added dangling files

functions_reference.R

@@ -0,0 +1,349 @@
+```{r}
+
+# Load some new libraries used by functions below
+
+library(RColorBrewer)
+library(hrbrthemes) # Used for ipsum theme etc.
+library(ggeasy) # used for easy_center_title() which is not strictly necessary, but tidier than theme(plot.title = element_text(hjust = 0.5))
+
+# Define colour palettes
+# TODO: confirm final colour scheme for charts and normalise across usage of different themes
+coul3 <- brewer.pal(3, "RdYlBu") # Using RdYlBu range to generate 3 colour palette: https://colorbrewer2.org/#type=diverging&scheme=RdYlBu&n=5
+coul4 <- brewer.pal(4, "RdYlBu")
+coul5 <- brewer.pal(5, "RdYlBu")
+coul6 <- brewer.pal(6, "RdYlBu")
+coul7 <- brewer.pal(7, "RdYlBu")
+coul4_reversed <- c("#2C7BB6", "#ABD9E9", "#FDAE61", "#D7191C")
+coul6_reversed <- c("#4575B4", "#91BFDB" , "#E0F3F8" , "#FEE090", "#FC8D59", "#D73027")
+white <- "#ffffff"
+purple <- "#590048"
+ochre <- "#B18839"
+ochre_12 <- wheel(ochre, num = 12)
+purple_12 <- wheel(purple, num = 12)
+
+# Reusable Functions ------------------------------------------------------
+
+# Importing code for colortools() now deprecated and removed from CRAN here. Some minor modifications to update code, but generally all credit here goes to Gaston Sanchez
+
+setColors <- function(color, num) {
+  # convert to RGB
+  rgb_col = col2rgb(color)
+  # convert to HSV
+  hsv_col = rgb2hsv(rgb_col)[,1]
+  # get degree
+  hue = hsv_col[1]
+  sat = hsv_col[2]
+  val = hsv_col[3]
+  cols = seq(hue, hue + 1, by=1/num)
+  cols = cols[1:num]
+  cols[cols > 1] <- cols[cols > 1] - 1
+  # get colors with hsv
+  colors = hsv(cols, sat, val)
+  # transparency
+  if (substr(color, 1, 1) == "#" && nchar(color) == 9)
+    ({
+      alpha = substr(color, 8, 9)
+      colors = paste(colors, alpha, sep="")
+    })
+  colors
+}
+
+complementary <- function(color, plot=TRUE, bg="white", labcol=NULL, cex=0.8, title=TRUE) {	
+  tmp_cols = setColors(color, 12)
+  comp_colors <- tmp_cols[c(1, 7)]
+  
+  # plot
+  if (plot)
+    ({
+      # labels color
+      if (is.null(labcol)) 
+        ({
+          lab_col = rep("", 12)
+          if (mean(col2rgb(bg)) > 127)
+            ({
+              lab_col[c(1, 7)] <- "black"
+              lab_col[c(2:6,8:12)] <- col2HSV(bg)
+            }) else ({
+              lab_col[c(1, 7)] <- "white"
+              lab_col[c(2:6,8:12)] <- col2HSV(bg)
+            })
+        }) else ({
+          lab_col = rep(labcol, 12)
+          if (mean(col2rgb(bg)) > 127)
+            ({
+              lab_col[c(1, 7)] <- labcol
+              lab_col[c(2:6,8:12)] <- col2HSV(bg)
+            }) else ({
+              lab_col[c(1, 7)] <- labcol
+              lab_col[c(2:6,8:12)] <- col2HSV(bg)
+            })
+        })	
+      # hide non-adjacent colors
+      tmp_cols[c(2:6,8:12)] <- paste(substr(tmp_cols[c(2:6,8:12)],1,7), "0D", sep="")
+      pizza(tmp_cols, labcol=lab_col, bg=bg, cex=cex)
+      # title
+      if (title)
+        title(paste("Complementary (opposite) color of: ", tmp_cols[1]), 
+              col.main=lab_col[1], cex.main=0.8)
+    })
+  # result
+  comp_colors
+}
+
+sequential <- function(color, percentage=5, what="saturation", s=NULL, v=NULL, alpha=NULL, fun="linear", plot=TRUE, verbose=TRUE)  {
+  # convert to HSV
+  col_hsv = rgb2hsv(col2rgb(color))[,1]
+  # transparency
+  if (is.null(alpha))
+    alpha = 1
+  if (substr(color, 1, 1) == "#" && nchar(color) == 9)
+    alpha = substr(color, 8, 9)
+  # get hue, saturation, and value
+  hue = col_hsv[1]
+  if (is.null(s)) s = col_hsv[2]
+  if (is.null(v)) v = col_hsv[3]
+  # sequence function
+  getseq = switch(fun, 
+                  linear = seq(0, 1, by=percentage/100),
+                  sqrt = sqrt(seq(0, 1, by=percentage/100)),
+                  log = log1p(seq(0, 1, by=percentage/100)),
+                  log10 = log10(seq(0, 1, by=percentage/100))
+  )
+  # what type of sequence?
+  if (what == "saturation") ({
+    sat = getseq
+    fixed = paste("v=", round(v,2), " and alpha=", alpha, sep="")
+    if (is.numeric(alpha))
+      seq_col = hsv(hue, s=sat, v=v, alpha=alpha)
+    if (is.character(alpha)) ({
+      seq_col = hsv(hue, s=sat, v=v)
+      seq_col = paste(seq_col, alpha, sep="")
