fit_gMSM: Estimate any parametric MSM with previously fitted weights.

In osofr/stremr: Streamlined Estimation for Static, Dynamic and Stochastic Treatment Regimes in Longitudinal Data

Description

Estimate the causal MSM for a particular stochastic, dynamic or static intervention on the treatment/exposure and monitoring processes based on the user-specified formula.

Usage

fit_gMSM(
  wts_data,
  form,
  family,
  OData,
  use_weights = TRUE,
  stabilize = TRUE,
  trunc_weights = 10^6,
  weights = NULL,
  getSEs = TRUE,
  return_wts = FALSE,
  tvals = NULL,
  tmax = NULL,
  rule.var = "rule.name",
  verbose = getOption("stremr.verbose")
)

Arguments

wts_data	A list of data.tables, each data set is a result of calling the function getIPWeights. Must contain the treatment/monitoring rule-specific estimated IPTW weights. This argument can be also a single data.table obtained with data.table::rbindlist(wts_data).
form	Formula for the logistic MSM
family	MSM family link function, passed directly to glm().
OData	The object returned by function fitPropensity. Contains the input dat and the previously fitted propensity score models for the exposure, monitoring and right-censoring.
use_weights	Logical value. Set to FALSE to ignore the weights in wts_data and fit a "crude" MSM that does not adjust for the possible confounding due to non-random assignment of the exposure/censoring and monitoring indicators.
stabilize	Set to TRUE to stabilize the weights by the empirical conditional probability of having followed the rule at time-point t, given the subject has followed the rule all the way up to time-point t.
trunc_weights	Specify the numeric weight truncation value. All final weights exceeding the value in trunc_weights will be truncated.
weights	Optional data.table with additional observation-time-specific weights. Must contain columns ID, t and weight. The column named weight is merged back into the original data according to (ID, t).
getSEs	A logical indicator. Set to TRUE to evaluate the standard errors for the estimated survival by using the MSM influence curve.
return_wts	Return the data.table with subject-specific IP weights as part of the output. Note: for large datasets setting this to TRUE may lead to extremely large object sizes!
tvals	Vector of time-points for Y(t), default (NULL) is to use all available time-points.
tmax	Maximum value of the follow-up period. All person-time observations above this value will be excluded from the MSM model.
rule.var	The column name in wts_data that identifies each unique regimen, can be integer, continuous, character or factor.
verbose	Set to TRUE to print messages on status and information to the console. Turn this on by default using options(stremr.verbose=TRUE).

Value

MSM estimation results

See Also

fitPropensity, getIPWeights.

Examples

#-------------------------------------------------------------------
# Simulated data with informative right-censoring
#-------------------------------------------------------------------
require("data.table")
require("magrittr")
data(OdataCatCENS)
OdataDT <- as.data.table(OdataCatCENS, key=c("ID", "t"))
# Indicator that the person has never been treated in the past:
OdataDT[, "barTIm1eq0" := as.integer(c(0, cumsum(TI)[-.N]) %in% 0), by = ID]
OdataDT[, ("N.tminus1") := shift(get("N"), n = 1L, type = "lag", fill = 1L), by = ID]

#-------------------------------------------------------------------
# Regressions for modeling the exposure (TRT)
#-------------------------------------------------------------------
gform_TRT <- "TI ~ CVD + highA1c + N.tminus1"
# Fit a separate model for TRT (stratify) for each of the following subsets:
stratify_TRT <- list(
  TI=c(
       # MODEL TI AT t=0
       "t == 0L",
       # MODEL TRT INITATION WHEN MONITORED
       "(t > 0L) & (N.tminus1 == 1L) & (barTIm1eq0 == 1L)",
       # MODEL TRT INITATION WHEN NOT MONITORED
       "(t > 0L) & (N.tminus1 == 0L) & (barTIm1eq0 == 1L)",
       # MODEL TRT CONTINUATION (BOTH MONITORED AND NOT MONITORED)
       "(t > 0L) & (barTIm1eq0 == 1L)"
      ))

