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Package: ClinicoPath | ||
Type: Package | ||
Package: ClinicoPath | ||
Title: Analysis for Clinicopathological Research | ||
Version: 0.0.1.0002 | ||
Date: 2020-03-17 | ||
Version: 0.0.1.0004 | ||
Date: 2020-03-29 | ||
Authors@R: | ||
person(given = "Serdar", | ||
family = "Balci", | ||
role = c("aut", "cre"), | ||
email = "drserdarbalci@gmail.com", | ||
comment = c(ORCID = "0000-0002-7852-3851")) | ||
Maintainer: Serdar Balci <drserdarbalci@gmail.com> | ||
Description: Analysis for Clinicopathological Research | ||
ClinicoPath help researchers to generate natural language summaries of their | ||
dataset, generate cross tables with statistical tests, and survival analysis | ||
with survival tables, survival plots, and natural language summaries. | ||
Description: Analysis for Clinicopathological Research | ||
ClinicoPath help researchers to generate natural language summaries of | ||
their dataset, generate cross tables with statistical tests, and | ||
survival analysis with survival tables, survival plots, and natural | ||
language summaries. | ||
License: GPL-3 | ||
Encoding: UTF-8 | ||
LazyData: true | ||
Roxygen: list(markdown = TRUE) | ||
URL: https://github.com/sbalci/ClinicoPathJamoviModule/, | ||
https://sbalci.github.io/ClinicoPathJamoviModule/ | ||
BugReports: | ||
https://github.com/sbalci/ClinicoPathJamoviModule/issues/ | ||
Depends: | ||
R (>= 3.6) | ||
Imports: | ||
jmvcore (>= 0.8.5), | ||
R6, | ||
caret, | ||
correlation, | ||
dplyr, | ||
survival, | ||
survminer, | ||
explore, | ||
FFTrees, | ||
finalfit, | ||
arsenal, | ||
purrr, | ||
forcats, | ||
ggalluvial, | ||
ggplot2, | ||
ggstatsplot, | ||
glue, | ||
irr, | ||
janitor, | ||
ggplot2, | ||
forcats, | ||
jmvcore (>= 0.8.5), | ||
jsonlite, | ||
knitr, | ||
networkD3, | ||
purrr, | ||
R6, | ||
report, | ||
rlang, | ||
scales, | ||
survival, | ||
survminer, | ||
tableone, | ||
tangram, | ||
rlang, | ||
knitr, | ||
remotes, | ||
tibble, | ||
tidyr, | ||
utils | ||
Suggests: | ||
rmarkdown, | ||
tidyselect, | ||
kableExtra, | ||
ggstatsplot, | ||
ggalluvial, | ||
caret, | ||
irr | ||
yarrr, | ||
circlize, | ||
randomForest | ||
VignetteBuilder: | ||
knitr | ||
Remotes: | ||
r-lib/tidyselect, | ||
ndphillips/FFTrees, | ||
easystats/parameters, | ||
easystats/bayestestR, | ||
easystats/effectsize, | ||
easystats/correlation, | ||
easystats/modelbased, | ||
easystats/insight, | ||
easystats/bayestestR, | ||
easystats/performance, | ||
easystats/parameters, | ||
easystats/report | ||
Suggests: | ||
effectsize, | ||
emmeans, | ||
rmarkdown, | ||
igraph, | ||
iterators, | ||
rms, | ||
commonmark, | ||
sass | ||
Encoding: UTF-8 | ||
LazyData: true | ||
Roxygen: list(markdown = TRUE) | ||
RoxygenNote: 7.0.2 | ||
VignetteBuilder: knitr | ||
URL: https://github.com/sbalci/ClinicoPathJamoviModule/, https://sbalci.github.io/ClinicoPathJamoviModule/ | ||
BugReports: https://github.com/sbalci/ClinicoPathJamoviModule/issues/ |
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# This file is a generated template, your changes will not be overwritten | ||
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competingsurvivalClass <- if (requireNamespace('jmvcore')) R6::R6Class( | ||
"competingsurvivalClass", | ||
inherit = competingsurvivalBase, | ||
private = list( | ||
.run = function() { | ||
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# https://finalfit.org/articles/survival.html#death-status | ||
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# `self$data` contains the data | ||
# `self$options` contains the options | ||
# `self$results` contains the results object (to populate) | ||
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}) | ||
) |
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# This file is automatically generated, you probably don't want to edit this | ||
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competingsurvivalOptions <- if (requireNamespace('jmvcore')) R6::R6Class( | ||
"competingsurvivalOptions", | ||
