MSLT: Multistate life table: survival function and exposure...
In Biograph: Explore Life Histories
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Examples
Description
The function MSLT.S estimates the multistate survival function from cumulative transition rates.
The function MSLT.e uses the multistate life table method to estimate expected state occupation times by state.
Usage
1
2
Arguments
rates
transition rates. Either the Nelson-Aalen estimators or the occurrence-exposure rates.
SS
The multistate survival function. An object of class 'MSLT.S'
radix
The radix, which is the distribution of the population by state at the initial (reference) age
Details
The multistate life table is produced by two functions: (1) MSLT.S produces the multistate survival function and (2) MSLT.e generates expected sojourn times: total and by state. MSLT.S uses the MatrixExp function of the msm package. MSLT.e applies the multistate life table method that incorporates equations that infer expected sojourn times from transition rates and the associated transition probabilities.
Value
The function MSLT.S returns:
S
The multistate survival function
P
Age-specific transition probabilities
The function MSLT.e returns an object with the following components:
L
For each state, the expected sojourn time by age. It is the number of time units (years, months) a person at the beginning of his or her career (e.g. at birth or at a reference age) may expect to spend in the given state during each age interval.
e0
The total expected sojourn time in each state. If life histories are considered from birth, e0 gives the life expectancy by state. If life histories are truncated at a given age, the life expectancy is the total expected sojourn time in a state between birth and that maximum age.
e.p
Population-based life expectancies by age and state. Population-based measures are independent on the state occupied at the reference age.
e.s
Status-based life expectancies by age and state. Status-based measures depend on the state occupied at the reference age.
Author(s)
Frans Willekens
References
Rogers, A. (1975) Introduction to multiregional mathematical demography. Wiley, New York
Willekens, F. (1987) The marital status life-table. In: J. Bongaarts, T. Burch and K.W. Wachter eds. Family demography: models and applications. Oxford: Clarendon Press. pages 125-149.
Palloni, A. (2001) Increment-decrement life tables. In: S.H. Preston, P. Heuveline and M. Guillot Demography. Measuring and modelling population processes. Blackwell, Oxford, Chapter12, pp. 256-272.
See Also
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
# a. The multistate life table based on Nelson-Aalen estimators
# The example obtains Nelson-Aalen estimators of the cumulative transition rates
# using the mavna package. It derives the multistate life survival function
# from the transition rates and the expected sojourn times from the survival function.
# The radix is the number of persons by state at the reference age
# (e.g. at the start of the life history).
data(GLHS)
z <- Parameters (GLHS)
cr <- Cumrates (irate=3,Bdata=GLHS)
S.e <- MSLT.S(cr$astr[,,,1]) # expected
radix <- c(10000,0)
mslt.e <- MSLT.e (S.e,radix)
S.u <- MSLT.S(cr$astr[,,,2]) # upper
mslt.u <- MSLT.e (S.u,radix)
S.l <- MSLT.S(cr$astr[,,,3]) # lower
mslt.l <- MSLT.e (S.l,radix)
# b. The multistate life table based on occurrence-exposure rates
cr <- Cumrates (irate=3,Bdata=GLHS)
S <- MSLT.S(cr$oe)
radix <- c(10000,0)
mslt <- MSLT.e (S,radix)
Example output
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
[1] ". . . . . . Removing intrastate transitions . . . . . "
[1] . . . . . . Removes intrastate transitions . . . .
[1] . . . . Intrastate transitions removed. Recalculating transitions . . . .
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
[1] A new Biograph object without intrastate transitions is returned.
[1] ". . . . . . Estimating rates . . . . ."
