R/dynamicGP.R
In pcats-api/pcatsAPIclientR: 'PCATS' API Client
Defines functions
dynamicGP
Documented in
dynamicGP
###################### DynamicResults###################################
#' @title Performs a data analysis for data with adaptive treatments.
#' @description Performs Bayesian's Gaussian process regression or Bayesian
#' additive regression tree for data with adaptive treatment(s).
#' @param datafile File to upload (.csv or .xls)
#' @param dataref Reference to already uploaded file.
#' @param method The method to be used. "GP" for GP method and "BART" for BART method. The default value is "BART".
#' @param stg1.outcome The name of the intermediate outcome variable for stage 1.
#' @param stg1.treatment The name of the treatment variable for stage 1.
#' @param stg1.x.explanatory A vector of the name of the explanatory variables for stage 1.
#' @param stg1.x.confounding A vector of the name of the confounding variables for stage 1.
#' @param stg1.tr.hte An optional vector specifying categorical variables which may have heterogeneous treatment effect with the treatment variable for stage 1.
#' @param stg1.outcome.bound_censor The default value is "neither".
#' "neither" if the intermediate outcome is not bounded or censored.
#' "bounded" if the intermediate outcome is bounded.
#' "censored" if the intermediate outcome is censored.
#' @param stg1.outcome.lb Stage 1 lower bound if the intermediate outcome is bounded.
#' @param stg1.outcome.ub Stage 1 upper bound if the intermediate outcome is bounded.
#' @param stg1.outcome.type Intermediate outcome type ("Continuous" or "Discrete") for stage 1.
#' @param stg1.outcome.censor.yn Censoring variable if the intermediate outcome is censored.
#' @param stg1.outcome.censor.lv lower variable of censored interval if the intermediate outcome is censored.
#' @param stg1.outcome.censor.uv upper variable of censored interval if the intermediate outcome is censored.
#' @param stg1.outcome.link function for the intermediate outcome; the default value is ``identity''.
#' "identity" if no transformation needed.
#' "log" for log transformation.
#' "logit" for logit transformation.
#' @param stg1.tr.values User-defined values for the calculation of ATE if the treatment variable is continuous for stage 1.
#' @param stg1.tr.type The type of treatment at stage 1. "Continuous" for continuous treatment and "Discrete" for categorical treatment. The default value is "Discrete".
#' @param stg1.time Time variable.
#' @param stg1.time.value Pre-specified time exposure.
#' @param stg1.c.margin An optional vector of user-defined values of c for PrTE at stage 1.
#' @param stg2.outcome The name of the outcome variable for stage 2.
#' @param stg2.treatment The name of the treatment variable for stage 2.
#' @param stg2.x.explanatory A vector of the name of the explanatory variables for stage 2.
#' @param stg2.x.confounding A vector of the name of the confounding variables for stage 2.
#' @param stg2.tr1.hte At stage 2, an optional vector specifying categorical variables which may have heterogeneous treatment effect with the stage 1 treatment variable
#' @param stg2.tr2.hte At stage 2, an optional vector specifying categorical variables which may have heterogeneous treatment effect with the stage 2 treatment variable
#' @param stg2.outcome.bound_censor The default value is "neither".
#' "neither" if the intermediate outcome is not bounded or censored.
#' "bounded" if the intermediate outcome is bounded.
#' "censored" if the intermediate outcome is censored.
#' @param stg2.outcome.lb Stage 2 lower bound if the outcome is bounded.
#' @param stg2.outcome.ub Stage 2 upper bound if the outcome is bounded.
#' @param stg2.outcome.type Outcome type ("Continuous" or "Discrete") for stage 2.
#' @param stg2.outcome.censor.yn Censoring variable if the outcome is censored.
#' @param stg2.outcome.censor.lv lower variable of censored interval if the outcome is censored.
#' @param stg2.outcome.censor.uv upper variable of censored interval if the outcome is censored.
#' @param stg2.outcome.link function for the outcome; the default value is ``identity''.
#' "identity" if no transformation needed.
#' "log" for log transformation.
#' "logit" for logit transformation.
#' @param stg2.tr.values User-defined values for the calculation of ATE if the treatment variable is continuous for stage 2.
#' @param stg2.tr.type The type of treatment at stage 2. "Continuous" for continuous treatment and "Discrete" for categorical treatment. The default value is "Discrete".
