In ekstroem/cleanR: A Suite of Checks for Identification of Potential Errors in a Data Frame as Part of the Data Screening Process

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library(knitr)
options(htmltools.dir.version = FALSE, cache=TRUE)
opts_chunk$set(comment = NA, prompt=TRUE)
#opts_chunk$set(dev.args=list(bg="transparent"), fig.width=15, fig.height=7)
source("kutheme.R")

The RESCueH project

---

class: center

Timeline followback (TLFB)

DF <- data.frame(day1=sample(1:25, 6),
                 day2=c(NA, NA, sample(1:25, 3), 88),
                 day3=c(NA, 99, 40, sample(1:25, 3)))
head(DF, 4)

---

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Timeline followback (TLFB)

head(DF, 6)

---

background-image: url(pics/mau.png) background-size: 80% class: center

Monthly Alcohol units

library(extrafont)
loadfonts()
library(ggplot2)
library(ggthemr)
claus <- define_palette(swatch = c('#eeeeee', '#FFFACD','#901A1E', 'lightblue', 'green', 'blue', 'brown', 'purple', 'yellow'),
  gradient = c(lower = 'red', upper = 'green'),
                        background = "#222222",
                        text = c("#eeeeee", "#eeeeee"),
                        line = c("#ee1e1e", "#6e6e6e"), # Axis lines
                        gridline = "#434343") # Gridlines

ggthemr(claus, layout="scientific", type = 'outer', spacing=1.2)

tlfb <- data.frame(units=dget("tlfb.txt"))

p <- ggplot(tlfb, aes(units)) + geom_dotplot() +
#     ggtitle("Baseline alcohol") +
     xlab("Units") + ylab("Frequency") +
     theme(text=element_text(size=24, family="Comic Sans MS"),
           axis.text.y=element_blank(),
           axis.ticks.y=element_blank())

theme_xkcd <- theme(

#  panel.background = element_rect(fill="transparent"),
#  plot.background = element_rect(fill="transparent"),

  #axis.ticks = element_line(colour=NA),
##  panel.grid = element_line(colour="white"),
  #axis.text.y = element_text(colour=NA),
##  axis.text.x = element_text(colour="black"),
  text = element_text(size=36, family="Humor Sans")
)
## p + theme_xkcd


# Rotate the dot plot
# p + coord_flip()



#p <- ggplot(mtcars, aes(x=wt, y=mpg)) + geom_point(size=3) +
#  ggtitle("Fuel Efficiency of 32 Cars") +
#  xlab("Weight (x1000 lb)") + ylab("Miles per Gallon") +
#  theme(text=element_text(size=16, family="Comic Sans MS"))
#p

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Reproducible research

What didn't we check?

--

• Need experts in relevant field
• Merge existing databases into megadatabases
• New technologies revive old data

---

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library(dataMaid)
data(toyData)

.small[

toyData

]

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dataMaid

library(dataMaid)
data(toyData)
makeDataReport(toyData) #<<

Documentation to be read and evaluated by a human.

See github.com/ekstroem/dataMaid for more info. Stable version on CRAN.

---

background-image: url(pics/flowchart2.png) background-size: 100% class: center

dataMaid flowchart

library(DiagrammeR)
library(DiagrammeRsvg)
library(svglite)
library(rsvg)

grViz("
  digraph {

graph[layout = neato,
      overlap=false,
      rankdir = 'LR', 
      bgcolor='#000000',
      sep=.2]

node[fontsize=20,
      fillcolor = DimGray,
      fontcolor = White,
      fillcolor='#222222',
      style=filled,
      color=White]

edge [color = White, penwidth=4]

  'data frame'  -> 'summarize'
    subgraph detail {
       rank='same';
       'summarize' -> 'visualize' -> 'check';
       'check' -> 'summarize'; }
'check' -> '.Rmd / render';
  }")

---

Part 1: Data cleaning summary

knitr::include_graphics('pics/summ.png', dpi = NA)

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Part 2: Summary table

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Part 3: Variable list

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background-image: url(pics/out2.png) background-size: 100%

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dataMaid common arguments

.small[

| Argument | Description | | ------------- |:--------------------------------| | mode | Tasks to perform. c("summarize", "visualize", "check") is default | | replace | Logical. Should existing dataMaid reports be overwritten? Default FALSE | | output | Output format. Choices are "pdf", "html", ""word" | | onlyProblematic | Logical. Show only variable with problems. Default FALSE | | maxProbVals | Maximum number of unique values printed. Positive int or Inf (default 10) |

]

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Exercise 2

1. Load the dataMaid package
2. Use makeDataReport() to generate a data report
3. Screen the bigPresidentData data for errors we did not find before.