inherit = jmvcore::Options, | ||
public = list( | ||
initialize = function( | ||
dep = NULL, | ||
group = NULL, | ||
alt = "notequal", | ||
varEq = TRUE, ...) { | ||
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super$initialize( | ||
package='ClinicoPath', | ||
name='competingsurvival', | ||
requiresData=TRUE, | ||
...) | ||
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private$..dep <- jmvcore::OptionVariable$new( | ||
"dep", | ||
dep) | ||
private$..group <- jmvcore::OptionVariable$new( | ||
"group", | ||
group) | ||
private$..alt <- jmvcore::OptionList$new( | ||
"alt", | ||
alt, | ||
options=list( | ||
"notequal", | ||
"onegreater", | ||
"twogreater"), | ||
default="notequal") | ||
private$..varEq <- jmvcore::OptionBool$new( | ||
"varEq", | ||
varEq, | ||
default=TRUE) | ||
|
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self$.addOption(private$..dep) | ||
self$.addOption(private$..group) | ||
self$.addOption(private$..alt) | ||
self$.addOption(private$..varEq) | ||
}), | ||
active = list( | ||
dep = function() private$..dep$value, | ||
group = function() private$..group$value, | ||
alt = function() private$..alt$value, | ||
varEq = function() private$..varEq$value), | ||
private = list( | ||
..dep = NA, | ||
..group = NA, | ||
..alt = NA, | ||
..varEq = NA) | ||
) | ||
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competingsurvivalResults <- if (requireNamespace('jmvcore')) R6::R6Class( | ||
inherit = jmvcore::Group, | ||
active = list( | ||
text = function() private$.items[["text"]]), | ||
private = list(), | ||
public=list( | ||
initialize=function(options) { | ||
super$initialize( | ||
options=options, | ||
name="", | ||
title="Competing Survival") | ||
self$add(jmvcore::Preformatted$new( | ||
options=options, | ||
name="text", | ||
title="Competing Survival"))})) | ||
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competingsurvivalBase <- if (requireNamespace('jmvcore')) R6::R6Class( | ||
"competingsurvivalBase", | ||
inherit = jmvcore::Analysis, | ||
public = list( | ||
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) { | ||
super$initialize( | ||
package = 'ClinicoPath', | ||
name = 'competingsurvival', | ||
version = c(1,0,0), | ||
options = options, | ||
results = competingsurvivalResults$new(options=options), | ||
data = data, | ||
datasetId = datasetId, | ||
analysisId = analysisId, | ||
revision = revision, | ||
pause = NULL, | ||
completeWhenFilled = FALSE) | ||
})) | ||
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#' Competing Survival | ||
#' | ||
#' | ||
#' @param data . | ||
#' @param dep . | ||
#' @param group . | ||
#' @param alt . | ||
#' @param varEq . | ||
#' @return A results object containing: | ||
#' \tabular{llllll}{ | ||
#' \code{results$text} \tab \tab \tab \tab \tab a preformatted \cr | ||
#' } | ||
#' | ||
#' @export | ||
competingsurvival <- function( | ||
data, | ||
dep, | ||
group, | ||
alt = "notequal", | ||
varEq = TRUE) { | ||
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if ( ! requireNamespace('jmvcore')) | ||
stop('competingsurvival requires jmvcore to be installed (restart may be required)') | ||
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if ( ! missing(dep)) dep <- jmvcore::resolveQuo(jmvcore::enquo(dep)) | ||
if ( ! missing(group)) group <- jmvcore::resolveQuo(jmvcore::enquo(group)) | ||
if (missing(data)) | ||
data <- jmvcore::marshalData( | ||
parent.frame(), | ||
`if`( ! missing(dep), dep, NULL), | ||
`if`( ! missing(group), group, NULL)) | ||
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options <- competingsurvivalOptions$new( | ||
dep = dep, | ||
group = group, | ||
alt = alt, | ||
varEq = varEq) | ||
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analysis <- competingsurvivalClass$new( | ||
options = options, | ||
data = data) | ||
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analysis$run() | ||
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analysis$results | ||
} |
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