diff --git a/DESCRIPTION b/DESCRIPTION index e54c852..6584ecb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Type: Package Package: ClinicoPathDescriptives Title: Descriptives Functions for Clinicopathological Research -Version: 0.0.2.0064 -Date: 2021-03-26 +Version: 0.0.2.0084 +Date: 2021-04-14 Authors@R: person(given = "Serdar", family = "Balci", @@ -42,10 +42,10 @@ Imports: kableExtra, finalfit, vtree, - DiagrammeRsvg + DiagrammeRsvg, + tangram, + arsenal Remotes: - spgarbet/tangram, - mayoverse/arsenal, carloscinelli/benford.analysis, yanlinlin82/ggvenn Encoding: UTF-8 diff --git a/R/agepyramid.h.R b/R/agepyramid.h.R index 8bf2d5f..427b2af 100644 --- a/R/agepyramid.h.R +++ b/R/agepyramid.h.R @@ -1,7 +1,7 @@ # This file is automatically generated, you probably don't want to edit this -agepyramidOptions <- if (requireNamespace('jmvcore')) R6::R6Class( +agepyramidOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "agepyramidOptions", inherit = jmvcore::Options, public = list( @@ -11,8 +11,8 @@ agepyramidOptions <- if (requireNamespace('jmvcore')) R6::R6Class( female = NULL, ...) { super$initialize( - package='ClinicoPathDescriptives', - name='agepyramid', + package="ClinicoPathDescriptives", + name="agepyramid", requiresData=TRUE, ...) @@ -50,7 +50,8 @@ agepyramidOptions <- if (requireNamespace('jmvcore')) R6::R6Class( ..female = NA) ) -agepyramidResults <- if (requireNamespace('jmvcore')) R6::R6Class( +agepyramidResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( + "agepyramidResults", inherit = jmvcore::Group, active = list( pyramidTable = function() private$.items[["pyramidTable"]], @@ -97,14 +98,14 @@ agepyramidResults <- if (requireNamespace('jmvcore')) R6::R6Class( "gender", "female")))})) -agepyramidBase <- if (requireNamespace('jmvcore')) R6::R6Class( +agepyramidBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "agepyramidBase", inherit = jmvcore::Analysis, public = list( initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) { super$initialize( - package = 'ClinicoPathDescriptives', - name = 'agepyramid', + package = "ClinicoPathDescriptives", + name = "agepyramid", version = c(1,0,0), options = options, results = agepyramidResults$new(options=options), @@ -143,8 +144,8 @@ agepyramid <- function( gender, female) { - if ( ! requireNamespace('jmvcore')) - stop('agepyramid requires jmvcore to be installed (restart may be required)') + if ( ! requireNamespace("jmvcore", quietly=TRUE)) + stop("agepyramid requires jmvcore to be installed (restart may be required)") if ( ! missing(age)) age <- jmvcore::resolveQuo(jmvcore::enquo(age)) if ( ! missing(gender)) gender <- jmvcore::resolveQuo(jmvcore::enquo(gender)) @@ -169,3 +170,4 @@ agepyramid <- function( analysis$results } + diff --git a/R/alluvial.h.R b/R/alluvial.h.R index 1e8624c..63211d7 100644 --- a/R/alluvial.h.R +++ b/R/alluvial.h.R @@ -1,7 +1,7 @@ # This file is automatically generated, you probably don't want to edit this -alluvialOptions <- if (requireNamespace('jmvcore')) R6::R6Class( +alluvialOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "alluvialOptions", inherit = jmvcore::Options, public = list( @@ -17,8 +17,8 @@ alluvialOptions <- if (requireNamespace('jmvcore')) R6::R6Class( mytitle = "Alluvial Plot", ...) { super$initialize( - package='ClinicoPathDescriptives', - name='alluvial', + package="ClinicoPathDescriptives", + name="alluvial", requiresData=TRUE, ...) @@ -103,7 +103,8 @@ alluvialOptions <- if (requireNamespace('jmvcore')) R6::R6Class( ..mytitle = NA) ) -alluvialResults <- if (requireNamespace('jmvcore')) R6::R6Class( +alluvialResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( + "alluvialResults", inherit = jmvcore::Group, active = list( todo = function() private$.items[["todo"]], @@ -155,14 +156,14 @@ alluvialResults <- if (requireNamespace('jmvcore')) R6::R6Class( "condensationvar"), visible="(condensationvar)"))})) -alluvialBase <- if (requireNamespace('jmvcore')) R6::R6Class( +alluvialBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "alluvialBase", inherit = jmvcore::Analysis, public = list( initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) { super$initialize( - package = 'ClinicoPathDescriptives', - name = 'alluvial', + package = "ClinicoPathDescriptives", + name = "alluvial", version = c(1,0,0), options = options, results = alluvialResults$new(options=options), @@ -210,8 +211,8 @@ alluvial <- function( usetitle = FALSE, mytitle = "Alluvial Plot") { - if ( ! requireNamespace('jmvcore')) - stop('alluvial requires jmvcore to be installed (restart may be required)') + if ( ! requireNamespace("jmvcore", quietly=TRUE)) + stop("alluvial requires jmvcore to be installed (restart may be required)") if ( ! missing(vars)) vars <- jmvcore::resolveQuo(jmvcore::enquo(vars)) if ( ! missing(condensationvar)) condensationvar <- jmvcore::resolveQuo(jmvcore::enquo(condensationvar)) @@ -241,3 +242,4 @@ alluvial <- function( analysis$results } + diff --git a/R/benford.h.R b/R/benford.h.R index eff9894..274f184 100644 --- a/R/benford.h.R +++ b/R/benford.h.R @@ -1,7 +1,7 @@ # This file is automatically generated, you probably don't want to edit this -benfordOptions <- if (requireNamespace('jmvcore')) R6::R6Class( +benfordOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "benfordOptions", inherit = jmvcore::Options, public = list( @@ -9,8 +9,8 @@ benfordOptions <- if (requireNamespace('jmvcore')) R6::R6Class( var = NULL, ...) { super$initialize( - package='ClinicoPathDescriptives', - name='benford', + package="ClinicoPathDescriptives", + name="benford", requiresData=TRUE, ...) @@ -30,7 +30,8 @@ benfordOptions <- if (requireNamespace('jmvcore')) R6::R6Class( ..var = NA) ) -benfordResults <- if (requireNamespace('jmvcore')) R6::R6Class( +benfordResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( + "benfordResults", inherit = jmvcore::Group, active = list( todo = function() private$.items[["todo"]], @@ -66,14 +67,14 @@ benfordResults <- if (requireNamespace('jmvcore')) R6::R6Class( renderFun=".plot", requiresData=TRUE))})) -benfordBase <- if (requireNamespace('jmvcore')) R6::R6Class( +benfordBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "benfordBase", inherit = jmvcore::Analysis, public = list( initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) { super$initialize( - package = 'ClinicoPathDescriptives', - name = 'benford', + package = "ClinicoPathDescriptives", + name = "benford", version = c(1,0,0), options = options, results = benfordResults$new(options=options), @@ -104,8 +105,8 @@ benford <- function( data, var) { - if ( ! requireNamespace('jmvcore')) - stop('benford requires jmvcore to be installed (restart may be required)') + if ( ! requireNamespace("jmvcore", quietly=TRUE)) + stop("benford requires jmvcore to be installed (restart may be required)") if ( ! missing(var)) var <- jmvcore::resolveQuo(jmvcore::enquo(var)) if (missing(data)) @@ -125,3 +126,4 @@ benford <- function( analysis$results } + diff --git a/R/crosstable.h.R b/R/crosstable.h.R index 54146fa..0bea816 100644 --- a/R/crosstable.h.R +++ b/R/crosstable.h.R @@ -1,7 +1,7 @@ # This file is automatically generated, you probably don't want to edit this -crosstableOptions <- if (requireNamespace('jmvcore')) R6::R6Class( +crosstableOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "crosstableOptions", inherit = jmvcore::Options, public = list( @@ -14,8 +14,8 @@ crosstableOptions <- if (requireNamespace('jmvcore')) R6::R6Class( pcat = "chisq", ...) { super$initialize( - package='ClinicoPathDescriptives', - name='crosstable', + package="ClinicoPathDescriptives", + name="crosstable", requiresData=TRUE, ...) @@ -83,7 +83,8 @@ crosstableOptions <- if (requireNamespace('jmvcore')) R6::R6Class( ..pcat = NA) ) -crosstableResults <- if (requireNamespace('jmvcore')) R6::R6Class( +crosstableResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( + "crosstableResults", inherit = jmvcore::Group, active = list( todo = function() private$.items[["todo"]], @@ -146,14 +147,14 @@ crosstableResults <- if (requireNamespace('jmvcore')) R6::R6Class( visible="(sty:nejm || sty:lancet || sty:hmisc)", refs="tangram"))})) -crosstableBase <- if (requireNamespace('jmvcore')) R6::R6Class( +crosstableBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "crosstableBase", inherit = jmvcore::Analysis, public = list( initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) { super$initialize( - package = 'ClinicoPathDescriptives', - name = 'crosstable', + package = "ClinicoPathDescriptives", + name = "crosstable", version = c(1,0,0), options = options, results = crosstableResults$new(options=options), @@ -200,8 +201,8 @@ crosstable <- function( cont = "mean", pcat = "chisq") { - if ( ! requireNamespace('jmvcore')) - stop('crosstable requires jmvcore to be installed (restart may be required)') + if ( ! requireNamespace("jmvcore", quietly=TRUE)) + stop("crosstable requires jmvcore to be installed (restart may be required)") if ( ! missing(vars)) vars <- jmvcore::resolveQuo(jmvcore::enquo(vars)) if ( ! missing(group)) group <- jmvcore::resolveQuo(jmvcore::enquo(group)) @@ -229,3 +230,4 @@ crosstable <- function( analysis$results } + diff --git a/R/reportcat.h.R b/R/reportcat.h.R index 2c277e7..5c71450 100644 --- a/R/reportcat.h.R +++ b/R/reportcat.h.R @@ -1,7 +1,7 @@ # This file is automatically generated, you probably don't want to edit this -reportcatOptions <- if (requireNamespace('jmvcore')) R6::R6Class( +reportcatOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "reportcatOptions", inherit = jmvcore::Options, public = list( @@ -9,8 +9,8 @@ reportcatOptions <- if (requireNamespace('jmvcore')) R6::R6Class( vars = NULL, ...) { super$initialize( - package='ClinicoPathDescriptives', - name='reportcat', + package="ClinicoPathDescriptives", + name="reportcat", requiresData=TRUE, ...) @@ -31,7 +31,8 @@ reportcatOptions <- if (requireNamespace('jmvcore')) R6::R6Class( ..vars = NA) ) -reportcatResults <- if (requireNamespace('jmvcore')) R6::R6Class( +reportcatResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( + "reportcatResults", inherit = jmvcore::Group, active = list( todo = function() private$.items[["todo"]], @@ -55,14 +56,14 @@ reportcatResults <- if (requireNamespace('jmvcore')) R6::R6Class( name="text", title=""))})) -reportcatBase <- if (requireNamespace('jmvcore')) R6::R6Class( +reportcatBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "reportcatBase", inherit = jmvcore::Analysis, public = list( initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) { super$initialize( - package = 'ClinicoPathDescriptives', - name = 'reportcat', + package = "ClinicoPathDescriptives", + name = "reportcat", version = c(1,0,0), options = options, results = reportcatResults$new(options=options), @@ -97,8 +98,8 @@ reportcat <- function( data, vars) { - if ( ! requireNamespace('jmvcore')) - stop('reportcat requires jmvcore to be installed (restart may be required)') + if ( ! requireNamespace("jmvcore", quietly=TRUE)) + stop("reportcat requires jmvcore to be installed (restart may be required)") if ( ! missing(vars)) vars <- jmvcore::resolveQuo(jmvcore::enquo(vars)) if (missing(data)) @@ -119,3 +120,4 @@ reportcat <- function( analysis$results } + diff --git a/R/summarydata.h.R b/R/summarydata.h.R index 5c91fac..2af0791 100644 --- a/R/summarydata.h.R +++ b/R/summarydata.h.R @@ -1,7 +1,7 @@ # This file is automatically generated, you probably don't want to edit this -summarydataOptions <- if (requireNamespace('jmvcore')) R6::R6Class( +summarydataOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "summarydataOptions", inherit = jmvcore::Options, public = list( @@ -9,8 +9,8 @@ summarydataOptions <- if (requireNamespace('jmvcore')) R6::R6Class( vars = NULL, ...) { super$initialize( - package='ClinicoPathDescriptives', - name='summarydata', + package="ClinicoPathDescriptives", + name="summarydata", requiresData=TRUE, ...) @@ -30,7 +30,8 @@ summarydataOptions <- if (requireNamespace('jmvcore')) R6::R6Class( ..vars = NA) ) -summarydataResults <- if (requireNamespace('jmvcore')) R6::R6Class( +summarydataResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( + "summarydataResults", inherit = jmvcore::Group, active = list( todo = function() private$.items[["todo"]], @@ -51,14 +52,14 @@ summarydataResults <- if (requireNamespace('jmvcore')) R6::R6Class( name="text", title=""))})) -summarydataBase <- if (requireNamespace('jmvcore')) R6::R6Class( +summarydataBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "summarydataBase", inherit = jmvcore::Analysis, public = list( initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) { super$initialize( - package = 'ClinicoPathDescriptives', - name = 'summarydata', + package = "ClinicoPathDescriptives", + name = "summarydata", version = c(1,0,0), options = options, results = summarydataResults$new(options=options), @@ -93,8 +94,8 @@ summarydata <- function( data, vars) { - if ( ! requireNamespace('jmvcore')) - stop('summarydata requires jmvcore to be installed (restart may be required)') + if ( ! requireNamespace("jmvcore", quietly=TRUE)) + stop("summarydata requires jmvcore to be installed (restart may be required)") if ( ! missing(vars)) vars <- jmvcore::resolveQuo(jmvcore::enquo(vars)) if (missing(data)) @@ -114,3 +115,4 @@ summarydata <- function( analysis$results } + diff --git a/R/tableone.h.R b/R/tableone.h.R index 9ee993e..fc015a9 100644 --- a/R/tableone.h.R +++ b/R/tableone.h.R @@ -1,7 +1,7 @@ # This file is automatically generated, you probably don't want to edit this -tableoneOptions <- if (requireNamespace('jmvcore')) R6::R6Class( +tableoneOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "tableoneOptions", inherit = jmvcore::Options, public = list( @@ -11,8 +11,8 @@ tableoneOptions <- if (requireNamespace('jmvcore')) R6::R6Class( excl = TRUE, ...) { super$initialize( - package='ClinicoPathDescriptives', - name='tableone', + package="ClinicoPathDescriptives", + name="tableone", requiresData=TRUE, ...) @@ -47,7 +47,8 @@ tableoneOptions <- if (requireNamespace('jmvcore')) R6::R6Class( ..excl = NA) ) -tableoneResults <- if (requireNamespace('jmvcore')) R6::R6Class( +tableoneResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( + "tableoneResults", inherit = jmvcore::Group, active = list( todo = function() private$.items[["todo"]], @@ -103,14 +104,14 @@ tableoneResults <- if (requireNamespace('jmvcore')) R6::R6Class( visible="(sty:t4)", refs="janitor"))})) -tableoneBase <- if (requireNamespace('jmvcore')) R6::R6Class( +tableoneBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "tableoneBase", inherit = jmvcore::Analysis, public = list( initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) { super$initialize( - package = 'ClinicoPathDescriptives', - name = 'tableone', + package = "ClinicoPathDescriptives", + name = "tableone", version = c(0,0,1), options = options, results = tableoneResults$new(options=options), @@ -158,8 +159,8 @@ tableone <- function( sty = "t1", excl = TRUE) { - if ( ! requireNamespace('jmvcore')) - stop('tableone requires jmvcore to be installed (restart may be required)') + if ( ! requireNamespace("jmvcore", quietly=TRUE)) + stop("tableone requires jmvcore to be installed (restart may be required)") if ( ! missing(vars)) vars <- jmvcore::resolveQuo(jmvcore::enquo(vars)) if (missing(data)) @@ -181,3 +182,4 @@ tableone <- function( analysis$results } + diff --git a/R/vartree.h.R b/R/vartree.h.R index e91a8a5..f720fe2 100644 --- a/R/vartree.h.R +++ b/R/vartree.h.R @@ -1,7 +1,7 @@ # This file is automatically generated, you probably don't want to edit this -vartreeOptions <- if (requireNamespace('jmvcore')) R6::R6Class( +vartreeOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "vartreeOptions", inherit = jmvcore::Options, public = list( @@ -34,8 +34,8 @@ vartreeOptions <- if (requireNamespace('jmvcore')) R6::R6Class( summarylocation = "leafonly", ...) { super$initialize( - package='ClinicoPathDescriptives', - name='vartree', + package="ClinicoPathDescriptives", + name="vartree", requiresData=TRUE, ...) @@ -253,7 +253,8 @@ vartreeOptions <- if (requireNamespace('jmvcore')) R6::R6Class( ..summarylocation = NA) ) -vartreeResults <- if (requireNamespace('jmvcore')) R6::R6Class( +vartreeResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( + "vartreeResults", inherit = jmvcore::Group, active = list( todo = function() private$.items[["todo"]], @@ -282,14 +283,14 @@ vartreeResults <- if (requireNamespace('jmvcore')) R6::R6Class( title="Pattern Table", visible="(ptable)"))})) -vartreeBase <- if (requireNamespace('jmvcore')) R6::R6Class( +vartreeBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "vartreeBase", inherit = jmvcore::Analysis, public = list( initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) { super$initialize( - package = 'ClinicoPathDescriptives', - name = 'vartree', + package = "ClinicoPathDescriptives", + name = "vartree", version = c(1,0,0), options = options, results = vartreeResults$new(options=options), @@ -374,8 +375,8 @@ vartree <- function( prunesmaller = 5, summarylocation = "leafonly") { - if ( ! requireNamespace('jmvcore')) - stop('vartree requires jmvcore to be installed (restart may be required)') + if ( ! requireNamespace("jmvcore", quietly=TRUE)) + stop("vartree requires jmvcore to be installed (restart may be required)") if ( ! missing(vars)) vars <- jmvcore::resolveQuo(jmvcore::enquo(vars)) if ( ! missing(percvar)) percvar <- jmvcore::resolveQuo(jmvcore::enquo(percvar)) @@ -432,3 +433,4 @@ vartree <- function( analysis$results } + diff --git a/R/venn.h.R b/R/venn.h.R index 1cbe181..e3008f6 100644 --- a/R/venn.h.R +++ b/R/venn.h.R @@ -1,7 +1,7 @@ # This file is automatically generated, you probably don't want to edit this -vennOptions <- if (requireNamespace('jmvcore')) R6::R6Class( +vennOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "vennOptions", inherit = jmvcore::Options, public = list( @@ -16,8 +16,8 @@ vennOptions <- if (requireNamespace('jmvcore')) R6::R6Class( var4true = NULL, ...) { super$initialize( - package='ClinicoPathDescriptives', - name='venn', + package="ClinicoPathDescriptives", + name="venn", requiresData=TRUE, ...) @@ -99,7 +99,8 @@ vennOptions <- if (requireNamespace('jmvcore')) R6::R6Class( ..var4true = NA) ) -vennResults <- if (requireNamespace('jmvcore')) R6::R6Class( +vennResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( + "vennResults", inherit = jmvcore::Group, active = list( todo = function() private$.items[["todo"]], @@ -135,14 +136,14 @@ vennResults <- if (requireNamespace('jmvcore')) R6::R6Class( renderFun=".plot", requiresData=TRUE))})) -vennBase <- if (requireNamespace('jmvcore')) R6::R6Class( +vennBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "vennBase", inherit = jmvcore::Analysis, public = list( initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) { super$initialize( - package = 'ClinicoPathDescriptives', - name = 'venn', + package = "ClinicoPathDescriptives", + name = "venn", version = c(1,0,0), options = options, results = vennResults$new(options=options), @@ -185,8 +186,8 @@ venn <- function( var4, var4true) { - if ( ! requireNamespace('jmvcore')) - stop('venn requires jmvcore to be installed (restart may be required)') + if ( ! requireNamespace("jmvcore", quietly=TRUE)) + stop("venn requires jmvcore to be installed (restart may be required)") if ( ! missing(var1)) var1 <- jmvcore::resolveQuo(jmvcore::enquo(var1)) if ( ! missing(var2)) var2 <- jmvcore::resolveQuo(jmvcore::enquo(var2)) @@ -223,3 +224,4 @@ venn <- function( analysis$results } + diff --git a/jamovi/0000.yaml b/jamovi/0000.yaml index 6bb520f..c001230 100644 --- a/jamovi/0000.yaml +++ b/jamovi/0000.yaml @@ -1,12 +1,12 @@ --- title: Descriptives Functions for Clinicopathological Research name: ClinicoPathDescriptives -version: 0.0.2.0064 +version: 0.0.2.0084 jms: '1.0' authors: - Serdar Balci maintainer: Serdar Balci -date: '2021-03-26' +date: '2021-04-14' type: R description: >- Descriptives Functions for Clinicopathological Research Descriptive functions @@ -85,6 +85,6 @@ datasets: - Alluvial Diagrams - Venn Diagrams usesNative: true -minApp: 1.2.19 +minApp: 1.8.0 ...