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Update manual

tags/v1.0.0
prise6 4 years ago
parent
commit
79cc1ecf07
7 changed files with 65 additions and 26 deletions
  1. 3
    1
      data-raw/sepsis.R
  2. BIN
      data/sepsis.rdata
  3. 13
    3
      man/VT.difft.Rd
  4. 1
    1
      man/VT.object.Rd
  5. 1
    1
      man/VT.tree.Rd
  6. 19
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      man/sepsis.Rd
  7. 28
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      man/vt.data.Rd

+ 3
- 1
data-raw/sepsis.R View File

@@ -22,7 +22,9 @@ sum(is.na(sepsis.csv$survival))
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 # For futures computation i need to impute missing values
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 # I use random forest imputation with randomForest package with simple parameters
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 # I need to make survival field as factor
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-sepsis.csv$survival <- factor(sepsis.csv$survival, levels = 0:1) 
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+sepsis.csv$survival <- factor(sepsis.csv$survival, levels = 0:1)
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+# reproducibility:
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+set.seed(123)
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 sepsis.imp <- with(sepsis.csv, rfImpute(y = survival, x = sepsis.csv[, -1], iter = 5, ntree = 500))
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 str(sepsis.imp)
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BIN
data/sepsis.rdata View File


+ 13
- 3
man/VT.difft.Rd View File

@@ -10,8 +10,14 @@ A reference class to represent difference between twin1 and twin2
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 \details{
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 Difft are calculated depending on the favorable outcome chosen. It is the
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 second level of the outcome. For example, if the outcome is 0 and 1, the
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-favorable outcome is 1. Then, \deqn{difft_i = twin1_i - twin2_i IF T_i =
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-1} \deqn{ difft_i = twin2_i - twin1_i IF T_i = 0}
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+favorable outcome is 1. Then, \deqn{difft_i = twin1_i - twin2_i if T_i = 1}
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+\deqn{ difft_i = twin2_i - twin1_i if T_i = 0}.
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+So \emph{absolute} method is :
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+\deqn{P(Y = 1 | T = 1) - P(Y = 1 | T =0)}
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+So \emph{relative} method is :
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+\deqn{P(Y = 1 | T = 1)/P(Y = 1 | T =0)}
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+So \emph{absolute} method is :
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+\deqn{logit(P(Y = 1 | T = 1)) - logit(P(Y = 1 | T =0))}
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 }
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 \section{Fields}{
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@@ -22,6 +28,9 @@ favorable outcome is 1. Then, \deqn{difft_i = twin1_i - twin2_i IF T_i =
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 \item{\code{twin2}}{vector of \eqn{E(Y|T = another treatment)}}
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+\item{\code{method}}{Method available to compute difft : c("absolute", "relative",
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+"logit"). Absolute is default value. See details.}
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+
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 \item{\code{difft}}{vector of difference between twin1 and twin2}
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 }}
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 \section{Methods}{
@@ -30,6 +39,7 @@ favorable outcome is 1. Then, \deqn{difft_i = twin1_i - twin2_i IF T_i =
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 \item{\code{computeDifft()}}{Compute difference between twin1 and twin2. See details.}
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 }}
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 \seealso{
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-\code{\link{VT.forest}}, \code{\link{VT.forest.one}}, \code{\link{VT.forest.double}}
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+\code{\link{VT.forest}}, \code{\link{VT.forest.one}},
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+  \code{\link{VT.forest.double}}
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 }
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+ 1
- 1
man/VT.object.Rd View File

@@ -40,7 +40,7 @@ treatments.}
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 \item{\code{getFormula()}}{Return formula : Y~T+X1+...+Xp. Usefull for cforest function.}
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-\item{\code{getIncidences()}}{Return incidence table of data.}
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+\item{\code{getIncidences(rule = NULL)}}{Return incidence table of data if rule set to NULL. Otherwise return incidence for the rule.}
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 \item{\code{getX(interactions = T, trt = NULL)}}{Return predictors (T,X,X*T,X*(1-T)). Or (T,X) if interactions is FALSE.
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 If trt is not NULL, return predictors for T = trt}

+ 1
- 1
man/VT.tree.Rd View File

@@ -70,7 +70,7 @@ screening field}
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 \item{\code{getInfos()}}{Return infos about tree}
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 \item{\code{getRules(only.leaf = F, only.fav = F, tables = T, verbose = T,
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-  compete = F)}}{Retrun subgroups discovered by the tree. See details.}
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+  compete = F)}}{Return subgroups discovered by the tree. See details.}
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 \item{\code{run(...)}}{Compute tree with rpart parameters}
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 }}

