update docs

sbalci · Jan 30, 2020 · 08473bf · 08473bf
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -27,9 +27,6 @@
 ### License
 ^LICENSE\.md$
 
-### Hex logo
-^img/
-
 ### Jamovi
 ^jamovi/
 .jmo$
@@ -47,3 +44,5 @@ build
 ^tests$
 
 ^\.github/
+^docs$
+^pkgdown$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -28,15 +28,16 @@ Imports:
     explore,
     tangram,
     irr,
-    rlang
+    rlang,
+    tidyselect
 Remotes:
     easystats/insight,
     easystats/parameters,
     easystats/report
 Suggests:
     remotes,
     devtools,
-    tidyselect,
+    lubridate,
     broom, 
     GGally, 
     gridExtra, 

diff --git a/R/agreement.b.R b/R/agreement.b.R
@@ -1,3 +1,8 @@
+#' Agreement
+#'
+#'
+#' @importFrom R6 R6Class
+#' @import jmvcore
 
 # This file is a generated template, your changes will not be overwritten
 
@@ -25,10 +30,14 @@ agreementClass <- if (requireNamespace('jmvcore')) R6::R6Class(
 
             result1 <- irr::agree(ratings)
 
-
             result2 <- irr::kappa2(ratings)
 
 
+
+
+
+
+
             self$results$text1$setContent(result1)
 
             self$results$text2$setContent(result2)

diff --git a/R/cluster.b.R b/R/cluster.b.R
@@ -0,0 +1,17 @@
+#' @importFrom R6 R6Class
+#' @import jmvcore
+#'
+# This file is a generated template, your changes will not be overwritten
+
+clusterClass <- if (requireNamespace('jmvcore')) R6::R6Class(
+    "clusterClass",
+    inherit = clusterBase,
+    private = list(
+        .run = function() {
+
+            # `self$data` contains the data
+            # `self$options` contains the options
+            # `self$results` contains the results object (to populate)
+
+        })
+)
diff --git a/R/cluster.h.R b/R/cluster.h.R
@@ -0,0 +1,137 @@
+
+# This file is automatically generated, you probably don't want to edit this
+
+clusterOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
+    "clusterOptions",
+    inherit = jmvcore::Options,
+    public = list(
+        initialize = function(
+            dep = NULL,
+            group = NULL,
+            alt = "notequal",
+            varEq = TRUE, ...) {
+
+            super$initialize(
+                package='ClinicoPath',
+                name='cluster',
+                requiresData=TRUE,
+                ...)
+
+            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)
+
+            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)
+)
+
+clusterResults <- 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="Cluster Analysis")
+            self$add(jmvcore::Preformatted$new(
+                options=options,
+                name="text",
+                title="Cluster Analysis"))}))
+
+clusterBase <- if (requireNamespace('jmvcore')) R6::R6Class(
+    "clusterBase",
+    inherit = jmvcore::Analysis,
+    public = list(
+        initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
+            super$initialize(
+                package = 'ClinicoPath',
+                name = 'cluster',
+                version = c(1,0,0),
+                options = options,
+                results = clusterResults$new(options=options),
+                data = data,
+                datasetId = datasetId,
+                analysisId = analysisId,
+                revision = revision,
+                pause = NULL,
+                completeWhenFilled = FALSE)
+        }))
+
+#' Cluster Analysis
+#'
+#' 
+#' @param data .
+#' @param dep .
+#' @param group .
+#' @param alt .
+#' @param varEq .
+#' @return A results object containing:
+#' \tabular{llllll}{
+#'   \code{results$text} \tab \tab \tab \tab \tab a preformatted \cr
+#' }
+#'
+#' @export
+cluster <- function(
+    data,
+    dep,
+    group,
+    alt = "notequal",
+    varEq = TRUE) {
+
+    if ( ! requireNamespace('jmvcore'))
+        stop('cluster requires jmvcore to be installed (restart may be required)')
+
+    if ( ! missing(dep)) dep <- jmvcore::resolveQuo(jmvcore::enquo(dep))
+    if ( ! missing(group)) group <- jmvcore::resolveQuo(jmvcore::enquo(group))
+    if (missing(data))
+        data <- jmvcore::marshalData(
+            parent.frame(),
+            `if`( ! missing(dep), dep, NULL),
+            `if`( ! missing(group), group, NULL))
+
+
+    options <- clusterOptions$new(
+        dep = dep,
+        group = group,
+        alt = alt,
+        varEq = varEq)
+
+    analysis <- clusterClass$new(
+        options = options,
+        data = data)
+
+    analysis$run()
+
+    analysis$results
+}
diff --git a/R/correlation.b.R b/R/correlation.b.R
@@ -1,4 +1,6 @@
-
+#' @importFrom R6 R6Class
+#' @import jmvcore
+#'
 # This file is a generated template, your changes will not be overwritten
 