+    })
+  })
+  if (what == "value") ({
+    val = getseq
+    fixed = paste("s=", round(s,2), " and alpha=", alpha, sep="")
+    if (is.numeric(alpha))
+      seq_col = hsv(hue, s=s, v=val, alpha=alpha)
+    if (is.character(alpha)) ({
+      seq_col = hsv(hue, s=s, v=val)
+      seq_col = paste(seq_col, alpha, sep="")
+    })
+  })
+  if (what == "alpha") ({
+    alpha = getseq
+    fixed = paste("s=", round(s,2), " and v=", round(v,2), sep="")
+    seq_col = hsv(hue, s=s, v=v, alpha=alpha)
+  })
+  # if plot TRUE
+  if (plot)
+    ({
+      n = length(seq(0, 1, by=percentage/100))
+      fx = unlist(fixed)
+      #dev.new()
+      plot(0, 0, type="n", xlim=c(0,1), ylim=c(0,1), axes=FALSE, xlab="", ylab="")
+      rect(0:(n-1)/n, 0, 1:n/n, 1, col=seq_col, border="lightgray")
+      mtext(seq_col, side=1, at=0.5:(n)/n, cex=0.8, las=2)
+      title(paste("Sequential colors based on ", what, "\n with fixed ", fx, sep=""),
+            cex.main=0.9)
+    })
+  # result
+  if (verbose)
+    seq_col
+}
+
+wheel <- function(color, num=12, bg="gray95", border=NULL, init.angle=105, cex=1, lty=NULL, main=NULL, verbose=TRUE, ...) {
+  if (!is.numeric(num) || any(is.na(num) | num < 0)) 
+    stop("\n'num' must be positive")
+  x <- rep(1, num)
+  x <- c(0, cumsum(x)/sum(x))
+  dx <- diff(x)
+  nx <- length(dx)
+  # set colors
+  col = setColors(color, num)
+  labels = col
+  # labels color
+  labcol = ifelse( mean(col2rgb(bg)) > 127, "black", "white")
+  # prepare plot window
+  par(bg = bg)
+  plot.new()
+  pin <- par("pin")
+  xlim <- ylim <- c(-1, 1)
+  if (pin[1L] > pin[2L]) 
+    xlim <- (pin[1L]/pin[2L]) * xlim
+  else ylim <- (pin[2L]/pin[1L]) * ylim
+  dev.hold()
+  on.exit(dev.flush())
+  plot.window(xlim, ylim, "", asp = 1)
+  # get ready to plot
+  if (is.null(border[1])) ({
+    border <- rep(bg, length.out = nx)    
+  }) else ({
+    border <- rep(border, length.out = nx)    
+  })
+  if (!is.null(lty))
+    lty <- rep(NULL, length.out = nx)
+  angle <- rep(45, length.out = nx)
+  radius = seq(1, 0, by=-1/num)[1:num]
+  twopi <- -2 * pi
+  t2xy <- function(t, rad) ({
+    t2p <- twopi * t + init.angle * pi/180
+    list(x = rad * cos(t2p), y = rad * sin(t2p))
+  })
+  # plot colored segments
+  for (i in 1L:nx)
+    ({
+      n <- max(2, floor(200 * dx[i]))
+      P <- t2xy(seq.int(x[i], x[i + 1], length.out = n), rad=radius[1])
+      polygon(c(P$x, 0), c(P$y, 0), angle = angle[i], 
+              border = border[i], col = col[i], lty = lty[i])
+      P <- t2xy(mean(x[i + 0:1]), rad=radius[1])
+      lab <- labels[i]
+      if (!is.na(lab) && nzchar(lab)) ({
+        adjs = 0.5
+        if (P$x > 1e-08) adjs <- 0
+        if (P$x < -1e-08) adjs <- 1
+        lines(c(1, 1.05) * P$x, c(1, 1.05) * P$y)
+        text(1.1 * P$x, 1.1 * P$y, labels[i], xpd = TRUE, 
+             adj = adjs, cex=cex, col=labcol, ...)
+      })
+    })
+  # add title
+  title(main = main, ...)
+  # return color names
+  if (verbose)
+    col
+}
+
+# function to produce horizontal bar chart, colours drawn from "ochre" colour wheel defined above to match report
+plot_horizontal_bar <- function(x) {
+  ## code if a specific palette is needed for matching
+  fill = wheel(ochre, num = as.integer(count(x[1])))
+  #fill = scale_fill_brewer()
+  # make plot
+  ggplot(x, aes(x = n, y = response, fill = fill)) +
+    geom_col(colour = "white") +
+    ## add percentage labels
+    geom_text(aes(label = perc),
+              ## make labels left-aligned and white
+              hjust = 1, nudge_x = -.5, colour = "black", size=3) +
+    ## reduce spacing between labels and bars
+    scale_fill_identity(guide = "none") +
+    ## get rid of all elements except y axis labels + adjust plot margin
+    theme_ipsum_rc() +
+    theme(plot.margin = margin(rep(15, 4))) +
+    easy_center_title()
+}
+
+qualtrics_process_single_multiple_choice <- function(x) {
+  # create separate data frame
+  df <- as.data.frame(x)
+  # make column names coherent and simplified
+  names(df) <- c("response")
+  # filter out NA values
+  df <- filter(df, !is.na(response))
+  # generate new dataframe with sums per category and sort in descending order
+  sums <- df %>%
+    dplyr::count(response, sort = TRUE) %>% 
