866
3 3 1 1 867
1 2 1 0 868
10 1 12 5 869
20 27 5 20 870
4 10 4 2 871
0 0 1 6 872
82 20 0 0 873
0 0 0 7 874
26 2 0 6 875
2 0 0 0 876
16 40 20 12 877
0 0 3 3 878
0 2 0 0 879
7 76 86 103 880
6 3 3 1 881
0 0 0 0 882',
header = TRUE
)
dmeas <- Csnippet("lik = dnbinom(y, D, D/(D+C), give_log);")
rmeas <- Csnippet("y = rnbinom(D, D/(D+C));")
rinit <- Csnippet("
double tol=0.000001;
D = (sigma_D < tol || mu_D < tol) ? mu_D :
rgamma(pow(mu_D/sigma_D,2), pow(sigma_D,2)/mu_D);
if(D < tol) {D = tol;}
R = (sigma_R < tol || mu_R < tol) ? mu_R :
rgamma(pow(mu_R/sigma_R, 2), pow(sigma_R, 2)/mu_R);
X = (sigma_X < tol || mu_X < tol) ? mu_X :
rgamma(pow(mu_X/sigma_X, 2), pow(sigma_X, 2)/mu_X);
Z = (R < tol) ? 1/tol : rexp(1/R);
C = 0;
")
rproc <- Csnippet("
double Zcum, tol=0.000001;
C = 0;
Zcum = Z;
while(Zcum < 6){ // time in months within a 6 month observation interval
C += Z * X;
Z = (R < tol) ? 1/tol : rexp(1/R);
X = (sigma_X < tol || mu_X < tol) ? mu_X :
rgamma(pow(mu_X/sigma_X, 2), pow(sigma_X, 2)/mu_X);
Zcum += Z;
}
C += (6 - (Zcum - Z)) * X;
C *= pow(alpha, (int)t % 4);
Z = Zcum - 6;
")
# check for existing 'cdir' (to make 'testthat' package work)
cdir <- if (exists("cdir",inherits=FALSE)) cdir else NULL
template <- pomp(data=data.frame(t=1:4,y=NA),
times="t",
t0=0,
rprocess=discrete_time(step.fun=rproc,delta.t=1),
rmeasure=rmeas,
dmeasure=dmeas,
params=params,
paramnames=c("mu_X","sigma_X","mu_D","sigma_D","mu_R","sigma_R","alpha"),
statenames=c("X","D","R","C","Z"),
obsnames="y",
partrans=parameter_trans(
log=c("mu_X","sigma_X","mu_D","sigma_D"),
logit="alpha"
),
rinit=rinit,
cdir=cdir
)
## build list of pomps
U <- nrow(contact_data)
poList <- setNames(vector(mode="list",length=U),
nm=paste0("unit",1:U))
for (u in seq_len(U)) {
poList[[u]] <- template
data_u <- pomp(
data.frame(t=time(template),y=as.numeric(contact_data[u,time(template)])),
times="t",
t0=timezero(template)
)
poList[[u]]@data <- data_u@data
}
## Construct panelPomp
panelPomp(object=poList,shared=coef(template))
}
cbreto/panelPomp documentation built on April 13, 2024, 12:23 a.m.
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Defines functions contacts
Documented in contacts
##' Contacts model
##'
##' A panel model for dynamic variation in sexual contacts, with
##' data from Vittinghof et al (1999). The model was developed by
##' Romero-Severson et al (2015) and discussed by \Breto et al (2020).
##'
##' @param params parameter vector.
##' @return
##' A \code{panelPomp} object.
