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Collection of functions for plotting relations, generating tables, and more.

Description

This is a collection of functions that I've found useful in my research.The package is inspired by Frank Harrell'sHmisc package. The main focusis on tables, plots, andknitr-integration.

Awesome tables

ThegetDescriptionStatsBy is a straight forward function thataims at helping you to generate descriptive table stratified by differentvariables. In other words, the function returns everything you need for generatingaTable 1 ready for publication. This function is accompanied by thedescribeMean,describeMedian,describeProp,anddescribeFactors functions.

ThemergeDesc allows you to merge a set of outputsgetDescriptionStatsByinto ahtmlTable with the rgroup arguments automaticallygenerated, seevignette("descriptives", package = "Gmisc") for adetailed workflow description.

Some fancy plots

The transition plot function,transitionPlot, is fordescriptive purposes. It tries to illustrate the size of changebetween one state and the next, i.e. a transition. This isbasically a graph of based upontable(var1, var2).

TheSingular value decompositionis a common method for reducing the number of variables. Unfortunatelythis compression can reduce the interpretability of the model. ThegetSvdMostInfluentialfunction tries to remedy that by identifying the most influentialelements from theV-matrix.

Other stuff

TheinsertRowAndKeepAttr simply adds a row while rememberingall the attributes previously set by using thecopyAllNewAttributes.ThemergeLists tries to merge lists that do not have identicalelements.

Author(s)

Maintainer: Max Gordonmax@gforge.se

See Also

Useful links:

• https://gforge.se

• Report bugs athttps://github.com/gforge/Gmisc/issues

Deprecated function(s) inGmisc

Description

Theforestplot2 has moved toforestplot package and changed name toforestplot

Usage

forestplot2(...)

Arguments

A reference class for generating transition plots

Description

This class simplifies the creating of transition plots. It alsoallows for advanced multi-column transitions.

Details

Transition plots are a type ofSankey diagrams. These are a specific typeof flow diagram, in which the width of the arrows is shown proportionallyto the flow quantity. SeeWikipediafor details.

Fields

id

Optional id. The render uses named viewports that require a unique id if multiple transition plotsare combined. In order to avoid having overlapping graphs we need to generate a unique id for each viewportand thus this variable exists. If left empty it will create a counter that is stored in theoptions("Gmisc.transitionClassCounter") and each viewport will have the name preceded withtc_[0-9]+. Set thisif you intend to useseekViewport.

transitions

This is a >= 3 dimensional array with the transitions. Should not be directly accessed.

box_width

The box width

box_txt

The texts of each box

box_label

Box labels

box_label_pos

The label's positions, either "top"/"bottom"

box_label_cex

The size of the box labels

box_cex

The font-size multiplier for the text within the boxes

arrow_type

The type of arrow to use, defaults to "gradient", but can also be "simple".The corresponding functions arebezierArrowGradient, andbezierArrowSmpl.Note ThebezierGrob has been deprecatedas it is no longer faster than the bezier arrows and there is a difference in design.

arrow_clr

The arrow color

arrow_rez

The resolution of the arrow

vertical_space

The space between the boxes

fill_clr

The box fill color

clr_bar

Shows a color bar if there are proportions. Can be"none","top","bottom"

clr_bar_clrs

Extracts the colors for the color bar from thefill_clr if none is provided

clr_bar_cex

The size of the ticks in the color bar

clr_bar_subspace

If little or no difference exists at the low/high proportions ofthe spectrum then it can be of interest to focus the color change to the center leaving the tails constant

clr_bar_labels

The labels of the color bars. Defaults to the dim names for the proportions.

txt_clr

The text color within the boxes

txt_gpar

Similar to 'txt_clr' but for more advanced styling with fontfamily (see [grid::gpar()]). *Note* thatcol & cex are overridden.

title

The plot title if any

title_cex

The font-size multiplier for the title

skip_shadows

Skip the shadow effect on the boxes

mar

The margins for the plot.

min_lwd

The minimum line width that is still shown. The pixels will most likelynot have the same fine resolution as the data and you therefore may want to hidelines that are smaller than a certain amount.

max_lwd

The maximum line width to show

lwd_prop_type

The line can either be proportional to the"set" of transitions(group of two box columns), to"all" transitions, or to each"box". It defaultsto"all".

data

Internal storage variable. Should not be accessed directly.

Methods

addBoxStyle(fill, txt, gpar)

Adds colors or extends existing one so that they match the transition matrix.The fill corresponds to the fill_clr and txt corresponds to the txt_clr. Ifthe colors are missing and the transitions consist of only two columns the defaultcolors will be used. If the matrix is being extended and these values are missing thevalues from the previous last column will be used for the default columns.

addTransitions(mtrx, label, txt, fill_clr, txt_clr, txt_gpar)

Add a transition matrix. The input has to be a numerical matrix between 2 and 3 dimensions.If you don't provide the txt field the box' text field will be deduced from the transition matrix'dimnames. The fill_clr and txt_clr are passed on to theaddBoxStyle function.

arrowWidths(set_no, add_width)

Retrieves the details regarding arrow sizes for each arrow within the transitiongroup

boxPositions(col)

The box positions as a list with scalars for the positions:

1. x The center x-position

2. y The center y-position

3. right The right edge

4. left The left edge

5. top The top edge

6. bottom The bottom edge

7. height The box height

8. width The box width

9. unit The unit used for the values (npc)

boxSizes(col)

Gets the size of the boxes. Thecol argument shouldbe either an integer or 'last'

getDim()

Gets the current dimensions of the transitions

getTransitionSet(no, reduce_dim = FALSE)

Gets a specific set of transitions. If thereduce_dim is setto TRUE it will only return a 2-dimensional matrix even if the originalhas a 3rd proportions dimension

getYProps(col)

Gets the proportions after removing thevertical_spacebetween the boxes

initialize(transitions, label, txt, fill_clr, txt_clr, txt_gpar, id, ...)

Set up a Transition object. Thetransitions should be a 2D or 3D matrixas defined in the$addTransitions section and not as later internally stored.

noCols()

Gets the number of columns, i.e. the number of transitions

noRows(no)

Gets the number of boxes in each row.If multiple rows the number of rows may differbetwen each transition matrix we therefore needto specify what transitions that we refer to.If no value is specified it returns all of them.

render(new_page = TRUE)

Call this to render the full graph. Thenew_page argumentis for creating a new plot, set this toFALSEif you want to combine this plot with another or if you haveadditional viewports that you intend to use.

trnstnSizes(set_no)

Gets the transitions per box as a 2D matrix. For the proportionsit also adds an attributeattr('props', prop_mtrx) thatis a 2D matrix with the corresponding proportions.

Examples

# Transitionsset.seed(1)n <- 10my_data <-  data.frame(    Var_a = sample(c(      "Test 1",      "Test 2",      "Test 3"    ),    size = n,    replace = TRUE,    prob = 3:1    ),    Var_b = sample(c(      "Test 1",      "Test 2",      "Test 3"    ),    size = n,    replace = TRUE,    prob = 1:3    )  )mtrx <- with(  my_data,  table(Var_a, Var_b))# Initialize the transition plottransitions <- getRefClass("Transition")$new(mtrx,                                             label = c("Before", "After"))# Render the plottransitions$render()

Align boxes

Description

Aligns a set ofboxGrob/boxPropGrob according to the first positional argument.

Usage

alignVertical(reference, ..., .position = c("center", "top", "bottom"))alignHorizontal(  reference,  ...,  .position = c("center", "left", "right"),  .sub_position = c("none", "left", "right"))

Arguments

Value

list with the boxes that are to be aligned

See Also

Other flowchart components:boxGrob(),boxPropGrob(),connectGrob(),coords(),distance(),moveBox(),spread

Examples

library(grid)grid.newpage()box <- boxGrob("A cool\nreference\nbox",               x = .5, y = .8,               box_gp = gpar(fill = "#ADB5C7"))another_box <- boxGrob("A horizontal box", x = .1, y =  .5)yet_another_box <- boxGrob("Another horizontal box", x = .8, y = .3)alignedBoxes <- alignHorizontal(box,                                another_box,                                yet_another_box,                                .position = "right")boxfor (b in alignedBoxes) {  print(b)}vert_box <- boxGrob("Vert",                     x = .8, y = .3,                    box_gp = gpar(fill = "darkgreen"),                    txt_gp = gpar(col = "white"))another_vert_box <- boxGrob("Another vertical",                             x = .1, y =  .5,                            box_gp = gpar(fill = "darkgreen"),                            txt_gp = gpar(col = "white"))alignedBoxes <- alignVertical(box,                              vert_box,                              another_vert_box,                              .position = "bottom")for (b in alignedBoxes) {  print(b)}

Checks if unit or number 0-1

Description

Checks if unit or number 0-1

Assert that its a string or number

Assert valid color

Usage

assert_unit(var, allow_missing = TRUE)assert_label(var, allow_missing = TRUE)assert_just(var, allow_missing = TRUE)

Arguments

Value

void

void

void

A bezier arrow with gradient

Description

This is an experimental addition to the originalbezierArrowSmplwith the addition of a gradient in the center of the arrow that fades.

