Skip to content

Jamovi files added #1

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
arcaldwell49 wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Jamovi files added #1

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
f1d5a56
Addition of jamovi function
arcaldwell49 Apr 20, 2018
44ef7a1
Changed for SWC from SESOI notation
arcaldwell49 Apr 20, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
292 changes: 292 additions & 0 deletions R/datambicorr.b.R
View file
Open in desktop

Large diffs are not rendered by default.

396 changes: 396 additions & 0 deletions R/datambicorr.h.R
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,396 @@

# This file is automatically generated, you probably don't want to edit this

dataMBIcorrOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
"dataMBIcorrOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
pairs = NULL,
pearson = TRUE,
spear = FALSE,
kendall = FALSE,
SWC = 0.1,
confint = 90,
desc = FALSE, ...) {

super$initialize(
package='mbir',
name='dataMBIcorr',
requiresData=TRUE,
...)

private$..pairs <- jmvcore::OptionPairs$new(
"pairs",
pairs,
suggested=list(
"continuous"),
permitted=list(
"continuous",
"nominal",
"ordinal"))
private$..pearson <- jmvcore::OptionBool$new(
"pearson",
pearson,
default=TRUE)
private$..spear <- jmvcore::OptionBool$new(
"spear",
spear,
default=FALSE)
private$..kendall <- jmvcore::OptionBool$new(
"kendall",
kendall,
default=FALSE)
private$..SWC <- jmvcore::OptionNumber$new(
"SWC",
SWC,
min=0.01,
max=0.9,
default=0.1)
private$..confint <- jmvcore::OptionNumber$new(
"confint",
confint,
min=50,
max=99.9,
default=90)
private$..desc <- jmvcore::OptionBool$new(
"desc",
desc,
default=FALSE)

self$.addOption(private$..pairs)
self$.addOption(private$..pearson)
self$.addOption(private$..spear)
self$.addOption(private$..kendall)
self$.addOption(private$..SWC)
self$.addOption(private$..confint)
self$.addOption(private$..desc)
}),
active = list(
pairs = function() private$..pairs$value,
pearson = function() private$..pearson$value,
spear = function() private$..spear$value,
kendall = function() private$..kendall$value,
SWC = function() private$..SWC$value,
confint = function() private$..confint$value,
desc = function() private$..desc$value),
private = list(
..pairs = NA,
..pearson = NA,
..spear = NA,
..kendall = NA,
..SWC = NA,
..confint = NA,
..desc = NA)
)

dataMBIcorrResults <- if (requireNamespace('jmvcore')) R6::R6Class(
inherit = jmvcore::Group,
active = list(
text = function() private$.items[["text"]],
mbi = function() private$.items[["mbi"]],
desc = function() private$.items[["desc"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="MBI for Correlation")
self$add(jmvcore::Preformatted$new(
options=options,
name="text",
title="MBI for Correlation"))
self$add(jmvcore::Table$new(
options=options,
name="mbi",
title="Magnitude Based Inference: Correlation",
rows="(pairs)",
clearWith=list(
"confint",
"SWC"),
columns=list(
list(
`name`="i1",
`title`="",
`type`="text",
`content`="($key)"),
list(
`name`="i2",
`title`="",
`type`="text",
`content`="($key)"),
list(
`name`="b[0]",
`title`="",
`type`="text",
`content`="Pearson's r",
`visible`="(pearson)"),
list(
`name`="correl[0]",
`title`="",
`type`="Number",
`visible`="(pearson)"),
list(
`name`="p[0]",
`title`="p",
`type`="Number",
`format`="zto,pvalue",
`visible`="(pearson)"),
list(
`name`="Negative[0]",
`type`="Number",
`title`="Negative (%)",
`visible`="(pearson)"),
list(
`name`="Trivial[0]",
`type`="Number",
`title`="Trivial (%)",
`visible`="(pearson)"),
list(
`name`="Positive[0]",
`type`="Number",
`title`="Positive (%)",
`visible`="(pearson)"),
list(
`name`="Inference[0]",
`title`="Inference",
`type`="text",
`visible`="(pearson)"),
list(
`name`="b[1]",
`title`="",
`type`="text",
`content`="Spearman's rho",
`visible`="(spear)"),
list(
`name`="correl[1]",
`title`="",
`type`="Number",
`visible`="(spear)"),
list(
`name`="p[1]",
`title`="p",
`type`="Number",
`format`="zto,pvalue",
`visible`="(spear)"),
list(
`name`="Negative[1]",
`type`="Number",
`title`="Negative (%)",
`visible`="(spear)"),
list(
`name`="Trivial[1]",
`type`="Number",
`title`="Trivial (%)",
`visible`="(spear)"),
list(
`name`="Positive[1]",
`type`="Number",
`title`="Positive (%)",
`visible`="(spear)"),
list(
`name`="Inference[1]",
`title`="Inference",
`type`="text",
`visible`="(spear)"),
list(
`name`="b[2]",
`title`="",
`type`="text",
`content`="Kendall's tau-b",
`visible`="(kendall)"),
list(
`name`="correl[2]",
`title`="",
`type`="Number",
`visible`="(kendall)"),
list(
`name`="p[2]",
`title`="p",
`type`="Number",
`format`="zto,pvalue",
`visible`="(kendall)"),
list(
`name`="Negative[2]",
`type`="Number",
`title`="Negative (%)",
`visible`="(kendall)"),
list(
`name`="Trivial[2]",
`type`="Number",
`title`="Trivial (%)",
`visible`="(kendall)"),
list(
`name`="Positive[2]",
`type`="Number",
`title`="Positive (%)",
`visible`="(kendall)"),
list(
`name`="Inference[2]",
`title`="Inference",
`type`="text",
`visible`="(kendall)"))))
self$add(jmvcore::Table$new(
options=options,
name="desc",
title="Descriptives",
visible="(desc)",
rows="(pairs)",
clearWith=list(
"group"),
columns=list(
list(
`name`="name[1]",
`title`="",
`type`="text"),
list(
`name`="n[1]",
`title`="N",
`type`="integer"),
list(
`name`="m[1]",
`title`="Mean",
`type`="number"),
list(
`name`="med[1]",
`title`="Median",
`type`="number"),
list(
`name`="sd[1]",
`title`="SD",
`type`="number"),
list(
`name`="se[1]",
`title`="SE",
`type`="number"),
list(
`name`="name[2]",
`title`="",
`type`="text"),
list(
`name`="n[2]",
`title`="N",
`type`="integer"),
list(
`name`="m[2]",
`title`="Mean",
`type`="number"),
list(
`name`="med[2]",
`title`="Median",
`type`="number"),
list(
`name`="sd[2]",
`title`="SD",
`type`="number"),
list(
`name`="se[2]",
`title`="SE",
`type`="number"))))}))