[1] " "
[1] "Cumrates: calls function Biograph.mvna . . . "
ID born start end sex edu marriage LMentry cohort path Tr1
1 1 351 0 52.66667 Male 17 679 555 1929-31 NJ 17.00000
2 2 357 0 52.16667 Female 10 762 593 1929-31 NJN 19.66667
3 3 473 0 42.50000 Female 11 870 688 1939-41 NJN 17.91667
4 4 604 0 31.58333 Female 13 872 872 1949-51 NJN 22.33333
5 5 377 0 50.50000 Male 11 701 583 1929-31 NJ 17.16667
Tr2 Tr3 Tr4 Tr5 Tr6 Tr7 Tr8 Tr9 Tr10 Tr11 Tr12
1 NA NA NA NA NA NA NA NA NA NA NA
2 44.66667 NA NA NA NA NA NA NA NA NA NA
3 29.66667 NA NA NA NA NA NA NA NA NA NA
4 26.91667 NA NA NA NA NA NA NA NA NA NA
5 NA NA NA NA NA NA NA NA NA NA NA
[1] No intra-state transitions present in the data.
[1] " Biograph.mvna: Calls function Biograph.long . . . "
[1] . . . . . Creating long format . . . . . .
[1] . . . . . running reshape . . . . .
[1] . . . . Sort data in long format . . . .
[1] . . . . Adjust long format for survival package etc . . .
[1] Biograph.mvna completed: Object produced by Biograph.mvna: .$mvna
[1] "Cumrates 88"
[1] ". . . . . . . . . . . . "
[1] ". . . . Running mvna . . . . . . "
[1] Computing occurrence-exposure rates
[1] Running Sequences.ind
[1] Running Occup
[1] The number of age groups is 54
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
[1] ". . . . Running Occup . . . . "
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
[1] "state_time: compute state.n"
[1] Running Trans
[1] Running RateTable
[1] Running Rates
[1] ". . . . . . Removing intrastate transitions . . . . . "
[1] . . . . . . Removes intrastate transitions . . . .
[1] . . . . Intrastate transitions removed. Recalculating transitions . . . .
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
[1] A new Biograph object without intrastate transitions is returned.
[1] ". . . . . . Estimating rates . . . . ."
[1] " "
[1] "Cumrates: calls function Biograph.mvna . . . "
ID born start end sex edu marriage LMentry cohort path Tr1
1 1 351 0 52.66667 Male 17 679 555 1929-31 NJ 17.00000
2 2 357 0 52.16667 Female 10 762 593 1929-31 NJN 19.66667
3 3 473 0 42.50000 Female 11 870 688 1939-41 NJN 17.91667
4 4 604 0 31.58333 Female 13 872 872 1949-51 NJN 22.33333
5 5 377 0 50.50000 Male 11 701 583 1929-31 NJ 17.16667
Tr2 Tr3 Tr4 Tr5 Tr6 Tr7 Tr8 Tr9 Tr10 Tr11 Tr12
1 NA NA NA NA NA NA NA NA NA NA NA
2 44.66667 NA NA NA NA NA NA NA NA NA NA
3 29.66667 NA NA NA NA NA NA NA NA NA NA
4 26.91667 NA NA NA NA NA NA NA NA NA NA
5 NA NA NA NA NA NA NA NA NA NA NA
[1] No intra-state transitions present in the data.
[1] " Biograph.mvna: Calls function Biograph.long . . . "
[1] . . . . . Creating long format . . . . . .
[1] . . . . . running reshape . . . . .
[1] . . . . Sort data in long format . . . .
[1] . . . . Adjust long format for survival package etc . . .
[1] Biograph.mvna completed: Object produced by Biograph.mvna: .$mvna
[1] "Cumrates 88"
[1] ". . . . . . . . . . . . "
[1] ". . . . Running mvna . . . . . . "
[1] Computing occurrence-exposure rates
[1] Running Sequences.ind
[1] Running Occup
[1] The number of age groups is 54
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
[1] ". . . . Running Occup . . . . "
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
[1] "state_time: compute state.n"
[1] Running Trans
[1] Running RateTable
[1] Running Rates
Biograph documentation built on May 1, 2019, 8:48 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Value Author(s) References See Also Examples
Description
The function MSLT.S estimates the multistate survival function from cumulative transition rates. The function MSLT.e uses the multistate life table method to estimate expected state occupation times by state.