Usage

bezierArrowGradient(  x = c(0.2, 0.7, 0.3, 0.9),  y = c(0.2, 0.2, 0.9, 0.9),  width = 0.05,  clr = "#000000",  default.units = "npc",  align_2_axis = TRUE,  grdt_type = c("triangle", "rectangle"),  grdt_prop = 0.8,  grdt_decrease_prop = 0.5,  grdt_clr_prop = 0.7,  grdt_line_width,  grdt_clr = "#2F4F2F",  vp = NULL,  gp = gpar(),  rm_intersect = 3L,  ...)

Arguments

Value

A grob ofgList-type

Note

The triangle section of the arrow is not currently included in the gradient.

Examples

library(grid)grid.newpage()arrowGrob <- bezierArrowGradient(  x = c(.1, .3, .6, .9),  y = c(0.2, 0.2, 0.9, 0.9))grid.draw(arrowGrob)

A simple bezier arrow

Description

This is an alternative to the grid packagesbezierGrobwith the advantage that it allows you to draw an arrow with a specificunit width. Note, it has only a end-arrow at this point.

Usage

bezierArrowSmpl(  x = c(0.2, 0.7, 0.3, 0.9),  y = c(0.2, 0.2, 0.9, 0.9),  width = 0.05,  clr = "#000000",  default.units = "npc",  arrow = list(),  rez = 200,  align_2_axis = TRUE,  name = NULL,  rm_intersect = 3L,  gp = gpar(),  vp = NULL)

Arguments

Value

grid::grob A grob of the class polygonGrob with attributes thatcorrespond to the bezier points.

Examples

library(grid)grid.newpage()arrowGrob <- bezierArrowSmpl(  x = c(.1, .3, .6, .9),  y = c(0.2, 0.2, 0.9, 0.9))grid.draw(arrowGrob)

Create a box with text

Description

Creates agrob box with text inside it.

Usage

boxGrob(  label,  y = unit(0.5, "npc"),  x = unit(0.5, "npc"),  width,  height,  just = "center",  bjust = "center",  txt_gp = getOption("boxGrobTxt", default = gpar(color = "black", cex = 1)),  box_gp = getOption("boxGrob", default = gpar(fill = "white")),  box_fn = roundrectGrob,  name = NULL)## S3 method for class 'box'print(x, ...)## S3 method for class 'box'plot(x, ...)## S3 method for class 'box'widthDetails(x)## S3 method for class 'box'heightDetails(x)

Arguments

Value

A grob

Theplot/print

To output thegrob objects to the plot either callploton the object orprint it. Note that R automatically prints any object that is outputtedto the console. The function calls in turn thegrid.draw function on the object.

S3 from thegrid package

Width and height functions address thecoords attribute for the corresponding information.ThewidthDetails andheightDetailsthat provide information on an object.

See Also

Other flowchart components:align,boxPropGrob(),connectGrob(),coords(),distance(),moveBox(),spread

Examples

library(grid)grid.newpage()boxGrob("My box")

Create a box with a color split

Description

Creates a grob box with text inside it and a color split in thehorizontal axes that allow indicating different proportions. Thebox can also have a title that spanse the two color areas andthat has its own background.

Usage

boxPropGrob(  label,  label_left,  label_right,  prop,  y = unit(0.5, "npc"),  x = unit(0.5, "npc"),  width,  height,  just = "center",  bjust = "center",  txt_gp = getOption("boxPropGrobTxt", default = gpar(color = "black")),  txt_left_gp = getOption("boxPropGrobLeftTxt", default = gpar(col = "black")),  txt_right_gp = getOption("boxPropGrobRightTxt", default = gpar(col = "black")),  box_left_gp = getOption("boxPropGrobLeft", default = gpar(fill = "#E6E8EF")),  box_right_gp = getOption("boxPropGrobRight", default = gpar(fill = "#FFFDF6")),  box_highlight_gp = getOption("boxPropGrobHighlight", default = gpar(fill = "#ffffff55",    col = NA)),  name = NULL)

Arguments

Value

A box grob

See Also

Other flowchart components:align,boxGrob(),connectGrob(),coords(),distance(),moveBox(),spread

Examples

library(grid)grid.newpage()boxPropGrob("Main label", "Left text", "Right text", prop = .3)

Gets offsetted lines

Description

The function calculates new points according to the offsetthat lie to the left/right of the provided line.

Usage

calculateLinesAndArrow(  x,  y,  offset,  end_x = -1,  end_y = -1,  arrow_offset = -1,  rm_intersect = 3L)

Arguments

Value

list(list(x = ..., y = ...)) Returns a list with the right/leftlines that in turn lists withx andy elements

Connect boxes with an arrow

Description

The function creates a grob that links two boxes together. It looks forwhich side it should attach the arrow, e.g. if the start is on top ofthe bottom it should attach to the bottom edge of ther start box and thento the top at the end.

Usage

connectGrob(  start,  end,  type = c("vertical", "horizontal", "L", "-", "Z", "N"),  subelmnt = c("right", "left"),  lty_gp = getOption("connectGrob", default = gpar(fill = "black")),  arrow_obj = getOption("connectGrobArrow", default = arrow(ends = "last", type =    "closed")))## S3 method for class 'connect_boxes'print(x, ...)## S3 method for class 'connect_boxes'plot(x, ...)

Arguments

Details

The exact positions of the line is stored at theattr(..., "line").If you want to draw your own custom line all you need to do is check whichattr(my_line, "line")$x andattr(my_line, "line")$y you wantto attach to and then create your own customlinesGrob.

Value

grob with an arrow

See Also

Other flowchart components:align,boxGrob(),boxPropGrob(),coords(),distance(),moveBox(),spread

Examples

library(grid)grid.newpage()# Initiate the boxes that we want to connectstart <- boxGrob("Top", x = .5, y = .8)end <- boxGrob("Bottom", x = .5, y = .2)side <- boxPropGrob("Side", "Left", "Right", prop = .3, x = .2, y = .8)sub_side_left <- boxGrob("Left", x = attr(side, "coords")$left_x, y = .5)sub_side_right <- boxGrob("Right", x = attr(side, "coords")$right_x, y = .5)exclude <- boxGrob("Exclude:\n - Too sick\n - Prev. surgery", x = .8, y = .5, just = "left")# Connect the boxes and print/plot themconnectGrob(start, end, "vertical")connectGrob(start, side, "horizontal")connectGrob(side, sub_side_left, "v", "l")connectGrob(side, sub_side_right, "v", "r")connectGrob(start, exclude, "L")# Print the grobsstartendsideexcludesub_side_leftsub_side_right

A function for converting a show_missing variable.

Description

The variable is supposed to be directly compatible withtable(..., useNA = show_missing). It throws an errorif not compatible. It is mostly useful for custom describe functions.

Usage

convertShowMissing(show_missing)

Arguments

Details

Deprecated: This function will be deprecatedas all functions now use the useNA style in order to complywith standard R naming.

Value

string

Get the box coordinates

Description

Retrieves the boxes"coords" attribute.

Usage

coords(box)

Arguments

Value

A list with the coordinates

See Also

Other flowchart components:align,boxGrob(),boxPropGrob(),connectGrob(),distance(),moveBox(),spread

Examples

box <- boxGrob("A test box")coords(box)

A simple thing to keep the attributes

Description

Skips the attributes that the to object already hasto avoid overwriting dim and other important attributes

Usage

copyAllNewAttributes(from, to, attr2skip = c(), attr2force = c())

Arguments

Value

object Theto argument object

Examples

a <- "test"attr(a, 'wow') <- 1000b <- ab <- copyAllNewAttributes(a, b)print(attr(b, 'wow'))

Get statistics for missing data

Description

This function calculates the amount of missing per row fordescribeMean,describeMedian and custom description functions.It will return invisibly when no missing values are present.