#' @param stg2.time Time variable.
#' @param stg2.time.value Pre-specified time exposure.
#' @param stg2.c.margin An optional vector of user-defined values of c for PrTE at stage 2.
#' @param burn.num numeric; the number of MCMC 'burn-in' samples, i.e. number of MCMC to be discarded. The default value is 500.
#' @param mcmc.num numeric; the number of MCMC samples after 'burn-in'. The default value is 500.
#' @param x.categorical A vector of the name of categorical variables in data.
#' @param mi.datafile File to upload (.csv or .xls) that contains the imputed data in the model.
#' @param mi.dataref Reference to already uploaded file that contains the imputed data in the model.
#' @param sheet If \code{datafile} or \code{dataref} points to an Excel file this variable specifies which sheet to load.
#' @param mi.sheet If \code{mi.datafile} or \code{mi.dataurl} points to an Excel file this variable specifies which sheet to load.
#' @param seed Sets the seed. The default value is 5000.
#' @param token Authentication token.
#' @param use.cache Use cached results (default True).
#' @return jobid
#' @export
#' @import httr
#' @import utils
#' @importFrom methods hasArg
#'
dynamicGP <- function(datafile = NULL,
dataref = NULL,
method = "BART",
# stage 1
stg1.outcome,
stg1.treatment,
stg1.x.explanatory = NULL,
stg1.x.confounding = NULL,
stg1.tr.hte = NULL,
stg1.tr.values = NULL,
stg1.tr.type = "Discrete",
stg1.time,
stg1.time.value = NULL,
stg1.outcome.type = "Continuous",
stg1.outcome.bound_censor = "neither",
stg1.outcome.lb = NULL,
stg1.outcome.ub = NULL,
stg1.outcome.censor.lv = NULL,
stg1.outcome.censor.uv = NULL,
stg1.outcome.censor.yn = NULL,
stg1.outcome.link = "identity",
stg1.c.margin = NULL,
# stage 2
stg2.outcome,
stg2.treatment,
stg2.x.explanatory = NULL,
stg2.x.confounding = NULL,
stg2.tr1.hte = NULL,
stg2.tr2.hte = NULL,
stg2.tr.values = NULL,
stg2.tr.type = "Discrete",
stg2.time,
stg2.time.value = NULL,
stg2.outcome.type = "Continuous",
stg2.outcome.bound_censor = "neither",
stg2.outcome.lb = NULL,
stg2.outcome.ub = NULL,
stg2.outcome.censor.lv = NULL,
stg2.outcome.censor.uv = NULL,
stg2.outcome.censor.yn = NULL,
stg2.outcome.link = "identity",
stg2.c.margin = NULL,
# common parameters
burn.num = 500,
mcmc.num = 500,
x.categorical = NULL,
mi.datafile = NULL,
mi.dataref = NULL,
sheet = NULL,
mi.sheet = NULL,
seed = 5000,
token = NULL,
use.cache = NULL) {
data <- NULL
if (!is.null(datafile)) {
data <- httr::upload_file(datafile)
}
mi.data <- NULL
if (!is.null(mi.datafile)) {
mi.data <- httr::upload_file(mi.datafile)
}
headers <- c()
if (!is.null(token)) {
headers <- c(headers, "Authorization" = paste("Bearer", token))
}
if (!hasArg(use.cache) && Sys.getenv("PCATS_USE_CACHE") != "") use.cache <- Sys.getenv("PCATS_USE_CACHE")
if (!is.null(use.cache) && (use.cache == T || use.cache == "1")) {
headers <- c(headers, "X-API-Cache" = "1")
}
if (!is.null(use.cache) && (use.cache == F || use.cache == "0")) {
headers <- c(headers, "X-API-Cache" = "0")
}
retry_count <- 5
while(1) {
jobid <- tryCatch({
res <- POST(
url = "https://pcats.research.cchmc.org/api/dynamicgp",
add_headers(headers),
encode = "multipart",
body = list(
data = data,
dataref = dataref,
stg1.outcome = stg1.outcome, stg1.treatment = stg1.treatment,
stg1.x.explanatory = stg1.x.explanatory, stg1.x.confounding = stg1.x.confounding,
stg1.tr.hte = stg1.tr.hte,
stg1.tr.values = stg1.tr.values,
stg1.tr.type = stg1.tr.type,
stg1.time = stg1.time,
stg1.time.value = stg1.time.value,
stg1.outcome.type = stg1.outcome.type,
stg1.outcome.bound_censor = stg1.outcome.bound_censor,
stg1.outcome.lb = stg1.outcome.lb, stg1.outcome.ub = stg1.outcome.ub,