Usage
1 2 |
Arguments
rates |
transition rates. Either the Nelson-Aalen estimators or the occurrence-exposure rates. |
SS |
The multistate survival function. An object of class 'MSLT.S' |
radix |
The radix, which is the distribution of the population by state at the initial (reference) age |
Details
The multistate life table is produced by two functions: (1) MSLT.S produces the multistate survival function and (2) MSLT.e generates expected sojourn times: total and by state. MSLT.S uses the MatrixExp function of the msm package. MSLT.e applies the multistate life table method that incorporates equations that infer expected sojourn times from transition rates and the associated transition probabilities.
Value
The function MSLT.S returns:
S |
The multistate survival function |
P |
Age-specific transition probabilities |
The function MSLT.e returns an object with the following components:
L |
For each state, the expected sojourn time by age. It is the number of time units (years, months) a person at the beginning of his or her career (e.g. at birth or at a reference age) may expect to spend in the given state during each age interval. |
e0 |
The total expected sojourn time in each state. If life histories are considered from birth, e0 gives the life expectancy by state. If life histories are truncated at a given age, the life expectancy is the total expected sojourn time in a state between birth and that maximum age. |
e.p |
Population-based life expectancies by age and state. Population-based measures are independent on the state occupied at the reference age. |
e.s |
Status-based life expectancies by age and state. Status-based measures depend on the state occupied at the reference age. |
Author(s)
Frans Willekens
References
Rogers, A. (1975) Introduction to multiregional mathematical demography. Wiley, New York
Willekens, F. (1987) The marital status life-table. In: J. Bongaarts, T. Burch and K.W. Wachter eds. Family demography: models and applications. Oxford: Clarendon Press. pages 125-149.
Palloni, A. (2001) Increment-decrement life tables. In: S.H. Preston, P. Heuveline and M. Guillot Demography. Measuring and modelling population processes. Blackwell, Oxford, Chapter12, pp. 256-272.
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | # a. The multistate life table based on Nelson-Aalen estimators
# The example obtains Nelson-Aalen estimators of the cumulative transition rates
# using the mavna package. It derives the multistate life survival function
# from the transition rates and the expected sojourn times from the survival function.
# The radix is the number of persons by state at the reference age
# (e.g. at the start of the life history).
data(GLHS)
z <- Parameters (GLHS)
cr <- Cumrates (irate=3,Bdata=GLHS)
S.e <- MSLT.S(cr$astr[,,,1]) # expected
radix <- c(10000,0)
mslt.e <- MSLT.e (S.e,radix)
S.u <- MSLT.S(cr$astr[,,,2]) # upper
mslt.u <- MSLT.e (S.u,radix)
S.l <- MSLT.S(cr$astr[,,,3]) # lower
mslt.l <- MSLT.e (S.l,radix)
# b. The multistate life table based on occurrence-exposure rates
cr <- Cumrates (irate=3,Bdata=GLHS)
S <- MSLT.S(cr$oe)
radix <- c(10000,0)
mslt <- MSLT.e (S,radix)
|
Example output
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
[1] ". . . . . . Removing intrastate transitions . . . . . "
[1] . . . . . . Removes intrastate transitions . . . .
[1] . . . . Intrastate transitions removed. Recalculating transitions . . . .
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
[1] A new Biograph object without intrastate transitions is returned.
[1] ". . . . . . Estimating rates . . . . ."
