Setup

Overview

See the “Code and logs” tab for, well, the code and logs.

Code and logs

###-----------------------------------------------------------------------------
### Setting paths and datafile name
###-----------------------------------------------------------------------------

basePath <- here::here();

### NOTE: until we add in the data, the repo isn't portable anyway,
###       so we might as well get the existing data from the old repo.

dataPath <- normalizePath(file.path(basePath, "..", "coronapreppers", "data"));

figureDataPath <- file.path(basePath, "figure_data");
metadataPath <- file.path(basePath, "metadata");
outputPath <- file.path(basePath, "images");

dataFilename <- "shield_gjames_21-09-20.csv";

###-----------------------------------------------------------------------------
### Setting URLs and column names
###-----------------------------------------------------------------------------

questionLabels_sheetURL <-
  "https://docs.google.com/spreadsheets/d/1BEX4W8XRGnuDk4Asa_pdKij3EIZBvhSPqHxFrDjM07k";

questionLabels_varNameCol <- "New variable name";
questionLabels_leftAnchorCol <- "English lo-anchor";
questionLabels_rightAnchorCol <- "English hi-anchor";
questionLabels_labelCol <- "Label short"; # "Label";
questionLabels_labelCol <- "Item english translation"; # "Label";

###-----------------------------------------------------------------------------
### Load data
###-----------------------------------------------------------------------------

#df <- read.csv("data/shield_gjames_21-06-10.csv")

### James: refactored a bit using paths defined above and to
### make this platform-independent
df <- df.raw <- read.csv(
  file.path(
    dataPath,
    dataFilename
  )
);

###-----------------------------------------------------------------------------
### Create new composite measure of intention and behavior
###-----------------------------------------------------------------------------

intentionVars <-
  grep("^intention_", names(df), value=TRUE);

### Note: intention response options are:
###   1 = I will wear a mask all the time
###   2 = I'm going to wear a mask part of the time
###   3 = I'm not going to wear a mask
###   4 = I'm not going to go at all
###
### We recode these so that the new categories reflect the
### risk due to potential unmasked exposure to SARS-CoV-2:
###   1 -> 0
###   2 -> 1
###   3 -> 2
###   4 -> 0

for (currentIntentionVar in intentionVars) {
  df[, paste0(currentIntentionVar, "_recoded")] <-
    ifelse(
      df[, currentIntentionVar] == 4,
      0,
      df[, currentIntentionVar] - 1
    );
}

df$intention_composite <-
  rowSums(df[, paste0(intentionVars, "_recoded")]);

### Behavior

behaviorVars <-
  grep("^behaviour_", names(df), value=TRUE);

behaviorVars_selected <-
  grep("indoors|unmasked", behaviorVars, value=TRUE);

### For these two behavior measures, the response
### options are different:
###
###   behaviour_indoors_nonhouseholders:
###     1 = Several times a day
###     2 = Every day
###     3 = 5-6 days
###     4 = 3-4 days
###     5 = 1-2 days
###     6 = Not at all
###
###   behaviour_unmasked:
###     1 = Every day
###     5-6 days
###     3-4 days
###     1-2 days
###     not at all
###
### These are recoded to ~ represent, respectively,
### 'mask wearing opportunities' and 'risk events'.

maskWearingOpportunities_recodingVector <-
  c(14/7, 1, 5.5/7, 3.5/7, 1.5/7, 0);

df[, paste0(behaviorVars_selected[1], "_recoded")] <-
  maskWearingOpportunities_recodingVector[
    df[, behaviorVars_selected[1]]
  ];

riskEvents_recodingVector <-
  c(1, 5.5/7, 3.5/7, 1.5/7, 0);

df[, paste0(behaviorVars_selected[2], "_recoded")] <-
  riskEvents_recodingVector[
    df[, behaviorVars_selected[2]]
  ];

df$behavior_composite <-
  df[, paste0(behaviorVars_selected[1], "_recoded")] *
  df[, paste0(behaviorVars_selected[2], "_recoded")];

df$behavior_composite_recoded <-
  df$behavior_composite * 5;

df$intention_behavior_composite <-
  rowMeans(
    df[,
       c('intention_composite',
         'behavior_composite_recoded')
      ],
    na.rm = TRUE);

### Invert the final measure so that higher scores represent the desirable
### behavior instead of the other way around.
df$intention_behavior_composite <-
  max(df$intention_behavior_composite, na.rm=TRUE) - 
  df$intention_behavior_composite;

###-----------------------------------------------------------------------------
### We now have two variables: a behavior composite that represents in which
### proportion of the situations where mask-wearing was the desirable behavior
### participants wore masks; and an intention-behavior composite, where this
### variable is averaged with intention.
###-----------------------------------------------------------------------------

### Use regular expressions to select variables:
###  - the | means "or";
###  - the ^ means "start of the text string"

determinantVars <- list(
  continuous =
    grep(
      
      ### We don't want intention as a determinant
      ### Also, leave out the SDT items because they're part of
      ### another study, and not easy to interpret as determinants
      ### as thet may measure two things.
      #   "^intention|^automaticity|attitude|^norms|^risk|^effective|^sdt",
      
      "^automaticity|attitude|^norms|^risk|^effective",
      
      names(df),
      value=TRUE
    ),
  dichotomous =
    grep(
      "barriers",
      names(df),
      value=TRUE
    )
);

### Superseded
#behaviorVarName <- "behaviour_unmasked";

### Using the new composite behavior measure
behaviorVarName <- "intention_behavior_composite";

#behaviorVarName_dichotomized <- "behaviour_unmasked_bool"; ### Redundant now
#
### Create dichotomized behavior measure
# df[, behaviorVarName_dichotomized] <-
#   ifelse(df[, behaviorVarName] < 5,
#          0,
#          1);

### Verify that
# table(df[, behaviorVarName],
#       df[, behaviorVarName_dichotomized]);

###-----------------------------------------------------------------------------
### Create factors for age and education
###-----------------------------------------------------------------------------

df$demographic_educationType <-
  ifelse(
    df$demographic_higher_education,
    "Theoretical",
    "Practical"
  );

df$demographic_educationType <-
  factor(
    df$demographic_educationType,
    levels = c("Practical", "Theoretical"),
    labels = c("Practical", "Theoretical"),
    ordered = TRUE
  );

ageRecodingVector <-
  c("18-29" = "Younger than 40",
    "30-39" = "Younger than 40",
    "40-49" = "40 to 59",
    "50-59" = "40 to 59",
    "60+" = "60 or older");

df$demographic_ageGroups <-
  ageRecodingVector[
    df$demographic_age
  ];

df$demographic_ageGroups <-
  factor(
    df$demographic_ageGroups,
    levels = unique(ageRecodingVector),
    labels = unique(ageRecodingVector),
    ordered=TRUE
  );

### Verify recoding

table(df$demographic_higher_education,
      df$demographic_educationType);