Usage

descGetMissing(  x,  html = TRUE,  number_first = TRUE,  percentage_sign = TRUE,  language = "en",  useNA.digits = 1,  ...)

Arguments

Value

vector A vector with the missing estimate

Describes factor variables

Description

A function that returns a description of proportions in afactor that contains the number of times a level occurs and the percentage

Usage

describeFactors(  x,  html = TRUE,  digits = 1,  digits.nonzero = NA,  number_first = TRUE,  useNA = c("ifany", "no", "always"),  useNA.digits = digits,  horizontal_proportions,  percentage_sign = TRUE,  language = "en",  ...)

Arguments

Value

A string formatted for printing either latex by HTML

See Also

getDescriptionStatsBy

Other descriptive functions:describeMean(),describeMedian(),describeProp(),getDescriptionStatsBy(),getPvalWilcox()

Examples

set.seed(1)describeFactors(sample(50, x = c("A", "B", "C"), replace = TRUE))n <- 500my_var <- factor(sample(size = n, x = c("A", "B", "C", NA), replace = TRUE))my_exp <- rbinom(n = n, size = 1, prob = 0.2)total <- table(my_var, useNA = "ifany")by(my_var,  INDICES = my_exp,  FUN = describeFactors,  useNA = "ifany",  horizontal_proportions = total)

Describe the mean

Description

A function that returns a description of a continuous variable usingthe mean together with the standard deviation. The standard deviationis used as it is "industry standard" to use mean with standard deviationand not because it's the only option.

Usage

describeMean(  x,  html = TRUE,  digits = 1,  digits.nonzero = NA,  number_first = TRUE,  useNA = c("ifany", "no", "always"),  useNA.digits = digits,  percentage_sign = TRUE,  plusmin_str,  language = "en",  ...)

Arguments

Value

string Returns a string formatted for either LaTeX or HTML

See Also

getDescriptionStatsBy

Other descriptive functions:describeFactors(),describeMedian(),describeProp(),getDescriptionStatsBy(),getPvalWilcox()

Examples

describeMean(1:10)describeMean(c(1:10, NA), useNA = "always")describeMean(c(1:10, NA), useNA = "no")

A function that returns a description median that containsthe interquartile range or the full range

Description

A function that returns a description median that containsthe interquartile range or the full range

Usage

describeMedian(  x,  iqr = TRUE,  html = TRUE,  digits = 1,  digits.nonzero = NA,  number_first = TRUE,  useNA = c("ifany", "no", "always"),  useNA.digits = digits,  percentage_sign = TRUE,  language = "en",  ...)

Arguments

Value

string A string formatted for either LaTeX or HTML

See Also

getDescriptionStatsBy

Other descriptive functions:describeFactors(),describeMean(),describeProp(),getDescriptionStatsBy(),getPvalWilcox()

Examples

describeMedian(1:10)describeMedian(c(1:10, NA), useNA = "ifany")

A function that returns a description proportion that containsthe number and the percentage

Description

A function that returns a description proportion that containsthe number and the percentage

Usage

describeProp(  x,  html = TRUE,  digits = 1,  digits.nonzero = NA,  number_first = TRUE,  useNA = c("ifany", "no", "always"),  useNA.digits = digits,  default_ref = NULL,  percentage_sign = TRUE,  language = "en",  ...)

Arguments

Value

string A string formatted for either LaTeX or HTML

See Also

Other descriptive functions:describeFactors(),describeMean(),describeMedian(),getDescriptionStatsBy(),getPvalWilcox()

Examples

describeProp(factor(sample(50, x = c("A", "B", NA), replace = TRUE)))

Get the distance between grid objects

Description

Retrieves the distance between two boxes as absolute"mm" units. The function alsoacceptscoords objects as well as aunit or a numeric input.

Usage

distance(  box1,  box2,  type = c("vertical", "horizontal", "euclidean"),  half = FALSE,  center = FALSE)## S3 method for class 'Gmisc_unit'print(x, ...)

Arguments

Value

Aunit in"mm" with an absolute value. The attributepositive indicates the direction of the value, i.e. if it isTRUE thedistance was calculated from the first to the second, otherwise it isFALSE.Foreuclidean distance thepositive attribute isNA. There is also thefrom andto attributes that has the coordinates that were used for thecalculations, foreuclidean distance this isNA.

See Also

Other flowchart components:align,boxGrob(),boxPropGrob(),connectGrob(),coords(),moveBox(),spread

Examples

box1 <- boxGrob("A test box", y = .8)box2 <- boxGrob("Another test box", y = .2)distance(box1, box2, "v")

Formatter wrapper forhtml_document, facilitates easier porting to docx

Description

This function adds the option of having adaptations needed for seemless integration withMS Word for importing html-documents in the .docx-format. The advantage of html documents isthe ability to create advanced formatting frequently needed in medical publicationsand that is available in thehtmlTable function. You can viewthe seriesfor more details regarding how to achievefast-track-publishing (ftp) together with knitr.

Usage

docx_document(  ...,  self_contained = FALSE,  mathjax = NULL,  theme = NULL,  highlight = NULL,  css = "rmarkdown/docx.css",  h1_style = "margin: 24pt 0pt 0pt 0pt;",  other_h_style = "margin: 10pt 0pt 0pt 0pt;",  remove_scripts = TRUE,  force_captions = FALSE,  css_max_width)

Arguments

Details

If you want to get equations into Word the currently best way is touse theword_document format.

Value

R Markdown output format to pass torender

Author(s)

Max Gordon

Examples

# Possible yaml configuration at the top of the Rmd doc## Not run: ---title: "Test"author: "Max Gordon"output:  Gmisc::docx_document---## End(Not run)

An alternative to the internaldo.call

Description

Thedo.call can be somewhat slow, especially when workingwith large objects. This function is based upon the suggestions from HadleyWickham on the R mailing list.Also thanks toTommy at StackOverflow forsuggestinghow to handle double and triple colon operators,::, furtherenhancing the function.

Usage

fastDoCall(what, args, quote = FALSE, envir = parent.frame())

Arguments

Note

While the function attempts to do most of whatdo.callcan it has limitations. It can currently not parse the example code from theoriginal function:do.call(paste, list(as.name("A"), as.name("B")), quote = TRUE)and the functionality ofquote has not been thoroughly tested.

Examples

fastDoCall("complex", list(imaginary = 1:3))## if we already have a list (e.g. a data frame)## we need c() to add further argumentstmp <- expand.grid(letters[1:2], 1:3, c("+", "-"))fastDoCall("paste", c(tmp, sep = ""))## examples of where objects will be found.A <- 2f <- function(x) print(x^2)env <- new.env()assign("A", 10, envir = env)assign("f", f, envir = env)f <- function(x) print(x)f(A)                                      # 2fastDoCall("f", list(A))                     # 2fastDoCall("f", list(A), envir = env)        # 4fastDoCall(f, list(A), envir = env)          # 2fastDoCall("f", list(quote(A)), envir = env) # 100fastDoCall(f, list(quote(A)), envir = env)   # 10fastDoCall("f", list(as.name("A")), envir = env) # 100eval(call("f", A))                      # 2eval(call("f", quote(A)))               # 2eval(call("f", A), envir = env)         # 4eval(call("f", quote(A)), envir = env)  # 100

Adds a figure caption number

Description

The function relies onoptions("fig_caption_no")in order to keep track of the last number. Ifyou want to force the caption function to skipcaptions while still using it in the knitr fig.cap optionthen simply setoptions(fig_caption_no = FALSE)

Usage

figCapNo(  str,  roman = getOption("fig_caption_no_roman", default = FALSE),  sprintf_str = getOption("fig_caption_no_sprintf", default = "Fig. %s: %s"))

Arguments

See Also

Other figure caption functions:figCapNoLast(),figCapNoNext()

Examples

## Not run: ```{r, fig.cap = pigCapNo("My nice plot")}plot(1:10 + rnorm(10), 1:10)```## End(Not run)org_opts <- options(fig_caption_no = 2,                    fig_caption_no_sprintf = "Figure %s: %s")figCapNo("A plot with caption number = 3")org_opts <- options(fig_caption_no = TRUE)figCapNo("A plot with caption number = 1")# Use default settingoptions(fig_caption_no_sprintf = NULL)figCapNo("A plot with caption number = 2")# Return the original settingsoptions(org_opts)

Gets the last figure caption number

Description

The function relies onoptions("fig_caption_no")in order to keep track of the last number.

