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Avoid mentioning colors for flexibility
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template.qmd

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@@ -175,15 +175,15 @@ from the context dataset. The distribution of the nuclotide diversity is assumed
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`r div_values[["norm.text"]]` be normal after performing a Shapiro-Wilk test
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(p-value of $`r div_values[["normal.pvalue"]]`$).
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The nucleotide diversity of the target samples is $`r format(div_values[["diversity"]], scientific = TRUE) `$ (red line in @fig-div).
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The nucleotide diversity of the target samples is $`r format(div_values[["diversity"]], scientific = TRUE) `$ (vertical line in @fig-div).
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Assuming the independence of the context samples, the `r div_values[["type.test"]]`
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p-value of the context samples having a nucleotide diversity (in orange in @fig-div)
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p-value of the context samples having a nucleotide diversity (smooth curve in @fig-div)
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as low as that of the target dataset is $`r div_values[["p.value"]]`$.
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![Analysis of the nucleotide diversity (π). The orange line describes
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![Analysis of the nucleotide diversity (π). The smooth curve describes
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a normal distribution with the same mean and standard deviation as the distribution
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of π from $`r div_values[["boot.reps"]]`$ subsets of $`r div_values[["sample.size"]]`$
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sequences from the context. The red vertical line indicates the π value of the
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sequences from the context. The vertical line indicates the π value of the
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target samples.](`r params$div`){#fig-div}
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## Evolutionary trajectory of the serially-sampled SARS-CoV-2 infection

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