#-------------------------------------------------------------------
# Regressions for modeling the categorical censoring (CENS)
#-------------------------------------------------------------------
gform_CENS <- c("CatC ~ highA1c")
# stratify by time-points (separate model for all t<16 and t=16)
stratify_CENS <- list(CatC=c("t < 16", "t == 16"))

#-------------------------------------------------------------------
# Regressions for modeling the monitoring regimen (MONITOR)
#-------------------------------------------------------------------
# Intercept only model, pooling across all time points t
gform_MONITOR <- "N ~ 1"

#-------------------------------------------------------------------
# Define the counterfactual monitoring regimen of interest
#-------------------------------------------------------------------
# probability of being monitored at each t is 0.1
OdataDT[, "gstar.N" := 0.1]

# Define two dynamic rules: dlow & dhigh
OdataDT <- defineIntervedTRT(OdataDT, theta = c(0,1), ID = "ID", t = "t", I = "highA1c",
                            CENS = "C", TRT = "TI", MONITOR = "N", tsinceNis1 = "lastNat1",
                            new.TRT.names = c("dlow", "dhigh"), return.allcolumns = TRUE)

#-------------------------------------------------------------------
# Import data into stremr object
#-------------------------------------------------------------------
OData <- importData(OdataDT, ID = "ID", t = "t", covars = c("highA1c", "lastNat1"),
                    CENS = "CatC", TRT = "TI", MONITOR = "N", OUTCOME = "Y.tplus1")

# ----------------------------------------------------------------------
# Look at the input data object
# ----------------------------------------------------------------------
print(OData)

# ----------------------------------------------------------------------
# Access the input data
# ----------------------------------------------------------------------
get_data(OData)

#-------------------------------------------------------------------
# Estimate Propensity scores
#-------------------------------------------------------------------
OData <- fitPropensity(OData, gform_CENS = gform_CENS, gform_TRT = gform_TRT,
                      stratify_TRT = stratify_TRT, gform_MONITOR = gform_MONITOR)

#-------------------------------------------------------------------
# Defining weights for two dynamic regimens "dlow" and "dhigh"
#-------------------------------------------------------------------
wts.St.dlow <- getIPWeights(OData, intervened_TRT = "dlow")
wts.St.dhigh <- getIPWeights(OData, intervened_TRT = "dhigh")

# ------------------------------------------------------------------
# Estimate survival with IPW-adjusted MSM for the hazard (logistic model)
# 1. Saturated model for time points 0 to 7
# 2. Smoothing with one hazard coefficient over time-points 8 to 11
# 3. Smoothing with one hazard coefficient over time-points 12 to 15
# ------------------------------------------------------------------
IPW_MSM_res <- survMSM(OData, wts_data = list(dlow = wts.St.dlow, dhigh = wts.St.dhigh),
                      tbreaks = c(1:8,12,16)-1,
                      est_name = "IPAW", getSEs = TRUE)
names(IPW_MSM_res)
# Survival estimates over time
IPW_MSM_res$St
# SE estimates for each time point:
IPW_MSM_res$IC.Var.S.d$dhigh$se.S
IPW_MSM_res$IC.Var.S.d$dlow$se.S
# MSM coefficient fits
IPW_MSM_res$MSM.fit

# ------------------------------------------------------------------
# Generate automatic html report with results of the analysis
# This assumes that pandoc is already installed
# For more information, go to: http://pandoc.org/installing.html
# ------------------------------------------------------------------
## Not run: 
make_report_rmd(OData, MSM = IPW_MSM_res,
  AddFUPtables = TRUE,
  RDtables = get_MSM_RDs(IPW_MSM_res, t.periods.RDs = c(12, 15), getSEs = FALSE),
  WTtables = get_wtsummary(IPW_MSM_res$wts_data,
    cutoffs = c(0, 0.5, 1, 10, 20, 30, 40, 50, 100, 150), by.rule = TRUE),
  file.name = "sim.data.example.fup",
  title = "Custom Report Title",
  author = "Jane Doe",
  y_legend = 0.95)

## End(Not run)

osofr/stremr documentation built on Jan. 25, 2022, 8:07 a.m.