Usage

figCapNoLast(roman = getOption("fig_caption_no_roman", FALSE))

Arguments

See Also

Other figure caption functions:figCapNo(),figCapNoNext()

Examples

org_opts <- options(fig_caption_no = 1)figCapNoLast()options(org_opts)

Gets the next figure caption number

Description

The function relies onoptions("fig_caption_no")in order to keep track of the last number.

Usage

figCapNoNext(roman = getOption("fig_caption_no_roman", default = FALSE))

Arguments

See Also

Other figure caption functions:figCapNo(),figCapNoLast()

Examples

org_opts <- options(fig_caption_no = 1)figCapNoNext()options(org_opts)

Translates "npc" widths into absolute units

Description

The "npc"unit is not absolute, i.e.it depends on the relation between height and width withinthe current viewport. We therefore need to change these valuesto the value most likely intended. This is believed to be themain direction of the arrow as specified by the first and lastbezier control pointsx andy.

Usage

getAbsoluteWidth(w, default.units, x = x, y = y)

Arguments

Value

The width transformed into aunit of "mm"

Gets the bezier points adjusted for an arrow

Description

Gets the bezier points adjusted for an arrow

Usage

getBezierAdj4Arrw(x, y, arrow_length, length_out = 100)

Arguments

Value

list

Creating of description statistics

Description

A function that returns a description statistic that can be usedfor creating a publication "table 1" when you want it by groups.The function identifies if the variable is a continuous, binaryor a factored variable. The format is inspired by NEJM, Lancet &BMJ.

Usage

getDescriptionStatsBy(  x,  ...,  by,  digits = 1,  digits.nonzero = NA,  html = TRUE,  numbers_first = TRUE,  statistics = FALSE,  statistics.sig_lim = 10^-4,  statistics.two_dec_lim = 10^-2,  statistics.suppress_warnings = TRUE,  useNA = c("ifany", "no", "always"),  useNA.digits = digits,  continuous_fn = describeMean,  prop_fn = describeProp,  factor_fn = describeFactors,  show_all_values = FALSE,  hrzl_prop = FALSE,  add_total_col,  total_col_show_perc = TRUE,  use_units = FALSE,  units_column_name = "Units",  default_ref = NULL,  NEJMstyle = FALSE,  percentage_sign = TRUE,  header_count = NULL,  missing_value = "-",  names_of_missing = NULL)## S3 method for class 'Gmisc_getDescriptionStatsBy'htmlTable(x, ...)## S3 method for class 'Gmisc_getDescriptionStatsBy'print(x, ...)## S3 method for class 'Gmisc_getDescriptionStatsBy'knit_print(x, ...)## S3 method for class 'Gmisc_getDescriptionStatsBy'length(x)

Arguments

Value

Returnsmatrix if a single value was provided, otherwise alistof matrices with the class"Gmisc_getDescriptionStatsBy".

Customizing statistics

You can specify what function that you want for statistic by providing a functionthat takes two argumentsx andby and returns a p-value. There area few functions already prepared for this seegetPvalAnova,getPvalChiSqgetPvalFishergetPvalKruskalgetPvalWilcox.The default functions used aregetPvalFisher andgetPvalWilcox (unless the byargument has more than three unique levels where it defaults togetPvalAnova).

If you want the function to select functions depending on the type of inputyou can provide a list with the names'continuous','proportion','factor' andthe function will choose accordingly. If you fail to define a certain categoryit will default to the above.

You can also use a custom function that returns a string with the attribute'colname'set that will be appended to the results instead of the p-value column.

See Also

Other descriptive functions:describeFactors(),describeMean(),describeMedian(),describeProp(),getPvalWilcox()

Examples

library(magrittr)library(dplyr)library(htmlTable)data(mtcars)mtcars %<>%  mutate(am = factor(am, levels = 0:1, labels = c("Automatic", "Manual")),         vs = factor(vs, levels = 0:1, labels = c("V-shaped", "straight")),         drat_prop = drat > median(drat),         drat_prop = factor(drat_prop,                            levels = c(FALSE, TRUE),                            labels = c("High ratio", "Low ratio")),         carb_prop = carb > 2,         carb_prop = factor(carb_prop,                            levels = c(FALSE, TRUE),                            labels = c("&le; 2", "&gt; 2")),         across(c(gear, carb, cyl), factor))# A simple bare-bone examplemtcars %>%  getDescriptionStatsBy(`Miles per gallon` = mpg,                        Weight = wt,                        `Carborators &le; 2` = carb_prop,                        by = am) %>%  htmlTable(caption  = "Basic continuous stats from the mtcars dataset")invisible(readline(prompt = "Press [enter] to continue"))# For labeling & units we use set_column_labels/set_column_unit that use# the Hmisc package annotation functionsmtcars %<>%  set_column_labels(am = "Transmission",                    mpg = "Gas",                    wt = "Weight",                    gear = "Gears",                    disp = "Displacement",                    vs = "Engine type",                    drat_prop = "Rear axel ratio",                    carb_prop = "Carburetors") %>%  set_column_units(mpg = "Miles/(US) gallon",                   wt = "10<sup>3</sup> lbs",                   disp = "cu.in.")mtcars %>%  getDescriptionStatsBy(mpg,                        wt,                        `Gear&dagger;` = gear,                        drat_prop,                        carb_prop,                        vs,                        by = am,                        header_count = TRUE,                        use_units = TRUE,                        show_all_values = TRUE)  %>%  addHtmlTableStyle(pos.caption = "bottom") %>%  htmlTable(caption  = "Stats from the mtcars dataset",            tfoot = "&dagger; Number of forward gears")invisible(readline(prompt = "Press [enter] to continue"))# Using the default parameter we canmtcars %>%  getDescriptionStatsBy(mpg,                        wt,                        `Gear&dagger;` = gear,                        drat_prop,                        carb_prop,                        vs,                        by = am,                        header_count = TRUE,                        use_units = TRUE,                        default_ref = c(drat_prop = "Low ratio",                                        carb_prop = "&gt; 2"))  %>%  addHtmlTableStyle(pos.caption = "bottom") %>%  htmlTable(caption  = "Stats from the mtcars dataset",            tfoot = "&dagger; Number of forward gears")invisible(readline(prompt = "Press [enter] to continue"))# We can also use liststll <- list()tll[["Gear (3 to 5)"]] <- getDescriptionStatsBy(mtcars$gear, mtcars$am)tll <- c(tll,         list(getDescriptionStatsBy(mtcars$disp, mtcars$am)))mergeDesc(tll,          htmlTable_args = list(caption  = "Factored variables")) %>%  htmlTable::addHtmlTableStyle(css.rgroup = "")invisible(readline(prompt = "Press [enter] to continue"))tl_no_units <- list()tl_no_units[["Gas (mile/gallons)"]] <-  getDescriptionStatsBy(mtcars$mpg, mtcars$am,                        header_count = TRUE)tl_no_units[["Weight (10<sup>3</sup> kg)"]] <-  getDescriptionStatsBy(mtcars$wt, mtcars$am,                        header_count = TRUE)mergeDesc(tl_no_units,          tll) %>%  htmlTable::addHtmlTableStyle(css.rgroup = "")invisible(readline(prompt = "Press [enter] to continue"))# Other settingsmtcars$mpg[sample(1:NROW(mtcars), size = 5)] <- NAgetDescriptionStatsBy(mtcars$mpg,                      mtcars$am,                      statistics = TRUE)invisible(readline(prompt = "Press [enter] to continue"))# Do the horizontal versiongetDescriptionStatsBy(mtcars$gear,                      mtcars$am,                      statistics = TRUE,                      hrzl_prop = TRUE)invisible(readline(prompt = "Press [enter] to continue"))mtcars$wt_with_missing <- mtcars$wtmtcars$wt_with_missing[sample(1:NROW(mtcars), size = 8)] <- NAgetDescriptionStatsBy(mtcars$wt_with_missing, mtcars$am, statistics = TRUE,                      hrzl_prop = TRUE, total_col_show_perc = FALSE)invisible(readline(prompt = "Press [enter] to continue"))## Not run:   ## There is also a LaTeX wrapper  tll <- list(    getDescriptionStatsBy(mtcars$gear, mtcars$am),    getDescriptionStatsBy(mtcars$col, mtcars$am))  latex(mergeDesc(tll),        caption  = "Factored variables",        file = "")## End(Not run)

Gets grid value

Description

Returns the raw value in units if the provided is of type unit elseit returns the default unit.