##    
##     Practical Theoretical
##   0      1219           0
##   1         0        1053

table(df$demographic_age,
      df$demographic_ageGroups);

##        
##         Younger than 40 40 to 59 60 or older
##   18-29             395        0           0
##   30-39             354        0           0
##   40-49               0      416           0
##   50-59               0      379           0
##   60+                 0        0         728

### For convenience later on
ageGroups <- levels(df$demographic_ageGroups);
eduGroups <- levels(df$demographic_educationType);

###-----------------------------------------------------------------------------
### Export processed data
###-----------------------------------------------------------------------------

write.csv(
  df,
  file = file.path(
    dataPath,
    "data--preprocessed-for-CIBER.csv"
  )
);

###-----------------------------------------------------------------------------
### Load labels, store local backup, prepare vectors
###-----------------------------------------------------------------------------

questionLabels_localBackupFilename <-
  file.path(metadataPath, "questionLabels.xlsx");

### Use tryCatch in case we're offline
tryCatch({
  
  googlesheets4::gs4_deauth();
  
  questionLabelDf <-
    as.data.frame(
      googlesheets4::read_sheet(questionLabels_sheetURL)
    );
  
  ### Store local backup in case we're offline next time and so that it
  ### gets archived along with the rest if we freeze an OSF registration
  openxlsx::write.xlsx(
    questionLabelDf,
    questionLabels_localBackupFilename,
    overwrite = TRUE
  );
  
}, error = function(e) {
  
  ### We're probably offline; try reading local copy, otherwise throw error
  if (file.exists(questionLabels_localBackupFilename)) {
    questionLabelDf <-
      openxlsx::read.xlsx(
        questionLabels_localBackupFilename
      );
  } else {
    stop("I cannot read the google sheet with the question labels, nor ",
         "do I manage to read the spreadsheet from the local backup file.");
  }
  
});

## v Reading from "Citizen Shield notes".

## v Range 'Variable names'.

## New names:
## * `` -> ...18
## * `` -> ...19
## * `` -> ...20
## * `` -> ...21
## * `` -> ...22

###-----------------------------------------------------------------------------
### Create vectors
###-----------------------------------------------------------------------------

questionLabels <-
  stats::setNames(
    questionLabelDf[, questionLabels_labelCol],
    nm = questionLabelDf[, questionLabels_varNameCol]
  );

leftAnchors <-
  stats::setNames(
    questionLabelDf[, questionLabels_leftAnchorCol],
    nm = questionLabelDf[, questionLabels_varNameCol]
  );

rightAnchors <-
  stats::setNames(
    questionLabelDf[, questionLabels_rightAnchorCol],
    nm = questionLabelDf[, questionLabels_varNameCol]
  );

###-----------------------------------------------------------------------------
### Wrap vectors with labels
###-----------------------------------------------------------------------------

questionLabel_maxWidth <- 60;
anchors_maxWidth <- 20;

wrapVector <- function(x, width) {
  res <-
    unlist(
      lapply(
        strwrap(x, width = width, simplify = FALSE),
        paste,
        collapse = "\n"
      )
    );
  names(res) <- names(x);
  return(res);
}

questionLabels_wrapped <-
  wrapVector(questionLabels, questionLabel_maxWidth);

# questionLabels_wrapped <- questionLabels <-
#   stats::setNames(determinantVars$continuous,
#                   nm=determinantVars$continuous);

leftAnchors_wrapped <-
  wrapVector(leftAnchors, anchors_maxWidth);

rightAnchors_wrapped <-
  wrapVector(rightAnchors, anchors_maxWidth);

fullLabels <-
  stats::setNames(
    wrapVector(
      paste0(
        questionLabels,
        " [ ",
        leftAnchors[names(questionLabels)],
        " | ",
        rightAnchors[names(questionLabels)],
        " ]"
      ),
      questionLabel_maxWidth
    ),
    nm = names(questionLabels)
  );

CIBER plots

Full sample

### No longer necessary, set-up now happens above and distinguishes
### continuous and dichotomous variables

# tmp <- df %>%
#   select(-behaviour_unmasked_bool, -behaviour_unmasked, -id, -demographic_age) %>%
#   as.data.frame()
# 
# determinants_list <- colnames(tmp)

### Rescale variables to 0-1 --- note that the way this is done now
### assumes that the scale max is observed at least once. If that
### assumption doesn't hold, we may want to extract the scale max
### values from the google sheet with the labels.
df[, determinantVars$continuous] <-
  lapply(
    df[, determinantVars$continuous],
    function(x) {
      return((x - 1) / (max(x, na.rm=TRUE) - 1));
    }
  );

ciberJitterWidth <- floor(100*1/7) / 100;

CIBERplots <- list();

CIBERplots$fullSample <-
  behaviorchange::CIBER(
    data=df,
    determinants = determinantVars$continuous,
    targets = behaviorVarName,
    orderBy = behaviorVarName,
    titleVarLabels = stats::setNames("mask wearing", nm=behaviorVarName),
    titleSuffix = "(full sample)",
    subQuestions = questionLabels_wrapped[determinantVars$continuous],
    leftAnchors = leftAnchors_wrapped[determinantVars$continuous],
    rightAnchors = rightAnchors_wrapped[determinantVars$continuous],
    jitterWidth = ciberJitterWidth,
    drawPlot = FALSE,
    returnPlotOnly = FALSE
  );

ufs::knitAndSave(
  CIBERplots$fullSample$output$plot,
  figCaption = paste0("CIBER plot for the full sample."),
  path = outputPath,
  figWidth = attr(CIBERplots$fullSample$output$plot, "width"),
  figHeight = attr(CIBERplots$fullSample$output$plot, "height"),
);

## Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments

CIBER plot for the full sample.

selectedDeterminants <-
  c("automaticity_carry_mask",
    "automaticity_put_on_mask",
    "effective_means_masks",
    "effective_means_distance",
    "inst_attitude_protects_others",
    "norms_family_friends",
    "norms_officials",
    "aff_attitude_difficult_breathing",
    "risk_fear_restrictions")

CIBERplot_fullSample_selection <-
  behaviorchange::CIBER(
    data=df,
    determinants = selectedDeterminants,
    targets = behaviorVarName,
    orderBy = behaviorVarName,
    titleVarLabels = stats::setNames("mask wearing", nm=behaviorVarName),
    titleSuffix = "(full sample, selection)",
    subQuestions = questionLabels_wrapped[selectedDeterminants],
    leftAnchors = leftAnchors_wrapped[selectedDeterminants],
    rightAnchors = rightAnchors_wrapped[selectedDeterminants],
    jitterWidth = ciberJitterWidth,
    drawPlot = FALSE,
    returnPlotOnly = FALSE,
    xbreaks = c(0, .2, .4, .6, .8, 1)
  );

ufs::knitAndSave(
  CIBERplot_fullSample_selection$output$plot,
  figCaption = paste0("CIBER plot for the full sample (selection)."),
  path = outputPath,
  figWidth = attr(CIBERplot_fullSample_selection$output$plot, "width"),
  figHeight = attr(CIBERplot_fullSample_selection$output$plot, "height"),
);

## Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments

CIBER plot for the full sample (selection).

