minApp 1.8.0

sbalci · Apr 14, 2021 · 4017dc0 · 4017dc0
1 parent 5e02f43
commit 4017dc0
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Showing 11 changed files with 107 additions and 89 deletions.
diff --git 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
@@ -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
@@ -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
@@ -1,16 +1,16 @@
 
 # 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(
         initialize = function(
             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
@@ -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
@@ -1,16 +1,16 @@
 
 # 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(
         initialize = function(
             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
 }
+