stg1.outcome.censor.lv = stg1.outcome.censor.lv, stg1.outcome.censor.uv = stg1.outcome.censor.uv,
stg1.outcome.censor.yn = stg1.outcome.censor.yn, stg1.outcome.link = stg1.outcome.link,
stg1.c.margin = stg1.c.margin,
# stage 2
stg2.outcome = stg2.outcome, stg2.treatment = stg2.treatment,
stg2.x.explanatory = stg2.x.explanatory, stg2.x.confounding = stg2.x.confounding,
stg2.tr1.hte = stg2.tr1.hte,
stg2.tr2.hte = stg2.tr2.hte,
stg2.tr.values = stg2.tr.values,
stg2.tr.type = stg2.tr.type,
stg2.time = stg2.time,
stg2.time.value = stg2.time.value,
stg2.outcome.type = stg2.outcome.type,
stg2.outcome.bound_censor = stg2.outcome.bound_censor,
stg2.outcome.lb = stg2.outcome.lb, stg2.outcome.ub = stg2.outcome.ub,
stg2.outcome.censor.lv = stg2.outcome.censor.lv, stg2.outcome.censor.uv = stg2.outcome.censor.uv,
stg2.outcome.censor.yn = stg2.outcome.censor.yn, stg2.outcome.link = stg2.outcome.link,
stg2.c.margin = stg2.c.margin,
burn.num = burn.num, mcmc.num = mcmc.num,
x.categorical = x.categorical,
method = method,
mi.data = mi.data,
mi.dataref = mi.dataref,
sheet = sheet,
mi.sheet = mi.sheet,
seed = seed
)
)
cont <- content(res)
jobid <- cont$jobid[[1]]
jobid
}, error = function(e) {
return("") # Catch connection errors
})
if (jobid != "") break;
retry_count <- retry_count - 1
if (retry_count == 0) break;
Sys.sleep(5-retry_count)
}
jobid
}
pcats-api/pcatsAPIclientR documentation built on June 13, 2025, 5:14 a.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.
Defines functions dynamicGP
Documented in dynamicGP
###################### DynamicResults###################################
#' @title Performs a data analysis for data with adaptive treatments.
#' @description Performs Bayesian's Gaussian process regression or Bayesian
#' additive regression tree for data with adaptive treatment(s).
#' @param datafile File to upload (.csv or .xls)
#' @param dataref Reference to already uploaded file.
#' @param method The method to be used. "GP" for GP method and "BART" for BART method. The default value is "BART".
#' @param stg1.outcome The name of the intermediate outcome variable for stage 1.
#' @param stg1.treatment The name of the treatment variable for stage 1.
#' @param stg1.x.explanatory A vector of the name of the explanatory variables for stage 1.
#' @param stg1.x.confounding A vector of the name of the confounding variables for stage 1.
#' @param stg1.tr.hte An optional vector specifying categorical variables which may have heterogeneous treatment effect with the treatment variable for stage 1.
#' @param stg1.outcome.bound_censor The default value is "neither".
#' "neither" if the intermediate outcome is not bounded or censored.
#' "bounded" if the intermediate outcome is bounded.
#' "censored" if the intermediate outcome is censored.
#' @param stg1.outcome.lb Stage 1 lower bound if the intermediate outcome is bounded.
#' @param stg1.outcome.ub Stage 1 upper bound if the intermediate outcome is bounded.
#' @param stg1.outcome.type Intermediate outcome type ("Continuous" or "Discrete") for stage 1.
#' @param stg1.outcome.censor.yn Censoring variable if the intermediate outcome is censored.
#' @param stg1.outcome.censor.lv lower variable of censored interval if the intermediate outcome is censored.
#' @param stg1.outcome.censor.uv upper variable of censored interval if the intermediate outcome is censored.
#' @param stg1.outcome.link function for the intermediate outcome; the default value is ``identity''.
#' "identity" if no transformation needed.
#' "log" for log transformation.
#' "logit" for logit transformation.
#' @param stg1.tr.values User-defined values for the calculation of ATE if the treatment variable is continuous for stage 1.