### Age

for (currentAgeGroup in levels(df$demographic_ageGroups)) {
  
  ufs::heading(currentAgeGroup,
               headingLevel = 2);

  CIBERplots[[currentAgeGroup]] <-
    behaviorchange::CIBER(
      data = df[df$demographic_ageGroups == currentAgeGroup, ],
      determinants = determinantVars$continuous,
      targets = behaviorVarName,
      orderBy = behaviorVarName,
      titleVarLabels = stats::setNames("mask wearing", nm=behaviorVarName),
      titleSuffix = paste0("(", currentAgeGroup, ")"),
      subQuestions = questionLabels_wrapped[determinantVars$continuous],
      leftAnchors = leftAnchors_wrapped[determinantVars$continuous],
      rightAnchors = rightAnchors_wrapped[determinantVars$continuous],
      jitterWidth = ciberJitterWidth,
      drawPlot = FALSE,
      returnPlotOnly = FALSE
    );

  ### Use `cat` as R inhibits output in for-loops
  cat(
    ufs::knitAndSave(
      CIBERplots[[currentAgeGroup]]$output$plot,
      figCaption = paste0("CIBER plot for age group: ", currentAgeGroup, "."),
      path = outputPath,
      figWidth = attr(CIBERplots[[currentAgeGroup]]$output$plot, "width"),
      figHeight = attr(CIBERplots[[currentAgeGroup]]$output$plot, "height"),
    )
  );
  
}

Younger than 40

## Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments

CIBER plot for age group: Younger than 40.

40 to 59

## Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments

CIBER plot for age group: 40 to 59.

60 or older

## Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments

CIBER plot for age group: 60 or older.

### Education

for (currentEduGroup in levels(df$demographic_educationType)) {
    
  ufs::heading(currentEduGroup,
               headingLevel = 2);

  CIBERplots[[currentEduGroup]] <-
    behaviorchange::CIBER(
      data = df[df$demographic_educationType == currentEduGroup, ],
      determinants = determinantVars$continuous,
      targets = behaviorVarName,
      orderBy = behaviorVarName,
      titleVarLabels = stats::setNames("mask wearing", nm=behaviorVarName),
      titleSuffix = paste0("(", currentEduGroup, ")"),
      subQuestions = questionLabels_wrapped[determinantVars$continuous],
      leftAnchors = leftAnchors_wrapped[determinantVars$continuous],
      rightAnchors = rightAnchors_wrapped[determinantVars$continuous],
      jitterWidth = ciberJitterWidth,
      drawPlot = FALSE,
      returnPlotOnly = FALSE
    );

  ### Use `cat` as R inhibits output in for-loops
  cat(
    ufs::knitAndSave(
      CIBERplots[[currentEduGroup]]$output$plot,
      figCaption = paste0("CIBER plot for education group: ", currentEduGroup, "."),
      path = outputPath,
      figWidth = attr(CIBERplots[[currentEduGroup]]$output$plot, "width"),
      figHeight = attr(CIBERplots[[currentEduGroup]]$output$plot, "height"),
    )
  );
 
}

Practical

## Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments

CIBER plot for education group: Practical.

Theoretical

## Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments

CIBER plot for education group: Theoretical.

Potential for Change Indices

Note: until we standardize the scales, these are incomparable, as they use the ‘room for improvement’ which is scale-dependent (i.e. it will always be smaller for a dichotomous variable).

Full sample

df_standardized <- df;

df_standardized[, determinantVars$continuous] <-
  lapply(
    df_standardized[, determinantVars$continuous],
    function(x) {
      lowestObservation <- min(x, na.rm = TRUE);
      highestObservation <- max(x, na.rm = TRUE);
      return(
        (x - lowestObservation) / highestObservation
      );
    }
  );

dstList <- list();

dstList$fullSample <-
  behaviorchange::determinant_selection_table(
    data=df_standardized,
    determinants = determinantVars$continuous,
    determinantLabels =
      paste0(questionLabels_wrapped[determinantVars$continuous],
             " [ ",
             leftAnchors_wrapped[determinantVars$continuous],
             " | ",
             rightAnchors_wrapped[determinantVars$continuous],
             " ]"),
    target = behaviorVarName,
    sortBy = 6
  );

print(
  behaviorchange:::knit_print.determinantSelectionTable(
    dstList[['fullSample']],
    render_preview = FALSE
  )
);

## No viewer found, probably documenting or testing

Determinant Selection Table

(Sub-)determinant	Current	Upper bound	Weight	Potential for Change Index
When I use a face mask, I feel or would feel … [ Very uncomfortable \| Very comfortable ]	0.431	1	0.36	0.205
How likely do you think you would get a coronavirus infection in your free time in the next month if you did nothing to protect yourself from it? [ Very unlikely \| Very likely ]	0.421	1	0.326	0.188
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I produce unnecessary waste \| I do not produce unnecessary waste ]	0.511	1	0.361	0.176
Consequences of measures taken to prevent the spread of the coronavirus… [ Doesn’t scare me \| Scares me ]	0.401	1	-0.287	-0.172
The fact that I would get infected myself .. [ Doesn’t scare me \| Scares me ]	0.535	1	0.365	0.17
If you got a coronavirus infection, how serious a threat would you rate it to your health? [ Not serious at all \| Very serious ]	0.567	1	0.389	0.168
Spread of coronavirus… [ Doesn’t scare me \| Scares me ]	0.582	1	0.388	0.163
When I use a face mask, I feel or would feel … [ Very anxious \| Very calm ]	0.593	1	0.381	0.155
When I use a face mask, I feel or would feel … [ Very insecure \| Very safe ]	0.66	1	0.413	0.141
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I get enough oxygen \| I don’t get enough oxygen ]	0.592	1	0.335	0.137
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ It decreases sense of community \| It increases sense of community ]	0.621	1	0.33	0.125
Taking a mask with you to a store or public transport, for example, has already become automatic for some and is done without thinking. For others, taking a mask with them is not automatic at all, but requires conscious thinking and effort. [ 1 Not at all automatic \| 7 Fully automatic ]	0.761	1	0.521	0.125
Using a face mask [ Ineffective \| Effective ]	0.776	1	0.52	0.117
Putting on a mask, for example in a shop or on public transport, has already become automatic for some and it happens without thinking. For others, putting on a mask is not automatic at all, but requires conscious thinking and effort. [ 1 Not at all automatic \| 7 Fully automatic ]	0.781	1	0.528	0.116
When I use a face mask, I feel or would feel … [ Very easy to breathe \| Very difficult to breathe ]	0.54	1	-0.248	-0.114
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I expose myself to coronavirus infection \| I protect myself from coronavirus infection ]	0.734	1	0.385	0.102
That my loved one would get infected… [ Doesn’t scare me \| Scares me ]	0.72	1	0.356	0.1
In the indoors spaces I visit, people on the site think I should… [ Not to use a mask \| Use a mask ]	0.802	1	0.476	0.094
When I use a face mask, I feel or would feel … [ Very irresponsible \| Very responsible ]	0.804	1	0.46	0.09
Who thinks you should use a face mask and who thinks not? In the following questions, by using a face mask, we mean holding a cloth or disposable face mask, surgical mask, or respirator on the face so that it covers the nose and mouth. The questions concern leisure time. My family and friends think I should .. [ Not to use a mask \| Use a mask ]	0.82	1	0.473	0.085
How likely do you think you will get a coronavirus infection in your free time in the next month? [ Very unlikely \| Very likely ]	0.187	1	0.085	0.069
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I expose others to coronavirus infection \| I protect others from coronavirus infection ]	0.863	1	0.477	0.066
Keeping a safety distance (2 meters) [ Ineffective \| Effective ]	0.826	1	0.358	0.062
Ventilation [ Ineffective \| Effective ]	0.754	1	0.239	0.059
People at risk think I should .. [ Not to use a mask \| Use a mask ]	0.889	1	0.398	0.044
If two unvaccinated people from different households meet indoors, what means do you think would be effective in preventing coronavirus infection? Hand washing and use of gloves [ Ineffective \| Effective ]	0.851	1	0.193	0.029
The authorities think I should .. [ Not to use a mask \| Use a mask ]	0.918	1	0.323	0.027