+ 19
- 20
man/sepsis.Rd View File

@@ -4,22 +4,17 @@
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 \name{sepsis}
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 \alias{sepsis}
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 \title{Clinical Trial for Sepsis desease}
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-\format{454 patients and 13 variables.
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-\describe{
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- \item{survival}{binary outcome}
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- \item{THERAPY}{1 for active treatment, 0 for control treatment}
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- \item{TIMFIRST}{Time from first sepsis-organ fail to start drug}
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- \item{AGE}{Patient age in years}
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- \item{BLLPLAT}{Baseline local platelets}
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- \item{blSOFA}{Sum of baselin sofa (cardiovascular, hematology, hepaticrenal, and respiration scores)}
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- \item{BLLCREAT}{Base creatinine}
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- \item{ORGANNUM}{Number of baseline organ failures}
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- \item{PRAPACHE}{Pre-infusion apache-ii score}
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- \item{BLGCS}{Base GLASGOW coma scale score}
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- \item{BLIL6}{Baseline serum IL-6 concentration}
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- \item{BLADL}{Baseline activity of daily living score}
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- \item{BLLBILI}{Baseline local bilirubin}
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-}}
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+\format{470 patients and 13 variables. \describe{ \item{survival}{binary
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+  outcome} \item{THERAPY}{1 for active treatment, 0 for control treatment}
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+  \item{TIMFIRST}{Time from first sepsis-organ fail to start drug}
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+  \item{AGE}{Patient age in years} \item{BLLPLAT}{Baseline local platelets}
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+  \item{blSOFA}{Sum of baselin sofa (cardiovascular, hematology,
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+  hepaticrenal, and respiration scores)} \item{BLLCREAT}{Base creatinine}
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+  \item{ORGANNUM}{Number of baseline organ failures}
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+  \item{PRAPACHE}{Pre-infusion apache-ii score} \item{BLGCS}{Base GLASGOW
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+  coma scale score} \item{BLIL6}{Baseline serum IL-6 concentration}
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+  \item{BLADL}{Baseline activity of daily living score}
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+  \item{BLLBILI}{Baseline local bilirubin} }}
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 \source{
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 \url{http://biopharmnet.com/wiki/Software_for_subgroup_identification_and_analysis}
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 }
@@ -27,21 +22,25 @@
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 data(sepsis)
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 }
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 \description{
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-Simulated clinical trial with two groups treatment about sepsis desease. See details.
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+Simulated clinical trial with two groups treatment about sepsis desease. See
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+details.
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 }
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 \details{
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 This dataset is taken from
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 \href{http://biopharmnet.com/wiki/Software_for_subgroup_identification_and_analysis}{SIDES
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 method}.
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-\code{Sepsis} contains simulated data on 454 subjects with a binary outcome
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+\code{Sepsis} contains simulated data on 470 subjects with a binary outcome
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 survival, that stores survival status for patient after 28 days of treatment,
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 value of 1 for subjects who died after 28 days and 0 otherwise. There are 11
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 covariates, listed below, all of which are numerical variables.
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 Note that contrary to the original dataset used in SIDES, missing values have
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-been imputed by random forest \code{(randomForest::rfImpute())}
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+been imputed by random forest \code{(randomForest::rfImpute())}. See file
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+data-raw/sepsis.R for more details.
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-True subgroup is \emph{PRAPACHE <= 26 & AGE <= 49.80}
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+True subgroup is \emph{PRAPACHE <= 26 & AGE <= 49.80}. \emph{NOTE:} This
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+subgroup is defined with the \emph{lower} event rate (survival = 1) in
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+treatement arm.
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 }
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+ 28
- 0
man/vt.data.Rd View File

@@ -0,0 +1,28 @@
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+% Generated by roxygen2 (4.1.1): do not edit by hand
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+% Please edit documentation in R/object.wrapper.R
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+\name{vt.data}
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+\alias{vt.data}
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+\title{Initialize virtual twins data}
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+\usage{
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+vt.data(dataset, outcome.field, treatment.field, interactions = TRUE, ...)
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+}
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+\arguments{
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+\item{dataset}{data.frame representing RCT's}
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+
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+\item{outcome.field}{name of the outcome's field in \code{dataset}}
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+
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+\item{treatment.field}{name of the treatment's field in \code{dataset}}
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+
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+\item{interactions}{logical. If running VirtualTwins with treatment's
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+interactions, set to TRUE (default value)}
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+
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+\item{...}{parameters of \code{\link{VT.object}}}
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+}
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+\value{
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+\code{VT.object}
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+}
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+\description{
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+\code{vt.data} is a wrapper of \code{\link{formatRCTDataset}} and
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+\code{\link{VT.object}}.
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+}
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+

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