#' @param stg1.tr.type The type of treatment at stage 1. "Continuous" for continuous treatment and "Discrete" for categorical treatment. The default value is "Discrete".
#' @param stg1.time Time variable.
#' @param stg1.time.value Pre-specified time exposure.
#' @param stg1.c.margin An optional vector of user-defined values of c for PrTE at stage 1.
#' @param stg2.outcome The name of the outcome variable for stage 2.
#' @param stg2.treatment The name of the treatment variable for stage 2.
#' @param stg2.x.explanatory A vector of the name of the explanatory variables for stage 2.
#' @param stg2.x.confounding A vector of the name of the confounding variables for stage 2.
#' @param stg2.tr1.hte At stage 2, an optional vector specifying categorical variables which may have heterogeneous treatment effect with the stage 1 treatment variable
#' @param stg2.tr2.hte At stage 2, an optional vector specifying categorical variables which may have heterogeneous treatment effect with the stage 2 treatment variable
#' @param stg2.outcome.bound_censor The default value is "neither".
#' "neither" if the intermediate outcome is not bounded or censored.
#' "bounded" if the intermediate outcome is bounded.
#' "censored" if the intermediate outcome is censored.
#' @param stg2.outcome.lb Stage 2 lower bound if the outcome is bounded.
#' @param stg2.outcome.ub Stage 2 upper bound if the outcome is bounded.
#' @param stg2.outcome.type Outcome type ("Continuous" or "Discrete") for stage 2.
#' @param stg2.outcome.censor.yn Censoring variable if the outcome is censored.
#' @param stg2.outcome.censor.lv lower variable of censored interval if the outcome is censored.
#' @param stg2.outcome.censor.uv upper variable of censored interval if the outcome is censored.
#' @param stg2.outcome.link function for the outcome; the default value is ``identity''.
#' "identity" if no transformation needed.
#' "log" for log transformation.
#' "logit" for logit transformation.
#' @param stg2.tr.values User-defined values for the calculation of ATE if the treatment variable is continuous for stage 2.
#' @param stg2.tr.type The type of treatment at stage 2. "Continuous" for continuous treatment and "Discrete" for categorical treatment. The default value is "Discrete".
#' @param stg2.time Time variable.
#' @param stg2.time.value Pre-specified time exposure.
#' @param stg2.c.margin An optional vector of user-defined values of c for PrTE at stage 2.
#' @param burn.num numeric; the number of MCMC 'burn-in' samples, i.e. number of MCMC to be discarded. The default value is 500.
#' @param mcmc.num numeric; the number of MCMC samples after 'burn-in'. The default value is 500.
#' @param x.categorical A vector of the name of categorical variables in data.
#' @param mi.datafile File to upload (.csv or .xls) that contains the imputed data in the model.
#' @param mi.dataref Reference to already uploaded file that contains the imputed data in the model.
#' @param sheet If \code{datafile} or \code{dataref} points to an Excel file this variable specifies which sheet to load.
#' @param mi.sheet If \code{mi.datafile} or \code{mi.dataurl} points to an Excel file this variable specifies which sheet to load.
#' @param seed Sets the seed. The default value is 5000.
#' @param token Authentication token.
#' @param use.cache Use cached results (default True).