##'
##' @author Edward L. Ionides
##'
##' @examples
##' \donttest{
##' contacts()
##' }
##' @export
##'
##' @references \breto2020
##'
##' \romeroseverson2015
##'
##' \vittinghoff1999
##' @family panelPomp examples
contacts <- function(params=c(mu_X=1.75,sigma_X=2.67,mu_D=3.81,
sigma_D=4.42,mu_R=0.04,sigma_R=0,alpha=0.90)){
contact_data <- read.table(
text = '"y1" "y2" "y3" "y4" "individual"
5 0 0 0 1
2 2 31 4 2
9 2 0 0 3
12 8 10 6 4
0 10 4 1 5
25 23 15 2 6
12 6 0 0 7
10 2 0 4 8
31 58 24 48 9
0 0 0 0 10
32 42 9 1 11
5 4 12 2 12
0 1 0 1 13
2 0 3 0 14
1 3 0 0 15
92 40 7 5 16
3 0 1 10 17
2 4 3 3 18
5 1 3 2 19
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214 0 2 0 830
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1 0 0 1 833
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4 4 42 18 835
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2 0 25 0 837
3 3 1 8 838
0 0 0 3 839
120 221 5 98 840
0 2 20 2 841
10 43 80 32 842
8 5 0 0 843
2 1 6 6 844
8 1 3 3 845
1 0 0 0 846
208 0 0 0 847
13 8 5 23 848
1 15 3 0 849
19 6 7 4 850
3 1 2 2 851
0 1 0 0 852
1 2 0 0 853
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0 0 2 2 856
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0 0 4 6 858
1 0 1 0 859
0 0 1 3 860
10 5 1 0 861
13 0 0 0 862
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6 0 0 0 866
3 3 1 1 867
1 2 1 0 868
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4 10 4 2 871
0 0 1 6 872
82 20 0 0 873
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0 0 3 3 878
0 2 0 0 879
7 76 86 103 880
6 3 3 1 881
0 0 0 0 882',
header = TRUE
)
dmeas <- Csnippet("lik = dnbinom(y, D, D/(D+C), give_log);")
rmeas <- Csnippet("y = rnbinom(D, D/(D+C));")
rinit <- Csnippet("
double tol=0.000001;
D = (sigma_D < tol || mu_D < tol) ? mu_D :
rgamma(pow(mu_D/sigma_D,2), pow(sigma_D,2)/mu_D);
if(D < tol) {D = tol;}
R = (sigma_R < tol || mu_R < tol) ? mu_R :
rgamma(pow(mu_R/sigma_R, 2), pow(sigma_R, 2)/mu_R);
X = (sigma_X < tol || mu_X < tol) ? mu_X :
rgamma(pow(mu_X/sigma_X, 2), pow(sigma_X, 2)/mu_X);
Z = (R < tol) ? 1/tol : rexp(1/R);
C = 0;
")
rproc <- Csnippet("
double Zcum, tol=0.000001;
C = 0;
Zcum = Z;
while(Zcum < 6){ // time in months within a 6 month observation interval
C += Z * X;
Z = (R < tol) ? 1/tol : rexp(1/R);
X = (sigma_X < tol || mu_X < tol) ? mu_X :
rgamma(pow(mu_X/sigma_X, 2), pow(sigma_X, 2)/mu_X);
Zcum += Z;
}
C += (6 - (Zcum - Z)) * X;
C *= pow(alpha, (int)t % 4);
Z = Zcum - 6;
")
# check for existing 'cdir' (to make 'testthat' package work)
cdir <- if (exists("cdir",inherits=FALSE)) cdir else NULL
template <- pomp(data=data.frame(t=1:4,y=NA),
times="t",
t0=0,
rprocess=discrete_time(step.fun=rproc,delta.t=1),
rmeasure=rmeas,
dmeasure=dmeas,
params=params,
paramnames=c("mu_X","sigma_X","mu_D","sigma_D","mu_R","sigma_R","alpha"),
statenames=c("X","D","R","C","Z"),
obsnames="y",
partrans=parameter_trans(
log=c("mu_X","sigma_X","mu_D","sigma_D"),
logit="alpha"
),
rinit=rinit,
cdir=cdir
)
## build list of pomps
U <- nrow(contact_data)
poList <- setNames(vector(mode="list",length=U),
nm=paste0("unit",1:U))
for (u in seq_len(U)) {
poList[[u]] <- template
data_u <- pomp(
data.frame(t=time(template),y=as.numeric(contact_data[u,time(template)])),
times="t",
t0=timezero(template)
)
poList[[u]]@data <- data_u@data
}
## Construct panelPomp
panelPomp(object=poList,shared=coef(template))
}
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