pfree.calc: Probability of freedom over time
In RSurveillance: Design and Analysis of Disease Surveillance Activities
Description
Usage
Arguments
Value
Examples
View source: R/freedom_functions_1.R
Description
Calculates the probability (confidence) of disease freedom for
given prior, sep and p.intro over 1 or more time periods
Usage
1
pfree.calc(sep, p.intro, prior = 0.5, discount.1 = TRUE)
Arguments
sep
population sensitivity for each time period (vector)
p.intro
probability of introduction for each time period (scalar
or vector of same length as sep)
prior
prior probability of freedom before surveillance (scalar)
discount.1
logical variable whether or not to discount first time period.
Value
data.frame with columns for sep, p.intro, discounted
prior, probability of freedom, equilibrium probability of freedom
and equilibrium prior
Examples
1
2
3
4
5
6
7
# examples for pfree.calc
pfree.calc(0.8, 0.01, 0.5)
pfree.calc(0.8, 0.01, 0.5, FALSE)
pfree.calc(rep(0.6,24), 0.01, 0.5)
pfree.calc(rep(0.6,24), 0.01, 0.5, FALSE)
pfree.calc(runif(10, 0.4, 0.6), 0.01, 0.5)
pfree.calc(runif(10, 0.4, 0.6), runif(10, 0.005, 0.015), 0.5)
Example output
Period SeP PIntro Discounted.prior PFree Equilibrium.PFree
1 1 0.8 0.01 0.495 0.8305369 0.9974747
Equilibrium.prior
1 0.9875
Period SeP PIntro Discounted.prior PFree Equilibrium.PFree
1 1 0.8 0 0.5 0.8333333 1
Equilibrium.prior
1 1
Period SeP PIntro Discounted.prior PFree Equilibrium.PFree
1 1 0.6 0.01 0.4950000 0.7101865 0.993266
2 2 0.6 0.01 0.7030846 0.8554894 0.993266
3 3 0.6 0.01 0.8469345 0.9325822 0.993266
4 4 0.6 0.01 0.9232564 0.9678208 0.993266
5 5 0.6 0.01 0.9581426 0.9828257 0.993266
6 6 0.6 0.01 0.9729975 0.9890211 0.993266
7 7 0.6 0.01 0.9791309 0.9915465 0.993266
8 8 0.6 0.01 0.9816310 0.9925705 0.993266
9 9 0.6 0.01 0.9826448 0.9929849 0.993266
10 10 0.6 0.01 0.9830550 0.9931524 0.993266
11 11 0.6 0.01 0.9832209 0.9932201 0.993266
12 12 0.6 0.01 0.9832879 0.9932474 0.993266
13 13 0.6 0.01 0.9833150 0.9932585 0.993266
14 14 0.6 0.01 0.9833259 0.9932630 0.993266
15 15 0.6 0.01 0.9833303 0.9932648 0.993266
16 16 0.6 0.01 0.9833321 0.9932655 0.993266
17 17 0.6 0.01 0.9833328 0.9932658 0.993266
18 18 0.6 0.01 0.9833331 0.9932659 0.993266
19 19 0.6 0.01 0.9833333 0.9932660 0.993266
20 20 0.6 0.01 0.9833333 0.9932660 0.993266
21 21 0.6 0.01 0.9833333 0.9932660 0.993266
22 22 0.6 0.01 0.9833333 0.9932660 0.993266
23 23 0.6 0.01 0.9833333 0.9932660 0.993266
24 24 0.6 0.01 0.9833333 0.9932660 0.993266
Equilibrium.prior
1 0.9833333
2 0.9833333
3 0.9833333
4 0.9833333
5 0.9833333
6 0.9833333
7 0.9833333
8 0.9833333
9 0.9833333
10 0.9833333
11 0.9833333
12 0.9833333
13 0.9833333
14 0.9833333
15 0.9833333
16 0.9833333
17 0.9833333
18 0.9833333
19 0.9833333
20 0.9833333
21 0.9833333
22 0.9833333
23 0.9833333
24 0.9833333
Period SeP PIntro Discounted.prior PFree Equilibrium.PFree