#' @return jobid
#' @export
#' @import httr
#' @import utils
#' @importFrom methods hasArg
#'
dynamicGP <- function(datafile = NULL,
dataref = NULL,
method = "BART",
# stage 1
stg1.outcome,
stg1.treatment,
stg1.x.explanatory = NULL,
stg1.x.confounding = NULL,
stg1.tr.hte = NULL,
stg1.tr.values = NULL,
stg1.tr.type = "Discrete",
stg1.time,
stg1.time.value = NULL,
stg1.outcome.type = "Continuous",
stg1.outcome.bound_censor = "neither",
stg1.outcome.lb = NULL,
stg1.outcome.ub = NULL,
stg1.outcome.censor.lv = NULL,
stg1.outcome.censor.uv = NULL,
stg1.outcome.censor.yn = NULL,
stg1.outcome.link = "identity",
stg1.c.margin = NULL,
# stage 2
stg2.outcome,
stg2.treatment,
stg2.x.explanatory = NULL,
stg2.x.confounding = NULL,
stg2.tr1.hte = NULL,
stg2.tr2.hte = NULL,
stg2.tr.values = NULL,
stg2.tr.type = "Discrete",
stg2.time,
stg2.time.value = NULL,
stg2.outcome.type = "Continuous",
stg2.outcome.bound_censor = "neither",
stg2.outcome.lb = NULL,
stg2.outcome.ub = NULL,
stg2.outcome.censor.lv = NULL,
stg2.outcome.censor.uv = NULL,
stg2.outcome.censor.yn = NULL,
stg2.outcome.link = "identity",
stg2.c.margin = NULL,
# common parameters
burn.num = 500,
mcmc.num = 500,
x.categorical = NULL,
mi.datafile = NULL,
mi.dataref = NULL,
sheet = NULL,
mi.sheet = NULL,
seed = 5000,
token = NULL,
use.cache = NULL) {
data <- NULL
if (!is.null(datafile)) {
data <- httr::upload_file(datafile)
}
mi.data <- NULL
if (!is.null(mi.datafile)) {
mi.data <- httr::upload_file(mi.datafile)
}
headers <- c()
if (!is.null(token)) {
headers <- c(headers, "Authorization" = paste("Bearer", token))
}
if (!hasArg(use.cache) && Sys.getenv("PCATS_USE_CACHE") != "") use.cache <- Sys.getenv("PCATS_USE_CACHE")
if (!is.null(use.cache) && (use.cache == T || use.cache == "1")) {
headers <- c(headers, "X-API-Cache" = "1")
}
if (!is.null(use.cache) && (use.cache == F || use.cache == "0")) {
headers <- c(headers, "X-API-Cache" = "0")
}
retry_count <- 5
while(1) {
jobid <- tryCatch({
res <- POST(
url = "https://pcats.research.cchmc.org/api/dynamicgp",
add_headers(headers),
encode = "multipart",
body = list(
data = data,
dataref = dataref,
stg1.outcome = stg1.outcome, stg1.treatment = stg1.treatment,
stg1.x.explanatory = stg1.x.explanatory, stg1.x.confounding = stg1.x.confounding,
stg1.tr.hte = stg1.tr.hte,
stg1.tr.values = stg1.tr.values,
stg1.tr.type = stg1.tr.type,
stg1.time = stg1.time,
stg1.time.value = stg1.time.value,
stg1.outcome.type = stg1.outcome.type,
stg1.outcome.bound_censor = stg1.outcome.bound_censor,
stg1.outcome.lb = stg1.outcome.lb, stg1.outcome.ub = stg1.outcome.ub,
stg1.outcome.censor.lv = stg1.outcome.censor.lv, stg1.outcome.censor.uv = stg1.outcome.censor.uv,
stg1.outcome.censor.yn = stg1.outcome.censor.yn, stg1.outcome.link = stg1.outcome.link,
stg1.c.margin = stg1.c.margin,
# stage 2
stg2.outcome = stg2.outcome, stg2.treatment = stg2.treatment,
stg2.x.explanatory = stg2.x.explanatory, stg2.x.confounding = stg2.x.confounding,
stg2.tr1.hte = stg2.tr1.hte,
stg2.tr2.hte = stg2.tr2.hte,
stg2.tr.values = stg2.tr.values,
stg2.tr.type = stg2.tr.type,
stg2.time = stg2.time,
stg2.time.value = stg2.time.value,
stg2.outcome.type = stg2.outcome.type,
stg2.outcome.bound_censor = stg2.outcome.bound_censor,
stg2.outcome.lb = stg2.outcome.lb, stg2.outcome.ub = stg2.outcome.ub,
stg2.outcome.censor.lv = stg2.outcome.censor.lv, stg2.outcome.censor.uv = stg2.outcome.censor.uv,
stg2.outcome.censor.yn = stg2.outcome.censor.yn, stg2.outcome.link = stg2.outcome.link,
stg2.c.margin = stg2.c.margin,
burn.num = burn.num, mcmc.num = mcmc.num,
x.categorical = x.categorical,
method = method,
mi.data = mi.data,
mi.dataref = mi.dataref,
sheet = sheet,
mi.sheet = mi.sheet,
seed = seed
)
)
cont <- content(res)
jobid <- cont$jobid[[1]]
jobid
}, error = function(e) {
return("") # Catch connection errors
})
if (jobid != "") break;
retry_count <- retry_count - 1
if (retry_count == 0) break;
Sys.sleep(5-retry_count)
}
jobid
}
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.