JMP: Joint Model for Palliative care studies

In gitlzg/JMP: Joint Model for Palliative care studies

Description

Joint Model for Palliative care studies

Usage

JMP(dat = NA, dataPath = NA, covariate.fields, qol.prefix,
  qol.time.prefix, id.field, survival.time.field, censoring.status.field,
  treatment.status.field, long.knot.nums = 2:11)

Arguments

dat	formatted R dataset. See example dataset: data(dat_JMP)
dataPath	path of the data set to read in (if dat not supplied)
covariate.fields	covariates adjusted for
qol.prefix	prefix of the longitudinal quality of life measurements
qol.time.prefix	prefix of the time variable for longitudinal quality of life measurements
id.field	id variable in the dataset
survival.time.field	survival time variable in the dataset
censoring.status.field	censoring variable (1 for death, 0 for censored)
treatment.status.field	treatment status (1 for treated,0 for control)
long.knot.nums	number of knots for nonparametric curves (default 2 to 11)

Details

A semiparametric joint model for terminal trend of quality of life (QOL) and survival

- For longitudinal QOL outcomes: semiparametric mixed effects submodel (only random intercept is used in this package)

Y_i(t^*) = β_μ(t^*) + A_i β_A(t^*) + X_i^T ψ_X + b_i + ε_i(t^*)

- For survival outcomes: Cox submodel

λ_i(t) = λ_0(t) exp(A_i α_A + \tilde{X}_i^T α_X)

Value

A list of analysis results

1. monthly QOL results:

- month: time variable

- nCtr, nTrt: observed number of patients in control and treatment group, respectively

- CtrQOL, TrtQOL: average monthly QOL in control and treatment group

- Ctr95%CIlow, Ctr95%CIhi: lower and upper bounds of 95

- Trt95%CIlow, Trt95%CIhi: lower and upper bounds of 95

- TrtEffect: monthly treatment effect

- pValueTrtEffect: p-value for monthly treatment effect

2. The overall p value for testing the entire model

3. knot.combinations: different combinations of knots for longitudinal and survival submodels with their corresponding AIC and BIC values

4. maximum likelihood estimates (mle) results

and

Four figures saved in the current working directory

1. estimated terminal trend in a png file called "Longitudinal_trajectories.png"

2. the time-varying treatment effect in a png file called "Longitudinal_spline_treatment_effect.png"

3. estimated survival function and in a png file "Survival_function.png"

4. estimated cumulative hazard function in a png file "Cumulative_hazard.png"

Author(s)

Zhigang Li <[e-mail]>

Meilin Jiang <[e-mail]>

References

Li Z, Frost HR, Tosteson TD, et al. A Semiparametric Joint Model for Terminal Trend of Quality of Life and Survival in Palliative Care Research. Statistics in Medicine. 2017;36:4692–4704. https://doi.org/10.1002/sim.7445

Examples

data(dat_JMP)

results <- JMP(dat=dat_JMP,
covariate.fields = c("sex", "qol_0"),
qol.prefix="qol_", qol.time.prefix="time_",
id.field = "id", survival.time.field = "survival_time",
censoring.status.field = "death", treatment.status.field = "trt")

# Extract monthly results from output
results$monthlyResults

# The overall p value for testing the entire model
results$overallPvalueModel

gitlzg/JMP documentation built on March 7, 2020, 6:35 a.m.