1 1 0.6 0.00 0.5000000 0.7142857 1.000000
2 2 0.6 0.01 0.7071429 0.8578856 0.993266
3 3 0.6 0.01 0.8493068 0.9337309 0.993266
4 4 0.6 0.01 0.9243936 0.9683203 0.993266
5 5 0.6 0.01 0.9586371 0.9830338 0.993266
6 6 0.6 0.01 0.9732035 0.9891062 0.993266
7 7 0.6 0.01 0.9792152 0.9915811 0.993266
8 8 0.6 0.01 0.9816653 0.9925845 0.993266
9 9 0.6 0.01 0.9826587 0.9929905 0.993266
10 10 0.6 0.01 0.9830606 0.9931547 0.993266
11 11 0.6 0.01 0.9832231 0.9932210 0.993266
12 12 0.6 0.01 0.9832888 0.9932478 0.993266
13 13 0.6 0.01 0.9833153 0.9932587 0.993266
14 14 0.6 0.01 0.9833261 0.9932630 0.993266
15 15 0.6 0.01 0.9833304 0.9932648 0.993266
16 16 0.6 0.01 0.9833321 0.9932655 0.993266
17 17 0.6 0.01 0.9833329 0.9932658 0.993266
18 18 0.6 0.01 0.9833331 0.9932659 0.993266
19 19 0.6 0.01 0.9833333 0.9932660 0.993266
20 20 0.6 0.01 0.9833333 0.9932660 0.993266
21 21 0.6 0.01 0.9833333 0.9932660 0.993266
22 22 0.6 0.01 0.9833333 0.9932660 0.993266
23 23 0.6 0.01 0.9833333 0.9932660 0.993266
24 24 0.6 0.01 0.9833333 0.9932660 0.993266
Equilibrium.prior
1 1.0000000
2 0.9833333
3 0.9833333
4 0.9833333
5 0.9833333
6 0.9833333
7 0.9833333
8 0.9833333
9 0.9833333
10 0.9833333
11 0.9833333
12 0.9833333
13 0.9833333
14 0.9833333
15 0.9833333
16 0.9833333
17 0.9833333
18 0.9833333
19 0.9833333
20 0.9833333
21 0.9833333
22 0.9833333
23 0.9833333
24 0.9833333
Period SeP PIntro Discounted.prior PFree Equilibrium.PFree
1 1 0.5461889 0.01 0.4950000 0.6835368 0.9916074
2 2 0.5804358 0.01 0.6767015 0.8330213 0.9926986
3 3 0.4652301 0.01 0.8246911 0.8979249 0.9883892
4 4 0.5546324 0.01 0.8889457 0.9472936 0.9918889
5 5 0.5597547 0.01 0.9378206 0.9716387 0.9920556
6 6 0.5058342 0.01 0.9619223 0.9808138 0.9901320
7 7 0.4035632 0.01 0.9710056 0.9825019 0.9850714
8 8 0.4248446 0.01 0.9726769 0.9841004 0.9863252
9 9 0.5836574 0.01 0.9742594 0.9891196 0.9927946
10 10 0.5985031 0.01 0.9792284 0.9915553 0.9932239
Equilibrium.prior
1 0.9816913
2 0.9827716
3 0.9785053
4 0.9819700
5 0.9821350
6 0.9802307
7 0.9752207
8 0.9764620
9 0.9828667
10 0.9832916
Period SeP PIntro Discounted.prior PFree Equilibrium.PFree
1 1 0.4336293 0.009174317 0.4954128 0.6341721 0.9879063
2 2 0.5006551 0.014358534 0.6250663 0.7695136 0.9854704
3 3 0.4438684 0.008933015 0.7626395 0.8524511 0.9887068
4 4 0.4256178 0.007662213 0.8459194 0.9052877 0.9895798
5 5 0.5369086 0.006093727 0.8997711 0.9509450 0.9947118
6 6 0.5114637 0.005906983 0.9453278 0.9725223 0.9943243
7 7 0.5871751 0.013165133 0.9597189 0.9829681 0.9906205
8 8 0.5209178 0.012483374 0.9706974 0.9857440 0.9883741
9 9 0.4625478 0.011260714 0.9746438 0.9862105 0.9867667
10 10 0.5822418 0.005391283 0.9808936 0.9919284 0.9961108
Equilibrium.prior
1 0.9788429
2 0.9713205
3 0.9798746
4 0.9819974
5 0.9886503
6 0.9884508
7 0.9775789
8 0.9760358
9 0.9756550
10 0.9907405
RSurveillance documentation built on July 2, 2020, 2:33 a.m.