Usage

getGridVal(x, default.units, axisTo = "x")

Arguments

Value

float

P-value extractors forgetDescriptionStatsBy

Description

These functions are the base functions for getting the descriptionp-values. You can provide your own functions but all functions shouldtake two arguments and return a p-value (numeric, non-formatted)

Usage

getPvalWilcox(x, by)getPvalAnova(x, by)getPvalFisher(x, by)getPvalChiSq(x, by)getPvalKruskal(x, by)

Arguments

Value

numeric Returns the p-value from that particular test

getPvalWilcox

Performs a two-sample two-sided Wilcoxon test (also known as the Mann-Whitney test),seewilcox.test.

getPvalAnova

Performs a standard Analysis of Variance modelthroughanova(lm(x ~ by))

getPvalFisher

Performs Fisher's exact test through thefisher.test.

getPvalChiSq

Performs a standard Chi-Squares analysisthroughchisq.test

getPvalKruskal

Performs a Kruskal-Wallis rank sum testthroughkruskal.test

See Also

Other descriptive functions:describeFactors(),describeMean(),describeMedian(),describeProp(),getDescriptionStatsBy()

Examples

set.seed(123)getPvalFisher(  sample(letters[1:3], size = 100, replace = TRUE),  sample(LETTERS[1:3], size = 100, replace = TRUE))getPvalWilcox(  rnorm(100),  sample(LETTERS[1:2], size = 100, replace = TRUE))

Gets the maximum contributor variables from svd()

Description

This function is inspired by Jeff Leeks Data Analysis course wherehe suggests that one way to use thesvd is to lookat the most influential rows for first columns in the V matrix.

Usage

getSvdMostInfluential(  mtrx,  quantile,  similarity_threshold,  plot_selection = TRUE,  plot_threshold = 0.05,  varnames = NULL)

Arguments

Details

This function expands on that idea and adds the option of choosingmore than just the most contributing variable for each row. For instancetwo variables may have a major impact on a certain component where the secondvariable has 95important in that particular component it makes sense to include itin the selection.

It is of course useful when you have many continuous variables and you wantto determine a subgroup to look at, i.e. finding the needle in the haystack.

Value

Returns a list with vector with the column numbersthat were picked in the "most_influential" variable and thesvd caluclation in the "svd"

Examples

org_par <- par(ask = TRUE)set.seed(1345)# Simulate data with a patterndataMatrix <- matrix(rnorm(15 * 160), ncol = 15)colnames(dataMatrix) <- c(    paste("Pos.3:", 1:3, sep = " #"),    paste("Neg.Decr:", 4:6, sep = " #"),    paste("No pattern:", 7:8, sep = " #"),    paste("Pos.Incr:", 9:11, sep = " #"),    paste("No pattern:", 12:15, sep = " #"))for (i in 1:nrow(dataMatrix)) {  # flip a coin  coinFlip1 <- rbinom(1, size = 1, prob = 0.5)  coinFlip2 <- rbinom(1, size = 1, prob = 0.5)  coinFlip3 <- rbinom(1, size = 1, prob = 0.5)  # if coin is heads add a common pattern to that row  if (coinFlip1) {    cols <- grep("Pos.3", colnames(dataMatrix))    dataMatrix[i, cols] <- dataMatrix[i, cols] + 3  }  if (coinFlip2) {    cols <- grep("Neg.Decr", colnames(dataMatrix))    dataMatrix[i, cols] <- dataMatrix[i, cols] - seq(from = 5, to = 15, length.out = length(cols))  }  if (coinFlip3) {    cols <- grep("Pos.Incr", colnames(dataMatrix))    dataMatrix[i, cols] <- dataMatrix[i, cols] + seq(from = 3, to = 15, length.out = length(cols))  }}# Illustrate dataheatmap(dataMatrix, Colv = NA, Rowv = NA, margins = c(7, 2), labRow = "")svd_out <- svd(scale(dataMatrix))library(lattice)b_clr <- c("steelblue", "darkred")key <- simpleKey(  rectangles = TRUE, space = "top", points = FALSE,  text = c("Positive", "Negative"))key$rectangles$col <- b_clrb1 <- barchart(as.table(svd_out$v[, 1]),               main = "First column",               horizontal = FALSE, col = ifelse(svd_out$v[, 1] > 0,                                                b_clr[1], b_clr[2]               ),               ylab = "Impact value",               scales = list(x = list(rot = 55, labels = colnames(dataMatrix), cex = 1.1)),               key = key)b2 <- barchart(as.table(svd_out$v[, 2]),               main = "Second column",               horizontal = FALSE, col = ifelse(svd_out$v[, 2] > 0,                                                b_clr[1], b_clr[2]               ),               ylab = "Impact value",               scales = list(x = list(rot = 55, labels = colnames(dataMatrix), cex = 1.1)),               key = key)b3 <- barchart(as.table(svd_out$v[, 3]),               main = "Third column",               horizontal = FALSE, col = ifelse(svd_out$v[, 3] > 0,                                                b_clr[1], b_clr[2]               ),               ylab = "Impact value",               scales = list(x = list(rot = 55, labels = colnames(dataMatrix), cex = 1.1)),               key = key)b4 <- barchart(as.table(svd_out$v[, 4]),               main = "Fourth column",               horizontal = FALSE, col = ifelse(svd_out$v[, 4] > 0,                                                b_clr[1], b_clr[2]               ),               ylab = "Impact value",               scales = list(x = list(rot = 55, labels = colnames(dataMatrix), cex = 1.1)),               key = key)# Note that the fourth has the no pattern columns as the# chosen pattern, probably partly because of the previous# patterns already had been identifiedprint(b1, position = c(0, 0.5, .5, 1), more = TRUE)print(b2, position = c(0.5, 0.5, 1, 1), more = TRUE)print(b3, position = c(0, 0, .5, .5), more = TRUE)print(b4, position = c(0.5, 0, 1, .5))# Let's look at how well the SVD identifies# the most influential columnsgetSvdMostInfluential(dataMatrix,                      quantile = .8,                      similarity_threshold = .9,                      plot_threshold = .05,                      plot_selection = TRUE)par(org_par)

Gets an angle

Description

Uses a vector to get an angle byatan2.

Usage

getVectorAngle(x, y, x_origo = NA, y_origo = NA)

Arguments

Value

angle in radians (seeatan2)

Generates a generalized Bézier line

Description

This is a general form of bezier line that can be used for cubic, quadratic,and more advanced Bézier lines.

Usage

gnrlBezierPoints(ctrl_points, length_out = 100L)

Arguments

Examples

library(grid)grid.newpage()l <- gnrlBezierPoints(data.frame(x = c(.1, -.1, .7, 1, 1, 0.1),                                 y = c(.9, 0, 1, .8, .4, .1)),                      length_out = 100)grid.lines(l[,1], l[,2], gp=gpar(col="#550000", lwd = 4))out_sizes <- 4:20clrs <- colorRampPalette(c("orange", "darkblue"))(length(out_sizes))for (i in out_sizes){   l <- gnrlBezierPoints(data.frame(x = c(.1, -.1, .7, 1, 1, 0.1),                                    y = c(.9, 0, 1, .8, .4, .1)),                         length_out = i)   grid.lines(l[,1], l[,2],   gp=gpar(col=clrs[which(i == out_sizes)]))}

An R alternative to the lodashhas in JavaScript

Description

This is a handy function for checking if item exist in a nested structure

Usage

has(sourceList, path)

Arguments

Value

Returns a boolean.

See Also

Other lodash similar functions:retrieve()

Examples

has(list(a = list(b = 1)), "a.b")

Insert a row into a matrix

Description

Inserts a row and keeps the attributescopyAllNewAttributes

Usage

insertRowAndKeepAttr(m, r, v = NA, rName = "")

Arguments

Value

matrix Returns a matrix with one more row than the provided matrixm

Author(s)

Max Gordon, Arne Henningsen

Examples

test <- matrix(1:4, ncol = 2)attr(test, "wow") <- 1000test <- insertRowAndKeepAttr(test, 2)print(attr(test, "wow"))

Just a simple help with interpreting the radians

Description

Just a simple help with interpreting the radians

Usage

isHorizontal(angle_radian)

Arguments

Value

boolean

A wrapper around thehtmlTable/latex function

Description

Calls thehtmlTable/latex after extracting thergroup/n.rgroup arguments.

Usage

## S3 method for class 'descMrg'latex(object, ...)## S3 method for class 'descMrg'htmlTable(x, ...)## S3 method for class 'descMrg'print(x, ...)## S3 method for class 'descMrg'knit_print(x, ...)

Arguments

Prepares a matrix forhtmlTable from a list

Description

By putting all the output from thegetDescriptionStatsByinto a list, naming each element that we want in anrgroup we canautomatically merge everything and create an object ready for thehtmlTable.

