make_report_rmd

Input data object returned by the function <code><a rd-options="" href="/link/importData?package=stremr&version=0.4" data-mini-rdoc="stremr::importData">importData</a></code>.

OData

The MSM object fits returned by the function <code><a rd-options="" href="/link/survMSM?package=stremr&version=0.4" data-mini-rdoc="stremr::survMSM">survMSM</a></code>.

Optional list of a resulting calls to <code>survNPMSM</code> or a result of a single call to <code><a rd-options="" href="/link/survNPMSM?package=stremr&version=0.4" data-mini-rdoc="stremr::survNPMSM">survNPMSM</a></code>.

NPMSM

Optional list of a resulting calls to <code>fitTMLE</code> or a result of a single call to <code><a rd-options="" href="/link/fitTMLE?package=stremr&version=0.4" data-mini-rdoc="stremr::fitTMLE">fitTMLE</a></code>.

TMLE

Optional list of a resulting calls to <code>fitSeqGcomp</code> or a result of a single call to <code><a rd-options="" href="/link/fitSeqGcomp?package=stremr&version=0.4" data-mini-rdoc="stremr::fitSeqGcomp">fitSeqGcomp</a></code>.

GCOMP

Table(s) with distribution(s) of the IPTW weights, a result of calling the function <code><a rd-options="" href="/link/get_wtsummary?package=stremr&version=0.4" data-mini-rdoc="stremr::get_wtsummary">get_wtsummary</a></code>

WTtables

Logical, set to <code>TRUE</code> to print tables describing the distribution of the maximum follow-up times
by rule (monitoring and treatment).

FUPtables

List of tables with risk differences returned by the function <code><a rd-options="" href="/link/get_MSM_RDs?package=stremr&version=0.4" data-mini-rdoc="stremr::get_MSM_RDs">get_MSM_RDs</a></code>.

MSM.RDtables

List of tables with risk differences returned by the function <code><a rd-options="" href="/link/get_TMLE_RDs?package=stremr&version=0.4" data-mini-rdoc="stremr::get_TMLE_RDs">get_TMLE_RDs</a></code>.

TMLE.RDtables

Logical, set to <code>TRUE</code> to plot KM survival curves when <code>NPMSM</code> argument is specified. Default is <code>FALSE</code>.

plotKM

printEstimateTables

Choose the Pandoc output format for the report file (html, pdf or word).
Note that the html report file is always produced in addition to any other selected format.

format

skip.modelfits

File name for the report file without extension. Default file name is assigned based on the current date.

file.name

Directory path where the report file(s) should be written. Default is to use the system temporary directory.

file.path

Open the report file with OS default viewer?

openFile

Serve the html report as a webpage via R package "rmote".

serve_html_rmote

keep_md

Keep the source .tex files for pdf output?

keep_tex

Save the data needed for generating this report as a list in a separate 'report_name.Rd' file.

save_report_data

Additional arguments may specify the report title (<code>author</code>), author (<code>title</code>).
Specifying the logical flag <code>only.coefs=TRUE</code> disables printing of all h2o-specific model summaries.
Additional set of arguments control the survival plotting, these are passed on to the function <code>f_plot_survest</code>:
<code>t_int_sel</code>, <code>y_lab</code>, <code>x_lab</code>, <code>miny</code>, <code>x_legend</code>, <code>y_legend</code>.


Generate report(s) with modeling stats and survival estimates using pandoc.


Analysis of longitudinal time-to-event or time-to-failure data.
Estimates the counterfactual discrete survival curve under static, dynamic and
stochastic interventions on treatment (exposure) and monitoring events over time.
Estimators (IPW, MSM-IPW, GCOMP, longitudinal TMLE) adjust for measured time-varying
confounding and informative right-censoring. Model fitting can be performed either
with GLM or H2O-3 machine learning libraries.
The exposure, monitoring and censoring variables can be coded as either binary,
categorical or continuous. Each can be multivariate (e.g., can use more than one
column of dummy indicators for different censoring events).
The input data needs to be in long format.

Oleg Sofrygin

stremr

Streamlined Estimation of Survival for Static, Dynamic and
Stochastic Treatment and Monitoring Regimes

make_report_rmd function

Input data object returned by the function <code><a rd-options='' href='importData'>importData</a></code>.

The MSM object fits returned by the function <code><a rd-options='' href='survMSM'>survMSM</a></code>.

Optional list of a resulting calls to <code>survNPMSM</code> or a result of a single call to <code><a rd-options='' href='survNPMSM'>survNPMSM</a></code>.

Optional list of a resulting calls to <code>fitTMLE</code> or a result of a single call to <code><a rd-options='' href='fitTMLE'>fitTMLE</a></code>.

Optional list of a resulting calls to <code>fitSeqGcomp</code> or a result of a single call to <code><a rd-options='' href='fitSeqGcomp'>fitSeqGcomp</a></code>.

Table(s) with distribution(s) of the IPTW weights, a result of calling the function <code><a rd-options='' href='get_wtsummary'>get_wtsummary</a></code>

List of tables with risk differences returned by the function <code><a rd-options='' href='get_MSM_RDs'>get_MSM_RDs</a></code>.

List of tables with risk differences returned by the function <code><a rd-options='' href='get_TMLE_RDs'>get_TMLE_RDs</a></code>.

make_report_rmd: Generate report(s) with modeling stats and survival estimates using pandoc.

Description

Usage

Arguments

Value