### Age

for (currentAgeGroup in levels(df$demographic_ageGroups)) {
  
  ufs::heading(currentAgeGroup,
               headingLevel = 2);

  dstList[[currentAgeGroup]] <-
    behaviorchange::determinant_selection_table(
      data=df_standardized[
        df_standardized$demographic_ageGroups == currentAgeGroup,
      ],
      determinants = determinantVars$continuous,
      determinantLabels =
        paste0(questionLabels_wrapped[determinantVars$continuous],
               " [ ",
               leftAnchors_wrapped[determinantVars$continuous],
               " | ",
               rightAnchors_wrapped[determinantVars$continuous],
               " ]"),
      target = behaviorVarName,
      sortBy = 6,
      headingLevel = 3
    );
      
  print(
    behaviorchange:::knit_print.determinantSelectionTable(
      dstList[[currentAgeGroup]],
      render_preview = FALSE
    )
  );

}

Younger than 40

## No viewer found, probably documenting or testing

Determinant Selection Table

(Sub-)determinant	Current	Upper bound	Weight	Potential for Change Index
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I produce unnecessary waste \| I do not produce unnecessary waste ]	0.405	1	0.38	0.227
When I use a face mask, I feel or would feel … [ Very uncomfortable \| Very comfortable ]	0.426	1	0.361	0.208
If you got a coronavirus infection, how serious a threat would you rate it to your health? [ Not serious at all \| Very serious ]	0.402	1	0.334	0.199
Spread of coronavirus… [ Doesn’t scare me \| Scares me ]	0.533	1	0.408	0.19
The fact that I would get infected myself .. [ Doesn’t scare me \| Scares me ]	0.447	1	0.342	0.189
When I use a face mask, I feel or would feel … [ Very anxious \| Very calm ]	0.559	1	0.396	0.175
How likely do you think you would get a coronavirus infection in your free time in the next month if you did nothing to protect yourself from it? [ Very unlikely \| Very likely ]	0.416	0.857	0.385	0.17
Taking a mask with you to a store or public transport, for example, has already become automatic for some and is done without thinking. For others, taking a mask with them is not automatic at all, but requires conscious thinking and effort. [ 1 Not at all automatic \| 7 Fully automatic ]	0.686	1	0.521	0.164
When I use a face mask, I feel or would feel … [ Very insecure \| Very safe ]	0.623	1	0.421	0.159
Consequences of measures taken to prevent the spread of the coronavirus… [ Doesn’t scare me \| Scares me ]	0.457	1	-0.284	-0.154
Putting on a mask, for example in a shop or on public transport, has already become automatic for some and it happens without thinking. For others, putting on a mask is not automatic at all, but requires conscious thinking and effort. [ 1 Not at all automatic \| 7 Fully automatic ]	0.725	1	0.549	0.151
Using a face mask [ Ineffective \| Effective ]	0.698	1	0.495	0.149
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I get enough oxygen \| I don’t get enough oxygen ]	0.581	1	0.351	0.147
When I use a face mask, I feel or would feel … [ Very easy to breathe \| Very difficult to breathe ]	0.523	1	-0.293	-0.14
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ It decreases sense of community \| It increases sense of community ]	0.612	1	0.346	0.134
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I expose myself to coronavirus infection \| I protect myself from coronavirus infection ]	0.67	1	0.351	0.116
That my loved one would get infected… [ Doesn’t scare me \| Scares me ]	0.707	1	0.393	0.115
When I use a face mask, I feel or would feel … [ Very irresponsible \| Very responsible ]	0.769	1	0.471	0.109
In the indoors spaces I visit, people on the site think I should… [ Not to use a mask \| Use a mask ]	0.748	1	0.43	0.108
How likely do you think you will get a coronavirus infection in your free time in the next month? [ Very unlikely \| Very likely ]	0.204	0.857	0.164	0.107
Who thinks you should use a face mask and who thinks not? In the following questions, by using a face mask, we mean holding a cloth or disposable face mask, surgical mask, or respirator on the face so that it covers the nose and mouth. The questions concern leisure time. My family and friends think I should .. [ Not to use a mask \| Use a mask ]	0.794	1	0.484	0.1
Keeping a safety distance (2 meters) [ Ineffective \| Effective ]	0.769	1	0.351	0.081
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I expose others to coronavirus infection \| I protect others from coronavirus infection ]	0.85	1	0.533	0.08
Ventilation [ Ineffective \| Effective ]	0.713	1	0.199	0.057
People at risk think I should .. [ Not to use a mask \| Use a mask ]	0.867	1	0.358	0.048
The authorities think I should .. [ Not to use a mask \| Use a mask ]	0.924	1	0.315	0.024
If two unvaccinated people from different households meet indoors, what means do you think would be effective in preventing coronavirus infection? Hand washing and use of gloves [ Ineffective \| Effective ]	0.82	1	0.11	0.02