Usage

mergeDesc(..., htmlTable_args = list())

Arguments

Value

matrix Returns a matrix object of class descList

Thergroup value

The value for thergroup is by default the name of the list element. If you havepassed a list without a name for that particular element or if you have passed amatrix it will look for a label set by theHmisc::label function.For those elements that have only one row norgroup is set, and the naming sequenceis the same as above but with an additionalrownames if the previoustwo turn out empty. All this behavior is exemplified in the example.

Thergroup value can be overridden by simply specifying a customrgroup whencalling thehtmlTable function.

Thecolnames of the matrix

The function chooses thecolnames from the first element inthetlist.

Examples

library(magrittr)library(dplyr)library(htmlTable)data(mtcars)mtcars %<>%  mutate(am = factor(am, levels = 0:1, labels = c("Automatic", "Manual")),         vs = factor(vs, levels = 0:1, labels = c("V-shaped", "straight")),         drat_prop = drat > median(drat),         drat_prop = factor(drat_prop,                            levels = c(FALSE, TRUE),                            labels = c("High ratio", "Low ratio")),         carb_prop = carb > 2,         carb_prop = factor(carb_prop,                            levels = c(FALSE, TRUE),                            labels = c("&le; 2", "&gt; 2")),         across(c(gear, carb, cyl), factor))# A simple bare-bone examplemtcars %>%  getDescriptionStatsBy(`Miles per gallon` = mpg,                        Weight = wt,                        `Carborators &le; 2` = carb_prop,                        by = am) %>%  htmlTable(caption  = "Basic continuous stats from the mtcars dataset")invisible(readline(prompt = "Press [enter] to continue"))# For labeling & units we use set_column_labels/set_column_unit that use# the Hmisc package annotation functionsmtcars %<>%  set_column_labels(am = "Transmission",                    mpg = "Gas",                    wt = "Weight",                    gear = "Gears",                    disp = "Displacement",                    vs = "Engine type",                    drat_prop = "Rear axel ratio",                    carb_prop = "Carburetors") %>%  set_column_units(mpg = "Miles/(US) gallon",                   wt = "10<sup>3</sup> lbs",                   disp = "cu.in.")mtcars %>%  getDescriptionStatsBy(mpg,                        wt,                        `Gear&dagger;` = gear,                        drat_prop,                        carb_prop,                        vs,                        by = am,                        header_count = TRUE,                        use_units = TRUE,                        show_all_values = TRUE)  %>%  addHtmlTableStyle(pos.caption = "bottom") %>%  htmlTable(caption  = "Stats from the mtcars dataset",            tfoot = "&dagger; Number of forward gears")invisible(readline(prompt = "Press [enter] to continue"))# Using the default parameter we canmtcars %>%  getDescriptionStatsBy(mpg,                        wt,                        `Gear&dagger;` = gear,                        drat_prop,                        carb_prop,                        vs,                        by = am,                        header_count = TRUE,                        use_units = TRUE,                        default_ref = c(drat_prop = "Low ratio",                                        carb_prop = "&gt; 2"))  %>%  addHtmlTableStyle(pos.caption = "bottom") %>%  htmlTable(caption  = "Stats from the mtcars dataset",            tfoot = "&dagger; Number of forward gears")invisible(readline(prompt = "Press [enter] to continue"))# We can also use liststll <- list()tll[["Gear (3 to 5)"]] <- getDescriptionStatsBy(mtcars$gear, mtcars$am)tll <- c(tll,         list(getDescriptionStatsBy(mtcars$disp, mtcars$am)))mergeDesc(tll,          htmlTable_args = list(caption  = "Factored variables")) %>%  htmlTable::addHtmlTableStyle(css.rgroup = "")invisible(readline(prompt = "Press [enter] to continue"))tl_no_units <- list()tl_no_units[["Gas (mile/gallons)"]] <-  getDescriptionStatsBy(mtcars$mpg, mtcars$am,                        header_count = TRUE)tl_no_units[["Weight (10<sup>3</sup> kg)"]] <-  getDescriptionStatsBy(mtcars$wt, mtcars$am,                        header_count = TRUE)mergeDesc(tl_no_units,          tll) %>%  htmlTable::addHtmlTableStyle(css.rgroup = "")invisible(readline(prompt = "Press [enter] to continue"))# Other settingsmtcars$mpg[sample(1:NROW(mtcars), size = 5)] <- NAgetDescriptionStatsBy(mtcars$mpg,                      mtcars$am,                      statistics = TRUE)invisible(readline(prompt = "Press [enter] to continue"))# Do the horizontal versiongetDescriptionStatsBy(mtcars$gear,                      mtcars$am,                      statistics = TRUE,                      hrzl_prop = TRUE)invisible(readline(prompt = "Press [enter] to continue"))mtcars$wt_with_missing <- mtcars$wtmtcars$wt_with_missing[sample(1:NROW(mtcars), size = 8)] <- NAgetDescriptionStatsBy(mtcars$wt_with_missing, mtcars$am, statistics = TRUE,                      hrzl_prop = TRUE, total_col_show_perc = FALSE)invisible(readline(prompt = "Press [enter] to continue"))## Not run:   ## There is also a LaTeX wrapper  tll <- list(    getDescriptionStatsBy(mtcars$gear, mtcars$am),    getDescriptionStatsBy(mtcars$col, mtcars$am))  latex(mergeDesc(tll),        caption  = "Factored variables",        file = "")## End(Not run)

Merging of multiple lists

Description

The merge allows for a recursive componentwhere the lists are compared on the subelement.If one does not contain that element it will get NAin for those parameters.

Usage

mergeLists(  ...,  lapplyOutput = NULL,  sortNames = getOption("Gmisc.mergeList.sort", default = TRUE))

Arguments

Value

Returns a list with all the given lists.

Examples

v1 <- list("a" = c(1, 2), b = "test 1", sublist = list(one = 20:21, two = 21:22))v2 <- list("a" = c(3, 4), b = "test 2", sublist = list(one = 10:11, two = 11:12, three = 1:2))mergeLists(v1, v2)

A helper function for mergeLists that does the actual work.

Description

A helper function for mergeLists that does the actual work.

Usage

mergeLists_internal(o_element, n_element)

Arguments

Value

list with the two merged

Move a boxGrob

Description

Moves aboxGrob/boxPropGrob by modifying it'sviewport.This can be useful if you want to create a series of boxes whose position are relativeto each other and depend on each box's width/height.

Usage

moveBox(  element,  x = NULL,  y = NULL,  space = c("absolute", "relative"),  just = NULL)

Arguments

Value

The element with updated

See Also

Other flowchart components:align,boxGrob(),boxPropGrob(),connectGrob(),coords(),distance(),spread

Examples

library(grid)grid.newpage()box <- boxGrob("A simple box", x = .5, y = .8)moveBox(box, x = -.2, space = "relative")

A path join function

Description

This function joins strings into a valid path. It is a simple version of python'sos.path.join and fixes simple problems such as having/not having trailing /in each section.

Usage

pathJoin(...)

Arguments

Value

string A string with the merged path

Examples

pathJoin("my_base_path/helpers", "superfunction.R")# 'my_base_path/helpers/superfunction.R'base_dir <- "/home/tester/images"out <- data.frame(filename = c("file1.png", "file2.png", "file3.png")) |>  dplyr::mutate(full_path = pathJoin(base_dir, filename))

Add a p-value column to the results

Description

Add a p-value column to the results

Usage

prAddDescStats(  results,  x,  by,  statistics,  statistics.suppress_warnings,  statistics.sig_lim,  statistics.two_dec_lim,  html)

Arguments

Value

results with added column

Add a units column to the results

Description

Add a units column to the results

Usage

prAddDescUnitColumn(results, x, use_units, units_column_name)

Arguments

Value

results with added column

Convert the by-list into a matrix compatible format

Description

Helper for [getDescriptionStatsBy] that fixes empty values in matrixso that they are compatible with the matrix

Usage

prAddEmptyVals(t, missing_value)

Arguments

Value

A fixed list

Add a total column to the results

Description

Add a total column to the results

Usage

prAddTotalDescColumn(  results,  x,  by,  numbers_first,  total_col_show_perc,  show_all_values,  useNA,  useNA.digits,  html,  digits,  continuous_fn,  factor_fn,  prop_fn,  percentage_sign,  default_ref,  header_count = NULL,  add_total_col)

Arguments

Value

results with added column

Add a sub-label toboxPropGrob

Description

Add a sub-label toboxPropGrob

Usage

prBuildSubLabel(label, prop, txt_gp, side = c("left", "right"))

Arguments

Value

AtextGrob with he additional attributeswidth andheight.