dataMBIcorrBase <- if (requireNamespace('jmvcore')) R6::R6Class(
"dataMBIcorrBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = 'mbir',
name = 'dataMBIcorr',
version = c(1,0,0),
options = options,
results = dataMBIcorrResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE)
}))

#' MBI for Correlation
#'
#'
#'
#' @examples
#' \dontrun{
#'
#' data('bugs', package = 'jmv')
#'
#' mbir::dataMBIcorr(
#' data = data,
#' pairs = list(
#' list(
#' i1="LDLF",
#' i2="LDHF")))
#'
#' #
#' # Magnitude Based Inference: Correlation
#' # -------------------------------------------------------------------------------------------------------------------------------------------------
#' # p Negative (\%) Trivial (\%) Positive (\%) Inference
#' # -------------------------------------------------------------------------------------------------------------------------------------------------
#' # LDLF LDHF Pearson's r 0.577 < .001 0.00 0.00 100 Almost Certainly Large Positive Correlation.
#' # -------------------------------------------------------------------------------------------------------------------------------------------------
#' #
#' #
#'}
#' @param data the data as a data frame
#' @param pairs a list of vectors of strings naming variables to pair from
#' \code{data}
#' @param pearson \code{TRUE} (default) or \code{FALSE}, provide Pearson's R
#' @param spear \code{TRUE} or \code{FALSE} (default), provide Spearman's rho
#' @param kendall \code{TRUE} or \code{FALSE} (default), provide Kendall's
#' tau-b
#' @param SWC a number, default (r=0.1) that defines the bounds for
#' magnitude-based inference
#' @param confint 90\% (default), confidence interval for magnitude-based
#' inference
#' @param desc \code{TRUE} or \code{FALSE} (default), provide descriptive
#' statistics
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$text} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$mbi} \tab \tab \tab \tab \tab a table \cr
#' \code{results$desc} \tab \tab \tab \tab \tab a table \cr
#' }
#'
#' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:
#'
#' \code{results$mbi$asDF}
#'
#' \code{as.data.frame(results$mbi)}
#'
#' @export
dataMBIcorr <- function(
data,
pairs,
pearson = TRUE,
spear = FALSE,
kendall = FALSE,
SWC = 0.1,
confint = 90,
desc = FALSE) {

if ( ! requireNamespace('jmvcore'))
stop('dataMBIcorr requires jmvcore to be installed (restart may be required)')

options <- dataMBIcorrOptions$new(
pairs = pairs,
pearson = pearson,
spear = spear,
kendall = kendall,
SWC = SWC,
confint = confint,
desc = desc)

results <- dataMBIcorrResults$new(
options = options)

analysis <- dataMBIcorrClass$new(
options = options,
data = data)

analysis$run()

analysis$results
}
Loading