40 to 59

## No viewer found, probably documenting or testing

Determinant Selection Table

(Sub-)determinant	Current	Upper bound	Weight	Potential for Change Index
When I use a face mask, I feel or would feel … [ Very uncomfortable \| Very comfortable ]	0.41	1	0.402	0.237
How likely do you think you would get a coronavirus infection in your free time in the next month if you did nothing to protect yourself from it? [ Very unlikely \| Very likely ]	0.425	1	0.337	0.193
Consequences of measures taken to prevent the spread of the coronavirus… [ Doesn’t scare me \| Scares me ]	0.404	1	-0.279	-0.166
The fact that I would get infected myself .. [ Doesn’t scare me \| Scares me ]	0.542	1	0.361	0.165
Spread of coronavirus… [ Doesn’t scare me \| Scares me ]	0.578	1	0.384	0.162
When I use a face mask, I feel or would feel … [ Very anxious \| Very calm ]	0.592	1	0.386	0.157
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I produce unnecessary waste \| I do not produce unnecessary waste ]	0.485	1	0.3	0.154
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I get enough oxygen \| I don’t get enough oxygen ]	0.574	1	0.361	0.154
When I use a face mask, I feel or would feel … [ Very insecure \| Very safe ]	0.648	1	0.399	0.141
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ It decreases sense of community \| It increases sense of community ]	0.614	1	0.355	0.137
If you got a coronavirus infection, how serious a threat would you rate it to your health? [ Not serious at all \| Very serious ]	0.578	1	0.31	0.131
When I use a face mask, I feel or would feel … [ Very easy to breathe \| Very difficult to breathe ]	0.562	1	-0.273	-0.12
Taking a mask with you to a store or public transport, for example, has already become automatic for some and is done without thinking. For others, taking a mask with them is not automatic at all, but requires conscious thinking and effort. [ 1 Not at all automatic \| 7 Fully automatic ]	0.764	1	0.492	0.116
That my loved one would get infected… [ Doesn’t scare me \| Scares me ]	0.705	1	0.389	0.115
Using a face mask [ Ineffective \| Effective ]	0.774	1	0.505	0.114
Putting on a mask, for example in a shop or on public transport, has already become automatic for some and it happens without thinking. For others, putting on a mask is not automatic at all, but requires conscious thinking and effort. [ 1 Not at all automatic \| 7 Fully automatic ]	0.784	1	0.521	0.113
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I expose myself to coronavirus infection \| I protect myself from coronavirus infection ]	0.739	1	0.395	0.103
In the indoors spaces I visit, people on the site think I should… [ Not to use a mask \| Use a mask ]	0.795	1	0.465	0.095
Who thinks you should use a face mask and who thinks not? In the following questions, by using a face mask, we mean holding a cloth or disposable face mask, surgical mask, or respirator on the face so that it covers the nose and mouth. The questions concern leisure time. My family and friends think I should .. [ Not to use a mask \| Use a mask ]	0.809	1	0.481	0.092
When I use a face mask, I feel or would feel … [ Very irresponsible \| Very responsible ]	0.797	1	0.44	0.089
How likely do you think you will get a coronavirus infection in your free time in the next month? [ Very unlikely \| Very likely ]	0.197	1	0.087	0.07
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I expose others to coronavirus infection \| I protect others from coronavirus infection ]	0.86	1	0.471	0.066
Keeping a safety distance (2 meters) [ Ineffective \| Effective ]	0.814	1	0.315	0.059
Ventilation [ Ineffective \| Effective ]	0.746	1	0.225	0.057
People at risk think I should .. [ Not to use a mask \| Use a mask ]	0.885	1	0.402	0.046
If two unvaccinated people from different households meet indoors, what means do you think would be effective in preventing coronavirus infection? Hand washing and use of gloves [ Ineffective \| Effective ]	0.843	1	0.189	0.03
The authorities think I should .. [ Not to use a mask \| Use a mask ]	0.913	1	0.317	0.027

60 or older

## No viewer found, probably documenting or testing

Determinant Selection Table

(Sub-)determinant	Current	Upper bound	Weight	Potential for Change Index
When I use a face mask, I feel or would feel … [ Very uncomfortable \| Very comfortable ]	0.46	1	0.319	0.172
How likely do you think you would get a coronavirus infection in your free time in the next month if you did nothing to protect yourself from it? [ Very unlikely \| Very likely ]	0.422	1	0.275	0.159
Consequences of measures taken to prevent the spread of the coronavirus… [ Doesn’t scare me \| Scares me ]	0.341	1	-0.206	-0.136
When I use a face mask, I feel or would feel … [ Very anxious \| Very calm ]	0.63	1	0.323	0.12
Spread of coronavirus… [ Doesn’t scare me \| Scares me ]	0.636	1	0.299	0.109
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ It decreases sense of community \| It increases sense of community ]	0.638	1	0.295	0.107
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I get enough oxygen \| I don’t get enough oxygen ]	0.624	1	0.283	0.106
When I use a face mask, I feel or would feel … [ Very easy to breathe \| Very difficult to breathe ]	0.534	1	-0.221	-0.103
When I use a face mask, I feel or would feel … [ Very insecure \| Very safe ]	0.711	1	0.354	0.102
The fact that I would get infected myself .. [ Doesn’t scare me \| Scares me ]	0.62	1	0.262	0.1
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I produce unnecessary waste \| I do not produce unnecessary waste ]	0.65	1	0.248	0.087
If you got a coronavirus infection, how serious a threat would you rate it to your health? [ Not serious at all \| Very serious ]	0.724	1	0.305	0.084
Taking a mask with you to a store or public transport, for example, has already become automatic for some and is done without thinking. For others, taking a mask with them is not automatic at all, but requires conscious thinking and effort. [ 1 Not at all automatic \| 7 Fully automatic ]	0.834	1	0.459	0.076
Putting on a mask, for example in a shop or on public transport, has already become automatic for some and it happens without thinking. For others, putting on a mask is not automatic at all, but requires conscious thinking and effort. [ 1 Not at all automatic \| 7 Fully automatic ]	0.836	1	0.434	0.071
Using a face mask [ Ineffective \| Effective ]	0.857	1	0.454	0.065
That my loved one would get infected… [ Doesn’t scare me \| Scares me ]	0.749	1	0.258	0.065
When I use a face mask, I feel or would feel … [ Very irresponsible \| Very responsible ]	0.846	1	0.419	0.064
In the indoors spaces I visit, people on the site think I should… [ Not to use a mask \| Use a mask ]	0.865	1	0.468	0.063
How likely do you think you will get a coronavirus infection in your free time in the next month? [ Very unlikely \| Very likely ]	0.159	0.857	0.09	0.063
Who thinks you should use a face mask and who thinks not? In the following questions, by using a face mask, we mean holding a cloth or disposable face mask, surgical mask, or respirator on the face so that it covers the nose and mouth. The questions concern leisure time. My family and friends think I should .. [ Not to use a mask \| Use a mask ]	0.859	1	0.423	0.06
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I expose myself to coronavirus infection \| I protect myself from coronavirus infection ]	0.796	1	0.291	0.059
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I expose others to coronavirus infection \| I protect others from coronavirus infection ]	0.879	1	0.415	0.05
Ventilation [ Ineffective \| Effective ]	0.806	1	0.214	0.042
The authorities think I should .. [ Not to use a mask \| Use a mask ]	0.916	1	0.424	0.036
People at risk think I should .. [ Not to use a mask \| Use a mask ]	0.918	1	0.418	0.034
Keeping a safety distance (2 meters) [ Ineffective \| Effective ]	0.899	1	0.265	0.027
If two unvaccinated people from different households meet indoors, what means do you think would be effective in preventing coronavirus infection? Hand washing and use of gloves [ Ineffective \| Effective ]	0.893	1	0.237	0.025