Fixes the caption for elements without caption

Description

Fixes the caption for elements without caption

Usage

prCaptionFix(outFile)

Arguments

Value

outFile The name of the file

Converts an object to coordinates

Description

Sometimes we have an object that can be either a box,a coprdinate, a unit or a numerical value and all wewant is alist of coordinates that we can use forcalculating distance, alignment and other things.

Usage

prConvert2Coords(obj)

Arguments

Value

Alist with all the points thatcoords returns

Creates coordinates for box

Description

Creates coordinates for box

Usage

prCreateBoxCoordinates(viewport_data, extra_coordinate_functions = NULL)

Arguments

Value

list of classcoords

A helper function for the description stats

Description

A helper function for the description stats

Usage

prDescGetAndValidateDefaultRef(x, default_ref)

Arguments

Value

integer The level number of interest

Helper to [getDescriptionStatsBy()]

Description

Helper to [getDescriptionStatsBy()]

Usage

prFactorDescs(  x,  by,  factor_fn,  hrzl_prop,  html,  digits,  digits.nonzero,  numbers_first,  useNA,  useNA.digits,  percentage_sign,  missing_value,  names_of_missing)

Arguments

Value

A [base::by] list

Fix rownames for descriptive results

Description

Helper for [getDescriptionStatsBy] that fixes row names

Usage

prFixDescRownames(results, t, name)

Arguments

Value

The results with fixed names

Helper to ftp_document

Description

Helper to ftp_document

Usage

prFtpHeaderStyle(output_str, h1_style, other_h_style)

Arguments

Value

string

Changes lines for XML-conformity

Description

Changes lines for XML-conformity

Usage

prFtpOtherChanges(output_str)

Arguments

Value

string Returns with changes

Removes other unwanted lines

Description

Removes other unwanted lines

Usage

prFtpOtherRemoval(output_str)

Arguments

Value

string Returns without the unwanted lines

Removes the <script>*</scrip>

Description

Removes the <script>*</scrip>

Usage

prFtpScriptRemoval(output_str)

Arguments

Value

string Returns without the script elements

Retrieve basic description stats by header

Description

Helper for [getDescriptionStatsBy] that retrieves the basicheader names.

Usage

prGetDescHeader(by, html, header_count, already_table_format = FALSE)

Arguments

Value

A vector with basic headers

Get statistics according to the type

Description

A simple function applied by thegetDescriptionStatsByfor the total column.

Usage

prGetStatistics(  x,  show_perc = FALSE,  html = TRUE,  digits = 1,  digits.nonzero = NA,  numbers_first = TRUE,  useNA = c("ifany", "no", "always"),  useNA.digits = digits,  show_all_values = FALSE,  continuous_fn = describeMean,  factor_fn = describeFactors,  prop_fn = factor_fn,  percentage_sign = TRUE,  default_ref = NULL)

Arguments

Value

A matrix or a vector depending on the settings

Just a simple acces to the gp$cex parameter

Description

Just a simple acces to the gp$cex parameter

Usage

prGetTextGrobCex(x)

Arguments

Value

numeric The cex value, 1 if no cex was present

Adds a title to the plot

Description

Adds the title and generates a newmain viewport below the title

Usage

prGridPlotTitle(  title,  base_cex,  cex_mult = 1.2,  fontface = "bold",  space_below = NULL)

Arguments

Value

NULL The function does not return a value

Helper to [getDescriptionStatsBy()]

Description

Helper to [getDescriptionStatsBy()]

Usage

prNumericDescs(  x,  by,  hrzl_prop,  continuous_fn,  html,  digits,  digits.nonzero,  numbers_first,  useNA,  useNA.digits,  percentage_sign,  missing_value,  names_of_missing)

Arguments

Value

A [base::by] list

Collapses a vector for throwing errors

Description

The function collapses a vector into an output useful when throwingerrors, e.g. 1:3 becomes '1', '2', '3'

Usage

prPasteVec(x)

Arguments

Helper to [getDescriptionStatsBy()]

Description

Helper to [getDescriptionStatsBy()]

Usage

prPropDescs(  x,  by,  name,  default_ref,  prop_fn,  html,  digits,  digits.nonzero,  numbers_first,  useNA,  useNA.digits,  percentage_sign,  missing_value,  names_of_missing,  NEJMstyle)

Arguments

Value

A [base::by] list

Pushes viewport with margins

Description

Agrid.layout object is used togenerate the margins. A second viewport selecting themid-row/col is used to create the effect of margins

Usage

prPushMarginViewport(bottom, left, top, right, name = "margin")

Arguments

Value

2 - the number of pushed viewports

Updates the css max-width

Description

Reads the file, changes the max-widthfor the body element.

Usage

prSetMaxWidth(max_width, css_file)

Arguments

Value

string The file name

Finds the matching colors for the new addition based on the original setof colors

Description

Finds the matching colors for the new addition based on the original setof colors

Usage

prTcMatchClr(add, org, no_cols, no_rows, is3D)

Arguments

Value

A list with colors that is appropriate for the transition object

Plots the arrows within a single transition set

Description

Plots the arrows within a single transition set

Usage

prTcPlotArrows(  trnstn_set,  widths,  type = c("simple", "gradient"),  clr,  rez,  origin_boxes,  target_boxes,  left_box_clrs,  add_width,  max_flow,  min_width,  max_width,  abs_arrow_width = FALSE,  clr_bar_subspace)

Arguments

Plots a column of boxes

Description

Takes a set of box settings and plots them.

Usage

prTcPlotBoxColumn(  box_positions,  proportions,  fill,  txt,  txt_clr,  txt_gpar,  cex)

Arguments

Value

void

Checks and prepares colors

Description

The colors need to match the size of the transition matrixand therefore we need to have this input check. The output isalways a matrix of the exact same dimensions as the transitionmatrix.

Usage

prTcValidateAndPrepClr(value, no_cols, no_rows, is3D)

Arguments

Value

matrix Returns a matrix of the same size as thetransition matrix

Gets the box position

Description

Gets the box position

Usage

prTpGetBoxPositions(  no,  side,  transitions,  prop_start_sizes,  prop_end_sizes,  tot_spacing,  box_width)

Arguments

Value

list(top, left, bottom, right, width, height)

Gets the color for the given box

Description

Gets the color for the given box

Usage

prTpGetBoxPropClr(clr, no_boxes, lengthOneOK = FALSE)

Arguments

Value

matrix With two columns and no_boxes rows.If function fails then returnNULL

Gets the text size for the box

Description

Gets the text size for the box

Usage

prTpGetBoxSizedTextGrob(  txt,  txt_clr,  txt_cex,  txt_gpar = NULL,  force_cex = FALSE,  ...)

Arguments

Gets a set of colors or just one color

Description

Used in order to illustrate the mix between twoproportions in thetransitionPlot.

Usage

prTpGetColors(colors, proportion, space = NULL, no = 101)

Arguments

Value

character The function can return both single colorsor multiple colors as character vector (seergb)

Plots the arrows

Description

Outputs all the arrows from a box row

Usage

prTpPlotArrows(  type,  box_row,  transition_flow,  max_flow,  min_lwd,  max_lwd,  clr,  box_clr,  transition_arrow_props,  prop_start_sizes,  prop_end_sizes,  tot_spacing,  box_width,  abs_arrow_width,  color_bar_subspace,  add_width = NA)

Arguments

Value

void

Plots the box for the transition plot

Description

Plots the box for the transition plot

Usage

prTpPlotBox(  bx,  bx_txt,  fill,  txt_clr,  txt_gpar = NULL,  cex,  line_col,  lwd,  prop = NA)

Arguments

Value

void

Plot boxes and arrows

Description

Outputs all the boxes and arrow

Usage

prTpPlotBoxes(  overlap_order,  transition_flow,  no_boxes,  box_width,  tot_spacing,  txt,  cex,  txt_gpar = NULL,  prop_start_sizes,  prop_end_sizes,  box_prop,  lwd_prop_total = lwd_prop_total,  fill_start_clr,  fill_end_clr,  txt_start_clr,  txt_end_clr,  lwd = 2,  line_col = "#000000",  min_lwd,  max_lwd,  overlap_add_width,  overlap_bg_clr,  type_of_arrow,  abs_arrow_width,  arrow_clr,  transition_arrow_props,  color_bar_subspace,  plot_arrows = TRUE,  proportion = FALSE)

Arguments

Value

void

Output boxes

Description

Outputs a list of boxes as produced by either thespread or align functions for boxGrobs.