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Description Usage Arguments Value Examples
View source: R/freedom_functions_1.R
Description
Calculates the probability (confidence) of disease freedom for given prior, sep and p.intro over 1 or more time periods
Usage
1 | pfree.calc(sep, p.intro, prior = 0.5, discount.1 = TRUE)
|
Arguments
sep |
population sensitivity for each time period (vector) |
p.intro |
probability of introduction for each time period (scalar or vector of same length as sep) |
prior |
prior probability of freedom before surveillance (scalar) |
discount.1 |
logical variable whether or not to discount first time period. |
Value
data.frame with columns for sep, p.intro, discounted
prior, probability of freedom, equilibrium probability of freedom
and equilibrium prior
Examples
1 2 3 4 5 6 7 | # examples for pfree.calc
pfree.calc(0.8, 0.01, 0.5)
pfree.calc(0.8, 0.01, 0.5, FALSE)
pfree.calc(rep(0.6,24), 0.01, 0.5)
pfree.calc(rep(0.6,24), 0.01, 0.5, FALSE)
pfree.calc(runif(10, 0.4, 0.6), 0.01, 0.5)
pfree.calc(runif(10, 0.4, 0.6), runif(10, 0.005, 0.015), 0.5)
|
Example output
Period SeP PIntro Discounted.prior PFree Equilibrium.PFree
1 1 0.8 0.01 0.495 0.8305369 0.9974747
Equilibrium.prior
1 0.9875
Period SeP PIntro Discounted.prior PFree Equilibrium.PFree
1 1 0.8 0 0.5 0.8333333 1
Equilibrium.prior
1 1
Period SeP PIntro Discounted.prior PFree Equilibrium.PFree
1 1 0.6 0.01 0.4950000 0.7101865 0.993266
2 2 0.6 0.01 0.7030846 0.8554894 0.993266
3 3 0.6 0.01 0.8469345 0.9325822 0.993266
4 4 0.6 0.01 0.9232564 0.9678208 0.993266
5 5 0.6 0.01 0.9581426 0.9828257 0.993266
6 6 0.6 0.01 0.9729975 0.9890211 0.993266
7 7 0.6 0.01 0.9791309 0.9915465 0.993266
8 8 0.6 0.01 0.9816310 0.9925705 0.993266
9 9 0.6 0.01 0.9826448 0.9929849 0.993266
10 10 0.6 0.01 0.9830550 0.9931524 0.993266
11 11 0.6 0.01 0.9832209 0.9932201 0.993266
12 12 0.6 0.01 0.9832879 0.9932474 0.993266
13 13 0.6 0.01 0.9833150 0.9932585 0.993266
14 14 0.6 0.01 0.9833259 0.9932630 0.993266
15 15 0.6 0.01 0.9833303 0.9932648 0.993266
16 16 0.6 0.01 0.9833321 0.9932655 0.993266
17 17 0.6 0.01 0.9833328 0.9932658 0.993266
18 18 0.6 0.01 0.9833331 0.9932659 0.993266
19 19 0.6 0.01 0.9833333 0.9932660 0.993266
20 20 0.6 0.01 0.9833333 0.9932660 0.993266
21 21 0.6 0.01 0.9833333 0.9932660 0.993266
22 22 0.6 0.01 0.9833333 0.9932660 0.993266
23 23 0.6 0.01 0.9833333 0.9932660 0.993266
24 24 0.6 0.01 0.9833333 0.9932660 0.993266
Equilibrium.prior
1 0.9833333
2 0.9833333
3 0.9833333
4 0.9833333
5 0.9833333
6 0.9833333
7 0.9833333
8 0.9833333
9 0.9833333
10 0.9833333
11 0.9833333
12 0.9833333
13 0.9833333
14 0.9833333
15 0.9833333
16 0.9833333
17 0.9833333
18 0.9833333
19 0.9833333
20 0.9833333
21 0.9833333
22 0.9833333
23 0.9833333
24 0.9833333
Period SeP PIntro Discounted.prior PFree Equilibrium.PFree