 correlationClass <- if (requireNamespace('jmvcore')) R6::R6Class(

diff --git a/R/crosstable.b.R b/R/crosstable.b.R
@@ -1,4 +1,6 @@
-
+#' @importFrom R6 R6Class
+#' @import jmvcore
+#'
 # This file is a generated template, your changes will not be overwritten
 
 crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(

diff --git a/R/decision.b.R b/R/decision.b.R
@@ -1,4 +1,6 @@
-
+#' @importFrom R6 R6Class
+#' @import jmvcore
+#'
 # This file is a generated template, your changes will not be overwritten
 
 decisionClass <- if (requireNamespace('jmvcore')) R6::R6Class(

diff --git a/R/decisioncalculator.b.R b/R/decisioncalculator.b.R
@@ -1,4 +1,6 @@
-
+#' @importFrom R6 R6Class
+#' @import jmvcore
+#'
 # This file is a generated template, your changes will not be overwritten
 
 decisioncalculatorClass <- if (requireNamespace('jmvcore')) R6::R6Class(

diff --git a/R/frequencies.b.R b/R/frequencies.b.R
@@ -1,4 +1,6 @@
-
+#' @importFrom R6 R6Class
+#' @import jmvcore
+#'
 # This file is a generated template, your changes will not be overwritten
 
 frequenciesClass <- if (requireNamespace('jmvcore')) R6::R6Class(

diff --git a/R/multisurvival.b.R b/R/multisurvival.b.R
@@ -1,4 +1,6 @@
-
+#' @importFrom R6 R6Class
+#' @import jmvcore
+#'
 # This file is a generated template, your changes will not be overwritten
 
 multisurvivalClass <- if (requireNamespace('jmvcore')) R6::R6Class(

diff --git a/R/report.b.R b/R/report.b.R
@@ -1,4 +1,6 @@
-
+#' @importFrom R6 R6Class
+#' @import jmvcore
+#'
 # This file is a generated template, your changes will not be overwritten
 
 reportClass <- if (requireNamespace('jmvcore')) R6::R6Class(

diff --git a/R/statsplot2.b.R b/R/statsplot2.b.R
@@ -1,4 +1,6 @@
-
+#' @importFrom R6 R6Class
+#' @import jmvcore
+#'
 # This file is a generated template, your changes will not be overwritten
 
 statsplot2Class <- if (requireNamespace('jmvcore')) R6::R6Class(
@@ -7,6 +9,10 @@ statsplot2Class <- if (requireNamespace('jmvcore')) R6::R6Class(
     private = list(
         .run = function() {
 
+            if(is.null(self$options$dep) || is.null(self$options$group))
+                return()
+
+
             mydata <- self$data
 
             mydep <- self$data[[self$options$dep]]
@@ -17,10 +23,26 @@ statsplot2Class <- if (requireNamespace('jmvcore')) R6::R6Class(
             plotData <- jmvcore::naOmit(plotData)
 
             image <- self$results$plot
+
             image$setState(plotData)
 
 
-            self$results$text1$setContent(plotData)
+            # self$results$text1$setContent(plotData)
+
+
+            # mydepType <- data.frame(vclass = class(mydep),
+            #                         vtypeof = typeof(mydep),
+            #                         vordered = is.ordered(mydep),
+            #                         vfactor = is.factor(mydep),
+            #                         vnumeric = is.numeric(mydep),
+            #                         vdouble = is.double(mydep),
+            #                         vcharacter = is.character(mydep),
+            #                         vdate = lubridate::is.Date(mydep),
+            #                         vdate2 = is.na.POSIXlt(mydep)
+            #                         )
+            # mygroupType <- class(mygroup)
+            # variableTypes <- list(mydepType, mygroupType)
+            # self$results$text1$setContent(variableTypes)
 
 
 

diff --git a/R/tree.b.R b/R/tree.b.R
@@ -0,0 +1,15 @@
+
+# This file is a generated template, your changes will not be overwritten
+
+treeClass <- if (requireNamespace('jmvcore')) R6::R6Class(
+    "treeClass",
+    inherit = treeBase,
+    private = list(
+        .run = function() {
+
+            # `self$data` contains the data
+            # `self$options` contains the options
+            # `self$results` contains the results object (to populate)
+
+        })
+)