+    dplyr::mutate(
+      response = forcats::fct_rev(forcats::fct_inorder(response))
+    )    
+  # add new column with percentages for each sum
+  sums <- sums %>% 
+    dplyr::mutate(perc = scales::percent(n / sum(n), accuracy = 1, trim = FALSE))
+}
+
+qualtrics_process_single_multiple_choice_unsorted_streamlined <- function(x) {
+  # create separate data frame
+  df <- as.data.frame(as_factor(x))
+  # make column names coherent and simplified
+  names(df) <- c("response")
+  # filter out NA values
+  df <- filter(df, !is.na(response))
+  # generate new dataframe with sums per category and sort in descending order
+  sums <- df %>%
+    dplyr::count(response, sort = FALSE) 
+  # add new column with percentages for each sum
+  sums <- sums %>% 
+    dplyr::mutate(perc = scales::percent(n / sum(n), accuracy = 1, trim = FALSE))
+}
+
+qualtrics_process_single_multiple_choice_basic <- function(x) {
+  # create separate data frame
+  df <- as_factor(x)
+  # make column names coherent and simplified
+  names(df) <- c("response")
+  # filter out NA values
+  df <- filter(df, !is.na(response))
+  # generate new dataframe with sums per category and sort in descending order
+  sums <- df %>%
+    dplyr::count(response, sort = FALSE) 
+  # add new column with percentages for each sum
+  sums <- sums %>% 
+    dplyr::mutate(perc = scales::percent(n / sum(n), accuracy = 1, trim = FALSE))
+}
+
+qualtrics_process_single_multiple_choice_unsorted <- function(x) {
+  # create separate data frame
+  df <- as.data.frame(x)
+  # make column names coherent and simplified
+  names(df) <- c("response")
+  # filter out NA values
+  df <- filter(df, !is.na(response))
+  # generate new dataframe with sums per category and sort in descending order
+  sums <- df %>%
+    dplyr::count(response, sort = FALSE) %>% 
+    dplyr::mutate(
+      response = forcats::fct_rev(forcats::fct_inorder(response))
+    )    
+  # add new column with percentages for each sum
+  sums <- sums %>% 
+    dplyr::mutate(perc = scales::percent(n / sum(n), accuracy = 1, trim = FALSE))
+}
+
+# function to produce a summary table of results for a single column using flextable
+
+chart_single_result_flextable <- function(.data, var) {
+  table <- table(.data)
+  # add calculations and convert to a flextable object
+  table %>%
+    prop.table %>% # turn this into a table of proportions
+    # flextable requires a dataframe
+    as.data.frame() %>%
+    set_names(c("Variable", "Count")) %>%
+    # arrange in descending order
+    arrange({{ var }}) %>%
+    # convert table object to a flextable()
+    flextable(defaults = TRUE) %>%
+    # adjust column widths automatically to fit widest values
+    style(part = 'body', pr_t=fp_text(font.family='Roboto')) %>%
+    style(part = 'header', pr_t=fp_text(font.family='Roboto')) %>%
+    # note, likert also uses set_caption() so need to specify flextable:: here
+    flextable::set_caption(caption, style = "Table Caption", autonum = run_autonum(seq_id = "tab", bkm = "figures", bkm_all = TRUE)) %>%
+    autofit() %>%
+    theme_vanilla() %>%
+    # format numbers in count column as rounded percentages
+    set_formatter( table, Count = function(x) sprintf( "%.1f%%", x*100 ))
+}
+
+chart_single_result_flextable_unsorted <- function(.data, var) {
+  table <- table(.data)
+  # add calculations and convert to a flextable object
+  table %>%
+    prop.table %>% # turn this into a table of proportions
+    # flextable requires a dataframe
+    as.data.frame() %>%
+    set_names(c("Variable", "Count")) %>%
+    # convert table object to a flextable()
+    flextable(defaults = TRUE) %>%
+    # adjust column widths automatically to fit widest values
+    style(part = 'body', pr_t=fp_text(font.family='Roboto')) %>%
+    style(part = 'header', pr_t=fp_text(font.family='Roboto')) %>%
+    # note, likert also uses set_caption() so need to specify flextable:: here
+    flextable::set_caption(caption, style = "Table Caption", autonum = run_autonum(seq_id = "tab", bkm = "figures", bkm_all = TRUE)) %>%
+    autofit() %>%
+    theme_vanilla() %>%
+    # format numbers in count column as rounded percentages
+    set_formatter( table, Count = function(x) sprintf( "%.1f%%", x*100 ))
+}
+```

