Description Usage Arguments Value References See Also Examples
Fits a semi-parametric regression model to estimate the effects on transition probabilities in a (possibly non-Markov) progressive illness-death model for a sequence of time.
1 |
formula |
an object of class formula which specifies the covariates. For example
|
data |
a data.frame of |
link |
a link function for |
s |
the current time for the transition probabilities; default is zero which reports the occupation probabilities. |
t |
the Future time for the transition probabilities; default is |
R |
the number of bootstrap replicates. Default is 199. |
by |
number: increment of the sequence from time |
trans |
the possible transition(s) for a progressive illness-death model. For |
ncores |
the number of cores to use for parallel execution. Default is the number of CPU cores on the current host. |
TPreg
returns an object of class TPreg
.
An object of class TPreg
is a list containing at least the following components:
co |
the list of:
|
call |
the matched call. |
transition |
the transition, this is equal to the |
s |
the current time for the transition probability. |
t |
the future time for the transition probability. |
n.misobs |
the number of missing observations. |
In addition, trans="all"
will have four lists: co11
, co12
, co13
, and co23
instead of co
and will give the information for all possible transitions in the progressive illness death model
Azarang, L. Scheike, TH. and de Una-Alvarez, J. (2017) Direct modeling of regression effects for transition probabilities in the progressive illness-death model, Statistics in Medicine 36, 1964-1976.
print.TPreg
, summary.TPreg
, and plot.TPreg
as generic functions.
1 2 3 4 5 6 | data(colonTPreg)
co11 <- TPreg( ~ Age + Nodes + treatment, colonTPreg, link = "logit", s = 50, R = 19, t = 200,
trans = "11", ncores = 1)
co11
summary(co11)
|
Loading required package: survival
Loading required package: foreach
Loading required package: doParallel
Loading required package: iterators
Loading required package: parallel
Warning message:
In TPreg(~Age + Nodes + treatment, colonTPreg, link = "logit", s = 50, :
Nodes variable in 'data' has missing value(s),
Call:
TPreg(formula = ~Age + Nodes + treatment, data = colonTPreg,
link = "logit", s = 50, t = 200, R = 19, trans = "11", ncores = 1)
Transition:
[1] "11"
(s,t):
[1] 50 200
Coefficients:
Estimate St.Err LW.L UP.L P.value
X.Intercept. 2.492609419 0.72041023 1.08060538 3.90461346 0.0005402031
Age -0.005980971 0.01181244 -0.02913336 0.01717142 0.6126264027
Nodes -0.074748098 0.02923819 -0.13205494 -0.01744125 0.0105724084
treatmentLev 0.039682347 0.24418653 -0.43892324 0.51828794 0.8709055616
treatmentLev.5FU 0.929566117 0.32475154 0.29305310 1.56607913 0.0042045690
[1] "18 observations deleted due to missingness from 'data'"
Call:
TPreg(formula = ~Age + Nodes + treatment, data = colonTPreg,
link = "logit", s = 50, t = 200, R = 19, trans = "11", ncores = 1)
(s,t):
[1] 50 200
Transition 11 :
Coefficients:
time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
1 56 58.363354 -0.401888881 6.26264521 -31.10806842 -9.4653733
2 185 2.636107 -0.007185251 -0.07924264 0.10143607 1.0470649
3 200 2.492609 -0.005980971 -0.07474810 0.03968235 0.9295661
Standard Errors:
time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
1 56 491.3913682 4.40435468 16.67490873 370.5809571 368.6372256
2 185 0.6884838 0.01042247 0.02954041 0.2612095 0.4063520
3 200 0.7204102 0.01181244 0.02923819 0.2441865 0.3247515
Lower limit:
time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
1 56 -904.763728 -9.03442405 -26.4201759 -757.4467443 -731.9943355
2 185 1.286679 -0.02761330 -0.1371418 -0.4105346 0.2506150
3 200 1.080605 -0.02913336 -0.1320549 -0.4389232 0.2930531
Upper limit:
time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
1 56 1021.490435 8.23064628 38.94546631 695.2306074 713.063589
2 185 3.985535 0.01324280 -0.02134344 0.6134067 1.843515
3 200 3.904613 0.01717142 -0.01744125 0.5182879 1.566079
p.value:
time X.Intercept. Age Nodes treatmentLev treatmentLev.5FU
1 56 0.9054562857 0.9272955 0.707234379 0.9331009 0.979515239
2 185 0.0001287392 0.4905717 0.007307052 0.6977702 0.009973593
3 200 0.0005402031 0.6126264 0.010572408 0.8709056 0.004204569
[1] "18 observation(s) deleted due to missingness from 'data'"
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