1 1 0.6 0.00 0.5000000 0.7142857 1.000000
2 2 0.6 0.01 0.7071429 0.8578856 0.993266
3 3 0.6 0.01 0.8493068 0.9337309 0.993266
4 4 0.6 0.01 0.9243936 0.9683203 0.993266
5 5 0.6 0.01 0.9586371 0.9830338 0.993266
6 6 0.6 0.01 0.9732035 0.9891062 0.993266
7 7 0.6 0.01 0.9792152 0.9915811 0.993266
8 8 0.6 0.01 0.9816653 0.9925845 0.993266
9 9 0.6 0.01 0.9826587 0.9929905 0.993266
10 10 0.6 0.01 0.9830606 0.9931547 0.993266
11 11 0.6 0.01 0.9832231 0.9932210 0.993266
12 12 0.6 0.01 0.9832888 0.9932478 0.993266
13 13 0.6 0.01 0.9833153 0.9932587 0.993266
14 14 0.6 0.01 0.9833261 0.9932630 0.993266
15 15 0.6 0.01 0.9833304 0.9932648 0.993266
16 16 0.6 0.01 0.9833321 0.9932655 0.993266
17 17 0.6 0.01 0.9833329 0.9932658 0.993266
18 18 0.6 0.01 0.9833331 0.9932659 0.993266
19 19 0.6 0.01 0.9833333 0.9932660 0.993266
20 20 0.6 0.01 0.9833333 0.9932660 0.993266
21 21 0.6 0.01 0.9833333 0.9932660 0.993266
22 22 0.6 0.01 0.9833333 0.9932660 0.993266
23 23 0.6 0.01 0.9833333 0.9932660 0.993266
24 24 0.6 0.01 0.9833333 0.9932660 0.993266
Equilibrium.prior
1 1.0000000
2 0.9833333
3 0.9833333
4 0.9833333
5 0.9833333
6 0.9833333
7 0.9833333
8 0.9833333
9 0.9833333
10 0.9833333
11 0.9833333
12 0.9833333
13 0.9833333
14 0.9833333
15 0.9833333
16 0.9833333
17 0.9833333
18 0.9833333
19 0.9833333
20 0.9833333
21 0.9833333
22 0.9833333
23 0.9833333
24 0.9833333
Period SeP PIntro Discounted.prior PFree Equilibrium.PFree
1 1 0.5461889 0.01 0.4950000 0.6835368 0.9916074
2 2 0.5804358 0.01 0.6767015 0.8330213 0.9926986
3 3 0.4652301 0.01 0.8246911 0.8979249 0.9883892
4 4 0.5546324 0.01 0.8889457 0.9472936 0.9918889
5 5 0.5597547 0.01 0.9378206 0.9716387 0.9920556
6 6 0.5058342 0.01 0.9619223 0.9808138 0.9901320
7 7 0.4035632 0.01 0.9710056 0.9825019 0.9850714
8 8 0.4248446 0.01 0.9726769 0.9841004 0.9863252
9 9 0.5836574 0.01 0.9742594 0.9891196 0.9927946
10 10 0.5985031 0.01 0.9792284 0.9915553 0.9932239
Equilibrium.prior
1 0.9816913
2 0.9827716
3 0.9785053
4 0.9819700
5 0.9821350
6 0.9802307
7 0.9752207
8 0.9764620
9 0.9828667
10 0.9832916
Period SeP PIntro Discounted.prior PFree Equilibrium.PFree
1 1 0.4336293 0.009174317 0.4954128 0.6341721 0.9879063
2 2 0.5006551 0.014358534 0.6250663 0.7695136 0.9854704
3 3 0.4438684 0.008933015 0.7626395 0.8524511 0.9887068
4 4 0.4256178 0.007662213 0.8459194 0.9052877 0.9895798
5 5 0.5369086 0.006093727 0.8997711 0.9509450 0.9947118
6 6 0.5114637 0.005906983 0.9453278 0.9725223 0.9943243
7 7 0.5871751 0.013165133 0.9597189 0.9829681 0.9906205
8 8 0.5209178 0.012483374 0.9706974 0.9857440 0.9883741
9 9 0.4625478 0.011260714 0.9746438 0.9862105 0.9867667
10 10 0.5822418 0.005391283 0.9808936 0.9919284 0.9961108
Equilibrium.prior
1 0.9788429
2 0.9713205
3 0.9798746
4 0.9819974
5 0.9886503
6 0.9884508
7 0.9775789
8 0.9760358
9 0.9756550
10 0.9907405
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