hacking_religion/chapter_2.qmd

@@ -27,6 +27,21 @@ The first thing to note here is that we've drawn in a different type of data fil
 
 One of the challenges we faced when running this study is how to gather responsible data from surveys regarding religious identity. We'll dive into this in depth as we do analysis and look at some of the agreements and conflicts in terms of respondent attribution. Just to set the stage, we used the following kinds of question to ask about religion and spirituality:
 
+::: {.callout-tip}
+### What is Religion?
+
+Breakout box about beliefs in the paranormal:
+
+World Values survey - cf. paranormal belief breakdown by generation analysis by Bobby Duffy (KCL)
+God heaven hell afterlife
+
+Draw on European 
+
+Theos, Faith of the Faithless Report (2012)
+:::
+
+
+
 
 ### "What is your religion?"
 

hacking_religion/index.qmd

@@ -7,9 +7,9 @@ Data science is quickly consolidating as a new field, with new tools and user co
 
 ## The hacker way
 
-It's worth emphasising at the outset that this isn't meant to be a generic data science book. My own training as a researcher lies in the field of religious ethics, and my engagement with digital technology has, from the very start, been a context for exploring matters of personal values, and social action. A fair bit of ink has been spilled in books, magazines, blogs, zines, and tweets unpacking what exactly it means to be a "hacker". Pressing beyond some of the more superficial cultural stereotypes, I want to explain a bit here about how hacking can be a much more substantial vision for ethical engagement with technology and social transformation. 
+It's worth emphasising at the outset that this isn't meant to be a generic data science book. My own training as a researcher lies in the field of religious ethics, and my engagement with digital technology has, from the very start, been a context for exploring matters of personal values, and social action. A fair bit of ink has been spilled in books, magazines, blogs and zines unpacking what exactly it means to be a "hacker". Pressing beyond some of the more superficial cultural stereotypes, I want to explain a bit here about how hacking can be a much more substantial vision for ethical engagement with technology and social transformation.
 
-Back in the 1980s Steven Levy tried to capture some of this in his book "Hackers: Heroes of the Computer Revolution". As Levy put it, the "hacker ethic" included: (1) sharing, (2) openness, (3) decentralisation, (4) free access to computers and (5) world improvement. The key point here is that hacking isn't just about writing and breaking code, or testing and finding weaknesses in computer systems and networks. It can be a more substantial ethical code.
+Back in the 1980s Steven Levy tried to capture some of this in his book "Hackers: Heroes of the Computer Revolution". As Levy put it, the "hacker ethic" included: (1) sharing, (2) openness, (3) decentralisation, (4) free access to computers and (5) world improvement. The key point here is that hacking isn't just about writing and breaking code, or testing and finding weaknesses in computer systems and networks. There is often a more substantial underpinning ethical code which dovetails with on-the-surface matters of curiosity and craft.
 
 This emphasis on ethics is especially important when we're doing data science because this kind of research work will put you in positions of influence and grant you power over others. You might think this seems a bit overstated, but it never ceases to amaze me how much bringing a bar chart which succinctly shows some sort of social trend can sway a conversation or decision making process. There is something unusually persuasive that comes with the combination of aesthetics, data and storytelling. I've met many people who have come to data science out of a desire to bring about social transformation in some sphere of life. People want to use technology and communication to make the world better. However, it's possible that this can quickly get out of hand. It's important to have a clear sense of what sorts of convictions guide your work in this field, a "hacker code" of sorts. With this in mind, I'd like to share with you my own set of principles: