add pilot indirect Source V2

experiments/pilot-indirectSource-V2/CoverStoriesHW/Background.txt

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+<p> <strong>Background:</strong> We are now at an age of great exploration and discovery. Humanity has reached the stars, venturing to distant planets in search of new frontiers and resources. One of these new worlds is a remote, resource-rich planet called <strong>Xelifan-3</strong></p>
+          <p>The year is 2184, and Xelifan-3 has become home to a small but determined group of colonists. Their survival depends on a rare plant known as <strong>Xeliherb</strong>, a life-sustaining resource native to the planet. This unique plant has extraordinary properties, providing essential nutrients necessary for survival on the planet. Furthermore, it holds potential as a key ingredient in medicines capable of curing diseases, which has attracted significant interest from scientists around the galaxy. </p> 
+          <p>However, xeliherb grows only <strong>sparsely</strong>, and its limited availability has made life on Xelifan-3 a constant struggle.</p>

experiments/pilot-indirectSource-V2/CoverStoriesHW/RoleColonist.txt

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+You are one of the <strong>colonists</strong>, part of the group that has risked everything to settle on Xelifan-3 in search of a new beginning.
+<br><br>
+The colony’s survival is entirely dependent on a steady supply of <strong>Xeliherb</strong>, but its scarcity has led to a sense of urgency and tension. You live on the frontlines, working closely with the land, and every discovery you make has an immediate impact on the well-being of the people around you.
+<br><br>
+As a colonist, your mission is not just about survival but about the future of humanity’s presence on Xelifan-3. You must work alongside explorers and scientists to identify new Xeliherb patches, navigate the dangerous environments of the planet, and ensure the plant is yield and harvested efficiently.
+<br><br>
+However, there can be tension between the colonists and scientists. While the colonists focus on immediate survival, the scientists are driven by long-term research goals, which can lead to differing perspectives. Each group’s unique experiences and priorities may influence how they view and interpret information about <strong>Xeliherb</strong>.
+<br><br>
+<strong>Will you trust the scientists’ distant analysis, or will you rely on your own experiences and the stories shared by other colonists to guide your decisions?</strong>

experiments/pilot-indirectSource-V2/CoverStoriesHW/RoleScientist.txt

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+<p>You are one of the <strong>scientist</strong>, part of an elite team tasked with uncovering the secrets of <strong>Xeliherb.</strong> The Xeliherb is not only a vital resource for the colony's survival, but it also represents a groundbreaking opportunity for scientific advancement. If its full potential can be unlocked, it could revolutionize medicine and become a powerful asset to humanity, well beyond the confines of Xelifan-3.
+            </p>
+            <p>Unlike the colonists, your mission is driven by discovery and innovation. You are going to conduct thorough research on Xeliherb, understanding its properties and developing new methods to maximize its yield. From your remote research stations or safe compounds, you receive data from the colonists and analyze the Xeliherb samples they send you. You must carefully interpret this information, using your scientific expertise to provide guidance on how to cultivate and harvest the plant more effectively.
+<br><br>However, there can be tension between the colonists and scientists. While the colonists focus on immediate survival, the scientists are driven by long-term research goals, which can lead to differing perspectives. Each group’s unique experiences and priorities may influence how they view and interpret information about <strong>Xeliherb</strong>.
+<br><br> <strong> Will you rely on the data and scientific methods you trust, or will you consider the colonists' on-the-ground experiences when advising on how to proceed?</strong>
+            </p>

experiments/pilot-indirectSource-V2/CoverStoriesHW/speakerJournal.txt

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+Now, it is time to make a decision.
+<br><br>
+After months of surviving the hostile environment of Xelifan-3, you and your fellow collegues receive a mysterious discovery. One evening, a weathered journal is found in the ruins of an old research outpost, a relic from a science team that explored the planet decades ago. The journal is fragile and faded, but its contents are shocking. It claims:
+<br><br>
+<strong>The presence of Xeliherb is associatied with another plant called Ralocrop.</strong>
+<br><br>
+Do you trust the words of a lost science team, written in a time long past, and act on this information? Or do you continue relying on the methods that have kept the colony alive so far, unsure if the connection between xeliherb and ralocrop is real?
+<br><br>
+<strong>Question: How likely are going to looking for more Ralocrop? Your decision will shape the colony’s future.</strong> 

experiments/pilot-indirectSource-V2/CoverStoriesHW/speakerScientist.txt

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+Now, it is time to make a decision.
+<br><br>
+While navigating the challenges of life on Xelifan-3, a breakthrough occurs. A member of your supporting science team, stationed at a remote research facility, shares an urgent discovery. During their latest field study, they found strong evidence suggesting:
+<br><br>
+<strong>The presence of Xeliherb is associatied with another plant called Ralocrop.</strong>
+<br><br>
+Do you trust the direct word of this scientist and their data? Or do you remain cautious, knowing that a failed experiment could threaten the colony’s delicate balance?
+<br><br>
+<strong>Question: How likely are going to looking for more Ralocrop? Your decision will shape the colony’s future.</strong> 

experiments/pilot-indirectSource-V2/README.md

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+# Pilot 'indirect sources'
+
+
+Live version of the experiment [here](https://magpie-ea.github.io/magpie3-causal-implicature/experiments/pilot-indirectSource/).

experiments/pilot-indirectSource-V2/analysis/analysis-script-pilot-v1.Rmd

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+---
+title: "Analysis Script Pilot Indirect Source v1"
+author: "Hening Wang"
+date: "2024-11-18"
+output: pdf_document
+editor_options: 
+  markdown: 
+    wrap: 72
+---
+Supress messages in this document so that the output is cleaner
+```{r setup, include=FALSE} 
+knitr::opts_chunk$set(warning = FALSE, message = FALSE) 
+```
+Import packages.
+```{r}
+rm(list = ls())
+
+options(warn = -1)
+library(tidyverse)
+library(lme4)
+library(lmerTest)
+library(ggplot2)
+library(aida)
+```
+
+Set up theme for ggplot.
+
+```{r}
+theme_set(theme_aida())
+
+##################################################
+## CSP-colors
+##################################################
+CSP_colors = c(
+  "#7581B3", "#99C2C2", "#C65353", "#E2BA78", "#5C7457", "#575463",
+  "#B0B7D4", "#66A3A3", "#DB9494", "#D49735", "#9BB096", "#D4D3D9",
+  "#414C76", "#993333"
+  )
+# setting theme colors globally
+scale_colour_discrete <- function(...) {
+  scale_colour_manual(..., values = CSP_colors)
+}
+scale_fill_discrete <- function(...) {
+  scale_fill_manual(..., values = CSP_colors)
+}
+```
+
+# Data Import & Preprocessing
+
+Import data
+
+```{r}
+data <- read.csv("../data/pilot-v1/results.csv")
+```
+
+Factorise variables: id, item, informationSource, listenerRole
+
+```{r}
+data$id <- as.factor(1:nrow(data))
+data$item <- as.factor(data$condition)
+data$informationSource <- as.factor(data$informationSource)
+data$listenerRole <- as.factor(data$listenerRole)
+```
+
+Recruitment criteria: 1. English native speakers 2. Approval rate \> 90%
+3. Completion \> 5 times 4. Not included in the prior studies of
+CommuniCause
+
+# Plots
+
+## A histogram showing the distribution of probs. 
+**Interpretation: Data is left-skewed.**
+
+```{r}
+ggplot(data, aes(x = probs)) +
+  geom_histogram(binwidth = 5, fill = CSP_colors[1]) +
+  labs(title = "Distribution of Slider Ratings",
+       x = "Slider Ratings",
+       y = "Frequency")
+
+```
+
+## Plot the dependent variable "probs" against conditions.
+
+**Interpretation:**
+
+1. No significant difference between conditions. 
+2. Perhaps due to:
+  + not enough sample size.
+  + the empirical distribution is severe skewed. This is problem of slider rating in general.
+  + manipulation too subtle.
+3. We can try to observe some trends though: 
+  + "Direct" information seems to have a higher mean rating than "indirect", as expected. 
+  + The role "scientist" seems to be more sensitive to indirectness of information. This could lead to a potential interaction as expected.
+
+Next step: It seems that manipulation did have some effects given 3.2, but it was too subtle to be statistically significant. We should probably rework the design of the study by addressing the three points in 2.
+
+```{r}
+ggplot(data, aes(x = informationSource, y = probs, fill = listenerRole)) +
+  geom_boxplot() +
+  labs(title = "Slider Ratings by Conditions",
+       x = "Information Source",
+       y = "Slider Ratings",
+       fill = "Listener Role")
+```
+
+## Plot transformed data
+
+Given that data is left-skewed. We perform a log transformation, and
+show a QQ plot after data transformation.
+
+It does not really help. Now the data is right-skewed.
+
+```{r}
+data$transformed_probs <- log(max(data$probs+1) - data$probs)
+qqnorm(data$transformed_probs)
+```
+
+Another empirical plot with transformed data.
+Nothing really interesting here.
+```{r}
+ggplot(data, aes(x = informationSource, y = transformed_probs, fill = listenerRole)) +
+  geom_boxplot() +
+  labs(title = "log transformed Slider Ratings by Conditions",
+       x = "Information Source",
+       y = "Slider Ratings",
+       fill = "Listener Role")
+```
+
+# Statistical Analysis
+**Note: Nothing is significant here.** 
+
+Fit a linear model with full interaction.
+```{r}
+model_full <- lm(probs ~ informationSource * listenerRole, data = data)
+summary(model_full)
+
+```
+
+Fit another lm with transformed data.
+
+```{r}
+model_full_transformed <- lm(transformed_probs ~ informationSource * listenerRole, data = data)
+summary(model_full_transformed)
+```

experiments/pilot-indirectSource-V2/analysis/analysis.Rproj

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