[1] " "
[1] "Cumrates: calls function Biograph.mvna . . . "
ID born start end sex edu marriage LMentry cohort path Tr1
1 1 351 0 52.66667 Male 17 679 555 1929-31 NJ 17.00000
2 2 357 0 52.16667 Female 10 762 593 1929-31 NJN 19.66667
3 3 473 0 42.50000 Female 11 870 688 1939-41 NJN 17.91667
4 4 604 0 31.58333 Female 13 872 872 1949-51 NJN 22.33333
5 5 377 0 50.50000 Male 11 701 583 1929-31 NJ 17.16667
Tr2 Tr3 Tr4 Tr5 Tr6 Tr7 Tr8 Tr9 Tr10 Tr11 Tr12
1 NA NA NA NA NA NA NA NA NA NA NA
2 44.66667 NA NA NA NA NA NA NA NA NA NA
3 29.66667 NA NA NA NA NA NA NA NA NA NA
4 26.91667 NA NA NA NA NA NA NA NA NA NA
5 NA NA NA NA NA NA NA NA NA NA NA
[1] No intra-state transitions present in the data.
[1] " Biograph.mvna: Calls function Biograph.long . . . "
[1] . . . . . Creating long format . . . . . .
[1] . . . . . running reshape . . . . .
[1] . . . . Sort data in long format . . . .
[1] . . . . Adjust long format for survival package etc . . .
[1] Biograph.mvna completed: Object produced by Biograph.mvna: .$mvna
[1] "Cumrates 88"
[1] ". . . . . . . . . . . . "
[1] ". . . . Running mvna . . . . . . "
[1] Computing occurrence-exposure rates
[1] Running Sequences.ind
[1] Running Occup
[1] The number of age groups is 54
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
[1] ". . . . Running Occup . . . . "
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
[1] "state_time: compute state.n"
[1] Running Trans
[1] Running RateTable
[1] Running Rates
[1] ". . . . . . Removing intrastate transitions . . . . . "
[1] . . . . . . Removes intrastate transitions . . . .
[1] . . . . Intrastate transitions removed. Recalculating transitions . . . .
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
[1] A new Biograph object without intrastate transitions is returned.
[1] ". . . . . . Estimating rates . . . . ."
[1] " "
[1] "Cumrates: calls function Biograph.mvna . . . "
ID born start end sex edu marriage LMentry cohort path Tr1
1 1 351 0 52.66667 Male 17 679 555 1929-31 NJ 17.00000
2 2 357 0 52.16667 Female 10 762 593 1929-31 NJN 19.66667
3 3 473 0 42.50000 Female 11 870 688 1939-41 NJN 17.91667
4 4 604 0 31.58333 Female 13 872 872 1949-51 NJN 22.33333
5 5 377 0 50.50000 Male 11 701 583 1929-31 NJ 17.16667
Tr2 Tr3 Tr4 Tr5 Tr6 Tr7 Tr8 Tr9 Tr10 Tr11 Tr12
1 NA NA NA NA NA NA NA NA NA NA NA
2 44.66667 NA NA NA NA NA NA NA NA NA NA
3 29.66667 NA NA NA NA NA NA NA NA NA NA
4 26.91667 NA NA NA NA NA NA NA NA NA NA
5 NA NA NA NA NA NA NA NA NA NA NA
[1] No intra-state transitions present in the data.
[1] " Biograph.mvna: Calls function Biograph.long . . . "
[1] . . . . . Creating long format . . . . . .
[1] . . . . . running reshape . . . . .
[1] . . . . Sort data in long format . . . .
[1] . . . . Adjust long format for survival package etc . . .
[1] Biograph.mvna completed: Object produced by Biograph.mvna: .$mvna
[1] "Cumrates 88"
[1] ". . . . . . . . . . . . "
[1] ". . . . Running mvna . . . . . . "
[1] Computing occurrence-exposure rates
[1] Running Sequences.ind
[1] Running Occup
[1] The number of age groups is 54
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
[1] ". . . . Running Occup . . . . "
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
[1] "state_time: compute state.n"
[1] Running Trans
[1] Running RateTable
[1] Running Rates
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.