Usage

## S3 method for class 'Gmisc_list_of_boxes'print(x, ...)

Arguments

An R alternative to the lodashget in JavaScript

Description

This is a handy function for retrieving items deep in a nested structurewithout causing error if not found

Usage

retrieve(sourceList, path, default = NA)

Arguments

Value

Returns a sub-element fromsourceList or thedefault value.

See Also

Other lodash similar functions:has()

Examples

source <- list(a = list(b = 1, `odd.name` = 'I hate . in names', c(1,2,3)))retrieve(source, "a.b")retrieve(source, "a.b.1")retrieve(source, "a.odd\\.name")retrieve(source, "a.not_in_list")

Add [Hmisc::label()] to multiple columns

Description

Add label attribute using 'dplyr' syntax using the [Hmisc::label()]

Usage

set_column_labels(x, ...)

Arguments

Value

The original data.frame

See Also

Other Hmisc helpers:set_column_units()

Examples

library(magrittr)data(mtcars)mtcars_with_labels <- mtcars %>%  set_column_labels(mpg = "Gas",                    cyl = "Cylinders",                    hp = "Strength")Hmisc::label(mtcars_with_labels$mpg)

Add [Hmisc::unit()] to multiple columns

Description

Add label attribute using 'dplyr' syntax using the [Hmisc::unit()]

Usage

set_column_units(x, ...)

Arguments

Value

The original data.frame

See Also

Other Hmisc helpers:set_column_labels()

Examples

library(magrittr)data(mtcars)mtcars_with_units <- mtcars %>%  set_column_units(wt = "1000 lbs")Hmisc::units(mtcars_with_units$wt)

Spread boxes

Description

Spreads a set ofboxGrob/boxPropGrob in either horizontal or vertical direction.

Usage

spreadVertical(..., .from = NULL, .to = NULL, .type = c("between", "center"))spreadHorizontal(..., .from = NULL, .to = NULL, .type = c("between", "center"))

Arguments

Value

list with the boxes that have been spread

See Also

Other flowchart components:align,boxGrob(),boxPropGrob(),connectGrob(),coords(),distance(),moveBox()

Examples

library(grid)grid.newpage()box1 <- boxGrob("B1", x = .2, y = .8)box2 <- boxGrob("B2\n\n\neach\nbox\neven\nspace\nbetween", x = .2, y = .8)box3 <- boxGrob("B3", x = .2, y = .8)box4 <- boxGrob("B4", x = .2, y = .8)box5 <- boxGrob("B5", x = .2, y = .8)spread_boxes <- spreadVertical(box1,                               box2,                               box3,                               a = box4,                               box5,                                .type = "between")for (b in spread_boxes) {  print(b)}box1 <- boxGrob("B1\n\nanother group\ncenter oriented", x = .6, y = .8)box2 <- boxGrob("B2", x = .6, y = .8)box3 <- boxGrob("B3", x = .6, y = .8)box4 <- boxGrob("B4", x = .6, y = .8)box5 <- boxGrob("B5", x = .6, y = .8)spread_boxes <- spreadVertical(box1,                               box2,                               box3,                               a = box4,                               box5,                                .type = "center")for (b in spread_boxes) {  print(b)}

A dense time-span text

Description

When adding a time span text we often don't want to write3 jun - 10 jun butshorten it to3 - 10 jun while retaining month and year info only if the spancrosses between months or years.

Usage

time2spanTxt(  times,  day_month_glue_txt = getOption("Gmisc_time2spanTxt_day_month", default =    "{mday(time)} {month(time, label = TRUE)}"),  full_year_format = getOption("Gmisc_time2spanTxt_full_year", default =    "{mday(time)} {month(time, label = TRUE)} {year(time)}"),  start_stop_glue_txt = getOption("Gmisc_time2spanTxt_template", default =    "{start} to {stop}"))

Arguments

Details

There are options that can be set using theoptions:

• Gmisc_time2spanTxt_day_month The date with day + month as formatted byglue where the time is passed astime.

• Gmisc_time2spanTxt_full_year The full date with day + month + year as formatted byglue where the time is passed astime.

• Gmisc_time2spanTxt_template The merge of the stop & start elements usingglue.

Value

string A string describing the time span

Examples

time2spanTxt(as.POSIXct(c("2020-01-02", "2020-03-01", NA)))# 2 jan to 1 mar

A transition plot

Description

This plot's purpose is to illustrate how states change before andafter. In my research I use it before surgery and after surgerybut it can be used in any situation where you have a change fromone state to another

Usage

transitionPlot(  transition_flow,  type_of_arrow = c("grid", "simple", "gradient"),  box_txt = rownames(transition_flow),  tot_spacing = 0.2,  box_width = 1/4,  fill_start_box = "darkgreen",  txt_start_clr = "white",  fill_end_box = fill_start_box,  txt_end_clr = txt_start_clr,  cex = 2,  min_lwd = if (type_of_arrow == "grid") 1 else unit(0.1, "mm"),  max_lwd = if (type_of_arrow == "grid") 6 else unit(5, "mm"),  lwd_prop_total = TRUE,  arrow_clr = "#000000",  abs_arrow_width = FALSE,  overlap_bg_clr = "#FFFFFF",  overlap_order = 1:nrow(transition_flow),  overlap_add_width = if (type_of_arrow == "grid") 1.5 else unit(1, "mm"),  box_prop,  mar = unit(rep(3, times = 4), "mm"),  main = NULL,  box_label = NULL,  box_label_pos = "top",  box_label_cex = cex,  color_bar = TRUE,  color_bar_cex = cex * 0.33,  color_bar_labels,  color_bar_subspace = NULL,  new_page = FALSE)

Arguments

Value

void

Examples

# This example does not run since it# takes a little while to assemble the# arrows and RMD Check complains that this# is more than allowed forlibrary(grid)par_org <- par(ask = TRUE)# Settingsno_boxes <- 3# Generate test settingtransition_matrix <- matrix(NA, nrow = no_boxes, ncol = no_boxes)transition_matrix[1, ] <- 200 * c(.5, .25, .25)transition_matrix[2, ] <- 540 * c(.75, .10, .15)transition_matrix[3, ] <- 340 * c(0, .2, .80)grid.newpage()transitionPlot(transition_matrix,  box_txt = c("First", "Second", "Third"),  type_of_arrow = "simple",  min_lwd = unit(1, "mm"),  max_lwd = unit(6, "mm"),  overlap_add_width = unit(1, "mm"))# Setup proportionsbox_prop <- cbind(c(1, 0, 0.5), c(.52, .2, .8))# From the Set2 Colorbrewerstart_box_clr <- c("#8DA0CB", "#FC8D62")# Darken the colors slightlyend_box_clr <- c(  colorRampPalette(c(start_box_clr[1], "#000000"))(10)[2],  colorRampPalette(c(start_box_clr[2], "#000000"))(10)[2])# Create a new gridgrid.newpage()transitionPlot(transition_matrix,  box_prop = box_prop,  fill_start_box = start_box_clr, fill_end_box = end_box_clr,  txt_start_clr = c("#FFFFFF", "#000000"), txt_end_clr = c("#FFFFFF", "#000000"),  box_txt = c("First", "Second", "Third"),  type_of_arrow = "gradient",  min_lwd = unit(1, "mm"),  max_lwd = unit(10, "mm"),  overlap_add_width = unit(1, "mm"))par(par_org)

Checks the input of a vector

Description

It checks that a vector makes sense in itsgrid parameters. It also creates an origoat point 0 if none is provided.

Usage

validateAndConvertVectorInputs(x, y, x_origo, y_origo)

Arguments

Value

list with the input variables checked andconverted if necessary.

Outputs an object

Description

Manually viewing a list object can be tricky where the natural printcan be hard to work through. The config format *yaml* is increadiblydense and useful not only for writing configs but also viewing themwhich 'yamlDump' helps with.

Usage

yamlDump(x)

Arguments

Value

void

Examples

some_fancy_list <- list(complex = list(some_data = 1:3,                                       other_data = list(name = "Max")),                        simple = "awesome overview")yamlDump(some_fancy_list)#complex:#  some_data:#  - 1#  - 2#  - 3#  other_data:#    name: Max#simple: awesome overview# If you got a character json you can also input it directly# and the function will automatically convert it to a listyamlDump('{"a":{"b":["1"]}}')