### Education

for (currentEduGroup in levels(df$demographic_educationType)) {
    
  ufs::heading(currentEduGroup,
               headingLevel = 2);

  dstList[[currentEduGroup]] <-
    behaviorchange::determinant_selection_table(
      data=df_standardized[
        df_standardized$demographic_educationType == currentEduGroup,
      ],
      determinants = determinantVars$continuous,
      determinantLabels =
        paste0(questionLabels_wrapped[determinantVars$continuous],
               " [ ",
               leftAnchors_wrapped[determinantVars$continuous],
               " | ",
               rightAnchors_wrapped[determinantVars$continuous],
               " ]"),
      target = behaviorVarName,
      sortBy = 6,
      headingLevel = 3
    );
  
  print(
    behaviorchange:::knit_print.determinantSelectionTable(
      dstList[[currentEduGroup]],
      render_preview = FALSE
    )
  );

}

Practical

## No viewer found, probably documenting or testing

Determinant Selection Table

(Sub-)determinant	Current	Upper bound	Weight	Potential for Change Index
When I use a face mask, I feel or would feel … [ Very uncomfortable \| Very comfortable ]	0.425	1	0.361	0.207
How likely do you think you would get a coronavirus infection in your free time in the next month if you did nothing to protect yourself from it? [ Very unlikely \| Very likely ]	0.418	1	0.339	0.197
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I produce unnecessary waste \| I do not produce unnecessary waste ]	0.52	1	0.378	0.181
The fact that I would get infected myself .. [ Doesn’t scare me \| Scares me ]	0.541	1	0.366	0.168
Spread of coronavirus… [ Doesn’t scare me \| Scares me ]	0.581	1	0.397	0.166
If you got a coronavirus infection, how serious a threat would you rate it to your health? [ Not serious at all \| Very serious ]	0.581	1	0.396	0.166
When I use a face mask, I feel or would feel … [ Very anxious \| Very calm ]	0.571	1	0.368	0.158
Consequences of measures taken to prevent the spread of the coronavirus… [ Doesn’t scare me \| Scares me ]	0.401	1	-0.259	-0.155
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I get enough oxygen \| I don’t get enough oxygen ]	0.572	1	0.343	0.147
When I use a face mask, I feel or would feel … [ Very insecure \| Very safe ]	0.662	1	0.399	0.135
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ It decreases sense of community \| It increases sense of community ]	0.625	1	0.351	0.132
Taking a mask with you to a store or public transport, for example, has already become automatic for some and is done without thinking. For others, taking a mask with them is not automatic at all, but requires conscious thinking and effort. [ 1 Not at all automatic \| 7 Fully automatic ]	0.753	1	0.527	0.13
Putting on a mask, for example in a shop or on public transport, has already become automatic for some and it happens without thinking. For others, putting on a mask is not automatic at all, but requires conscious thinking and effort. [ 1 Not at all automatic \| 7 Fully automatic ]	0.772	1	0.526	0.12
Using a face mask [ Ineffective \| Effective ]	0.773	1	0.513	0.117
When I use a face mask, I feel or would feel … [ Very easy to breathe \| Very difficult to breathe ]	0.557	1	-0.252	-0.112
That my loved one would get infected… [ Doesn’t scare me \| Scares me ]	0.719	1	0.364	0.102
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I expose myself to coronavirus infection \| I protect myself from coronavirus infection ]	0.732	1	0.378	0.101
In the indoors spaces I visit, people on the site think I should… [ Not to use a mask \| Use a mask ]	0.8	1	0.485	0.097
Who thinks you should use a face mask and who thinks not? In the following questions, by using a face mask, we mean holding a cloth or disposable face mask, surgical mask, or respirator on the face so that it covers the nose and mouth. The questions concern leisure time. My family and friends think I should .. [ Not to use a mask \| Use a mask ]	0.803	1	0.478	0.094
When I use a face mask, I feel or would feel … [ Very irresponsible \| Very responsible ]	0.801	1	0.468	0.093
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I expose others to coronavirus infection \| I protect others from coronavirus infection ]	0.853	1	0.478	0.07
Keeping a safety distance (2 meters) [ Ineffective \| Effective ]	0.818	1	0.383	0.07
How likely do you think you will get a coronavirus infection in your free time in the next month? [ Very unlikely \| Very likely ]	0.181	0.857	0.103	0.07
Ventilation [ Ineffective \| Effective ]	0.743	1	0.254	0.065
People at risk think I should .. [ Not to use a mask \| Use a mask ]	0.881	1	0.409	0.049
If two unvaccinated people from different households meet indoors, what means do you think would be effective in preventing coronavirus infection? Hand washing and use of gloves [ Ineffective \| Effective ]	0.86	1	0.243	0.034
The authorities think I should .. [ Not to use a mask \| Use a mask ]	0.912	1	0.346	0.031