Hunt for errors!

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.small[

toyData

]

---

Using dataMaid interactively

.footnotesize[

check(toyData$events)
check(toyData$events, 
        numericChecks = "identifyMissing")

]

???

check er de funktioner, der bliver checket for

Kan sætte specifikke (også i makeDataReport)

Vis, at det er en liste med 2 elementer, og den form, som de har.

---

Overview of check functions

.footnotesize[

allCheckFunctions()

]

.footnotesize[

----------------------------------------------------------------------------------
name                 description                     classes                      
-------------------- -------------------------------------------------------------
identifyCaseIssues   Identify case issues            character, factor            

identifyLoners       Identify levels with < 6 obs.   character, factor            

identifyMissing      Identify miscoded missing       character, Date, factor,     
                     values                          integer, labelled, logical,  
                                                          numeric                      

]

and more

---

Interactive dataMaid - visualizations

.pull-left[ .footnotesize[

visualize(toyData$events)

Can also check the available visual functions

allVisualFunctions()

] ]

.pull-right[

visualize(toyData$events)  # Visualize variable

]

---

Interactive dataMaid - summaries

.footnotesize[

summarize(toyData$events)

]

---

Using dataMaid interactively

.small[

> allSummaryFunctions()

-------------------------------------------------------------
name         description          classes                    
------------ -------------------- ---------------------------
centralValue Compute median       character, Date, factor,   
             or mode              integer, labelled, logical,
                                  numeric                    

countMissing Compute ratio of     character, Date, factor,   
             missing obs.         integer, labelled, logical,
                                  numeric                    

minMax       Find min and max     integer, numeric, Date     
             values                                                   
quartiles    Compute 1st and 3rd quartiles Date, integer, numeric     

uniqueValues Count number of unique values character, Date, factor,   
                                           integer, labelled, logical,
                                           numeric                    

variableType Data class of variable        character, Date, factor,   
                                           integer, labelled, logical,
                                           numeric                    
----------------------------------------------------------------------

]

---

Extending dataMaid

Custom check, visual, or summary functions.

Few requirements --- input and output formats.

Easiet to work with a template system and modify one of those.

Check vignette vignette("extending_dataMaid") for detailed instructions. Or the exercises!

---

Custom summaryFunction - template

.footnotesize[

mySummaryFunction <- function(v, ...) {
  val <- [ result of whatever summary we are doing ]
  res <- [ properly escaped version of val ]        
  summaryResult(list(feature = "[Feature name]", 
                     result = res,
                     value = val))
}

]

Example (centralValue for numeric/integer)

.footnotesize[

function (v, maxDecimals = 2) {
    v <- na.omit(v)
    val <- median(v)
    summaryResult(list(feature = "Median", result = round(val, 
        maxDecimals), value = val))
}

]

---

Custom checkFunction - template

.small[

isSSN <- function(v, nMax = NULL, ...) {
  out <- list(problem = FALSE, 
              message = "", 
              problemValues=NULL)
  if (class(v) %in% c("character", "factor", 
                      "labelled")) {
    if (any(grep("\\d{3}-\\d{2}-\\d{4}", v))) {
      out$problem <- TRUE
      out$message <- "Warning: Seems to contain SSNs."
      out$problemValues <- "Will not show"
    }  
  }
  out 
}

]

Using the function

.footnotesize[

DF <- data.frame(ids=c("111-22-3333","123-45-6789", 
                       "111-22-3333"),
                 id2=c("111223333", "123456789", "4728491283"), 
                 stringsAsFactors=FALSE)

check(DF, characterChecks = c("isSSN"))

]

---

class: inverse

Exercise 2b/2c

How to tailor dataMaid to work with your dataset:

• Work interactively with dataMaid (exercise 2b)
• Create new custom summary, check and visualization functions (exercise 2c)

Pick whatever you want. Or jump back and forth.

ekstroem/cleanR documentation built on Jan. 31, 2022, 8:58 a.m.