Theoretical

## No viewer found, probably documenting or testing

Determinant Selection Table

(Sub-)determinant	Current	Upper bound	Weight	Potential for Change Index
When I use a face mask, I feel or would feel … [ Very uncomfortable \| Very comfortable ]	0.438	1	0.357	0.201
Consequences of measures taken to prevent the spread of the coronavirus… [ Doesn’t scare me \| Scares me ]	0.402	1	-0.325	-0.194
How likely do you think you would get a coronavirus infection in your free time in the next month if you did nothing to protect yourself from it? [ Very unlikely \| Very likely ]	0.424	1	0.307	0.177
If you got a coronavirus infection, how serious a threat would you rate it to your health? [ Not serious at all \| Very serious ]	0.55	1	0.386	0.174
The fact that I would get infected myself .. [ Doesn’t scare me \| Scares me ]	0.528	1	0.366	0.173
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I produce unnecessary waste \| I do not produce unnecessary waste ]	0.501	1	0.341	0.17
Spread of coronavirus… [ Doesn’t scare me \| Scares me ]	0.582	1	0.377	0.158
When I use a face mask, I feel or would feel … [ Very anxious \| Very calm ]	0.619	1	0.395	0.15
When I use a face mask, I feel or would feel … [ Very insecure \| Very safe ]	0.658	1	0.436	0.149
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I get enough oxygen \| I don’t get enough oxygen ]	0.615	1	0.323	0.124
Taking a mask with you to a store or public transport, for example, has already become automatic for some and is done without thinking. For others, taking a mask with them is not automatic at all, but requires conscious thinking and effort. [ 1 Not at all automatic \| 7 Fully automatic ]	0.769	1	0.511	0.118
Using a face mask [ Ineffective \| Effective ]	0.779	1	0.53	0.117
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ It decreases sense of community \| It increases sense of community ]	0.617	1	0.304	0.116
When I use a face mask, I feel or would feel … [ Very easy to breathe \| Very difficult to breathe ]	0.52	1	-0.24	-0.115
Putting on a mask, for example in a shop or on public transport, has already become automatic for some and it happens without thinking. For others, putting on a mask is not automatic at all, but requires conscious thinking and effort. [ 1 Not at all automatic \| 7 Fully automatic ]	0.791	1	0.53	0.111
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I expose myself to coronavirus infection \| I protect myself from coronavirus infection ]	0.737	1	0.394	0.104
That my loved one would get infected… [ Doesn’t scare me \| Scares me ]	0.721	1	0.347	0.097
In the indoors spaces I visit, people on the site think I should… [ Not to use a mask \| Use a mask ]	0.804	1	0.462	0.09
When I use a face mask, I feel or would feel … [ Very irresponsible \| Very responsible ]	0.807	1	0.449	0.087
Who thinks you should use a face mask and who thinks not? In the following questions, by using a face mask, we mean holding a cloth or disposable face mask, surgical mask, or respirator on the face so that it covers the nose and mouth. The questions concern leisure time. My family and friends think I should .. [ Not to use a mask \| Use a mask ]	0.839	1	0.464	0.075
What consequences do you think it has if you use a face mask in your free time? If or when I use a face mask… [ I expose others to coronavirus infection \| I protect others from coronavirus infection ]	0.874	1	0.474	0.06
Keeping a safety distance (2 meters) [ Ineffective \| Effective ]	0.837	1	0.321	0.052
Ventilation [ Ineffective \| Effective ]	0.768	1	0.215	0.05
How likely do you think you will get a coronavirus infection in your free time in the next month? [ Very unlikely \| Very likely ]	0.194	1	0.059	0.048
People at risk think I should .. [ Not to use a mask \| Use a mask ]	0.899	1	0.38	0.038
If two unvaccinated people from different households meet indoors, what means do you think would be effective in preventing coronavirus infection? Hand washing and use of gloves [ Ineffective \| Effective ]	0.841	1	0.138	0.022
The authorities think I should .. [ Not to use a mask \| Use a mask ]	0.925	1	0.289	0.022

for (sampleName in names(dstList)) {
  
  write.csv(
    dstList[[sampleName]],
    file.path(
      figureDataPath,
      paste0(
        "determinant-selection-table-",
        sampleName,
        ".csv")
      ),
    row.names = FALSE
  );
  
  ### CIBERplots has the same names
  tmpDf <- CIBERplots[[sampleName]]$intermediate$meansDat;
  names(tmpDf)[1:3] <- c("mean_ci_lo", "mean_point", "mean_ci_hi");
  row.names(tmpDf) <- tmpDf$label;
  tmpDf[tmpDf$label, c("r_ci_lo", "r_point", "r_ci_hi")] <-
    CIBERplots[[sampleName]]$intermediate$assocDat[[1]][tmpDf$label, ];
  tmpDf$fullLabel <-
    fullLabels[tmpDf$label];
  
  write.csv(
    tmpDf,
    file.path(
      figureDataPath,
      paste0(
        "CIBER-plot-data-",
        sampleName,
        ".csv")
      ),
    row.names = FALSE
  );
  
}

SHAP plots

sampleLabels <-
  c(
    fullSample = "Full sample",
    `Practical` = "Education: practical",
    `Theoretical` = "Education: theoretical",
    `Younger than 40` = "Age: 18-39",
    `40 to 59` = "Age: 40-59",
    `60 or older` = "Age: 60+"
  );

shapFilenames <-
  c(
    fullSample = file.path(figureDataPath,
                           "All_shap_real_values.csv"),
    `Practical` = file.path(figureDataPath,
                            "Lower_Education_shap_real_values.csv"),
    `Theoretical` = file.path(figureDataPath,
                              "Higher_Education_shap_real_values.csv"),
    `Younger than 40` = file.path(figureDataPath,
                                  "18 - 39_shap_real_values.csv"),
    `40 to 59` = file.path(figureDataPath,
                           "40 - 59_shap_real_values.csv"),
    `60 or older` = file.path(figureDataPath,
                              "60+_shap_real_values.csv")
  );

shapDfs <-
  stats::setNames(
    lapply(
      shapFilenames,
      read.csv
    ),
    names(shapFilenames)
  );

shapDfs <-
  lapply(
    shapDfs,
    function(currentDf) {
      currentDf$label <-
        fullLabels[currentDf$variable];
      ### Reverse order because ggplot plots from bottom to top on Y axis
      currentDf$label <-
        factor(
          currentDf$label,
          levels = rev(unique(fullLabels[currentDf$variable])),
          ordered = TRUE
        );
      ### Store actual_value as factor, too
      currentDf$actualValue_factor <-
        factor(
          currentDf$actual_value,
          levels = seq(min(currentDf$actual_value, na.rm=TRUE),
                       max(currentDf$actual_value, na.rm=TRUE)),
          ordered = TRUE
        );
      return(currentDf);
    }
  );

shapPlots <-
  stats::setNames(
    lapply(
      names(shapDfs),
      function(currentSample) {
        return(
          ggplot2::ggplot(
            data = shapDfs[[currentSample]],
            mapping = ggplot2::aes_string(
              x = "shap_value",
              y = "label",
              fill = "actualValue_factor",
              color = "actualValue_factor"
            )
          ) +
            ggbeeswarm::geom_beeswarm(
              size = 2,
              alpha = .66
            ) +
            ggplot2::theme_minimal() +
            ggplot2::labs(title = sampleLabels[currentSample],
                          x = "SHAP Value",
                          y = NULL,
                          fill = "Score",
                          color = "Score")
        );
      }
    ),
    nm = names(shapDfs)
  );

for (currentSample in names(shapPlots)) {
  ufs::heading(sampleLabels[currentSample],
               headingLevel = 2);
  cat(
    ufs::knitAndSave(
      shapPlots[[currentSample]],
      path = outputPath,
      figCaption = paste0("SHAP values for ", sampleLabels[currentSample]),
      figWidth = 9,
      figHeight = 14
    )
  );
}

Full sample

## Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments

## Warning in f(...): The default behavior of beeswarm has changed in version
## 0.6.0. In versions <0.6.0, this plot would have been dodged on the y-axis. In
## versions >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis.
## Please set grouponX=TRUE/FALSE to avoid this warning and ensure proper axis
## choice.

## Warning in f(...): The default behavior of beeswarm has changed in version
## 0.6.0. In versions <0.6.0, this plot would have been dodged on the y-axis. In
## versions >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis.
## Please set grouponX=TRUE/FALSE to avoid this warning and ensure proper axis
## choice.

## Warning in f(...): The default behavior of beeswarm has changed in version
## 0.6.0. In versions <0.6.0, this plot would have been dodged on the y-axis. In
## versions >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis.
## Please set grouponX=TRUE/FALSE to avoid this warning and ensure proper axis
## choice.

## Warning in f(...): The default behavior of beeswarm has changed in version
## 0.6.0. In versions <0.6.0, this plot would have been dodged on the y-axis. In
## versions >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis.
## Please set grouponX=TRUE/FALSE to avoid this warning and ensure proper axis
## choice.

SHAP values for Full sample.

Education: practical

## Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning in f(...): The default behavior of beeswarm has changed in version
## 0.6.0. In versions <0.6.0, this plot would have been dodged on the y-axis. In
## versions >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis.
## Please set grouponX=TRUE/FALSE to avoid this warning and ensure proper axis
## choice.

SHAP values for Education: practical.

Education: theoretical

## Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning in f(...): The default behavior of beeswarm has changed in version
## 0.6.0. In versions <0.6.0, this plot would have been dodged on the y-axis. In
## versions >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis.
## Please set grouponX=TRUE/FALSE to avoid this warning and ensure proper axis
## choice.

SHAP values for Education: theoretical.

Age: 18-39

## Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning in f(...): The default behavior of beeswarm has changed in version
## 0.6.0. In versions <0.6.0, this plot would have been dodged on the y-axis. In
## versions >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis.
## Please set grouponX=TRUE/FALSE to avoid this warning and ensure proper axis
## choice.

SHAP values for Age: 18-39.

Age: 40-59

## Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning in f(...): The default behavior of beeswarm has changed in version
## 0.6.0. In versions <0.6.0, this plot would have been dodged on the y-axis. In
## versions >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis.
## Please set grouponX=TRUE/FALSE to avoid this warning and ensure proper axis
## choice.

SHAP values for Age: 40-59.

Age: 60+

## Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning in f(...): The default behavior of beeswarm has changed in version
## 0.6.0. In versions <0.6.0, this plot would have been dodged on the y-axis. In
## versions >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis.
## Please set grouponX=TRUE/FALSE to avoid this warning and ensure proper axis
## choice.

SHAP values for Age: 60+.

Combined plots

widths <- c(.8, .2);
plotWidths = 12;
plotHeights = 13;

for (i in names(CIBERplots)) {

  ufs::heading(i, headingLevel = 2);
  
  ufs::knitAndSave(
    patchwork::wrap_plots(CIBERplots[[i]]$output$plot,
                          shapPlots[[i]],
                          widths = widths),
    path = outputPath,
    figCaption = paste0("Combined plots for ", i),
    figWidth = plotWidths,
    figHeight = plotHeights
  )
  
}

fullSample

## Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments

## Warning in f(...): The default behavior of beeswarm has changed in version
## 0.6.0. In versions <0.6.0, this plot would have been dodged on the y-axis. In
## versions >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis.
## Please set grouponX=TRUE/FALSE to avoid this warning and ensure proper axis
## choice.

## Warning in f(...): The default behavior of beeswarm has changed in version
## 0.6.0. In versions <0.6.0, this plot would have been dodged on the y-axis. In
## versions >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis.
## Please set grouponX=TRUE/FALSE to avoid this warning and ensure proper axis
## choice.

## Warning in f(...): The default behavior of beeswarm has changed in version
## 0.6.0. In versions <0.6.0, this plot would have been dodged on the y-axis. In
## versions >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis.
## Please set grouponX=TRUE/FALSE to avoid this warning and ensure proper axis
## choice.

Younger than 40

## Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

40 to 59

## Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

60 or older

## Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

Practical

## Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

Theoretical

## Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

## Warning: The default behavior of beeswarm has changed in version 0.6.0. In
## versions <0.6.0, this plot would have been dodged on the y-axis. In versions
## >=0.6.0, grouponX=FALSE must be explicitly set to group on y-axis. Please set
## grouponX=TRUE/FALSE to avoid this warning and ensure proper axis choice.

Session information

utils::sessionInfo();

## R version 4.1.2 (2021-11-01)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19042)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=English_United States.1252 
## [2] LC_CTYPE=English_United States.1252   
## [3] LC_MONETARY=English_United States.1252
## [4] LC_NUMERIC=C                          
## [5] LC_TIME=English_United States.1252    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.7           svglite_2.0.0        here_1.0.1          
##  [4] rprojroot_2.0.2      digest_0.6.28        utf8_1.2.2          
##  [7] R6_2.5.1             cellranger_1.1.0     evaluate_0.14       
## [10] httr_1.4.2           ggplot2_3.3.5        highr_0.9           
## [13] pillar_1.6.4         rlang_0.4.12         ufs_0.5.2           
## [16] googlesheets4_1.0.0  curl_4.3.2           rstudioapi_0.13     
## [19] jquerylib_0.1.4      rmarkdown_2.11       textshaping_0.3.6   
## [22] labeling_0.4.2       webshot_0.5.2        googledrive_2.0.0   
## [25] stringr_1.4.0        pander_0.6.4         munsell_0.5.0       
## [28] vipor_0.4.5          compiler_4.1.2       xfun_0.27           
## [31] pkgconfig_2.0.3      systemfonts_1.0.3    ggbeeswarm_0.6.0    
## [34] htmltools_0.5.2      tidyselect_1.1.1     tibble_3.1.5        
## [37] gridExtra_2.3        fansi_0.5.0          viridisLite_0.4.0   
## [40] crayon_1.4.2         dplyr_1.0.7          withr_2.4.2         
## [43] grid_4.1.2           jsonlite_1.7.2       gtable_0.3.0        
## [46] lifecycle_1.0.1      magrittr_2.0.1       scales_1.1.1        
## [49] zip_2.2.0            cli_3.1.0            stringi_1.7.5       
## [52] farver_2.1.0         viridis_0.6.2        fs_1.5.0            
## [55] rmdpartials_0.5.8    xml2_1.3.2           bslib_0.3.1         
## [58] ellipsis_0.3.2       ragg_1.2.0           generics_0.1.1      
## [61] vctrs_0.3.8          openxlsx_4.2.4       kableExtra_1.3.4    
## [64] tools_4.1.2          beeswarm_0.4.0       behaviorchange_0.4.3
## [67] glue_1.4.2           purrr_0.3.4          fastmap_1.1.0       
## [70] yaml_2.2.1           colorspace_2.0-2     gargle_1.2.0        
## [73] rvest_1.0.2          knitr_1.36           patchwork_1.1.1     
## [76] sass_0.4.0

Multi Method approaches applied to COVID-19 protective behavior

Kaisa Saurio, James Twose, Gjalt-Jorn Peters, Matti Heino & Nelli Hankonen

2021-12-13 at 14:46:17 CET (UTC+0100)

Setup

Overview

Code and logs

CIBER plots

Full sample

Younger than 40

40 to 59

60 or older

Practical

Theoretical

Potential for Change Indices

Full sample

Younger than 40

40 to 59

60 or older

Practical

Theoretical

SHAP plots

Full sample

Education: practical

Education: theoretical

Age: 18-39

Age: 40-59

Age: 60+

Combined plots

fullSample

Younger than 40

40 to 59

60 or older

Practical

Theoretical

Session information