diff --git a/docs/404.html b/docs/404.html index 5acd4df..f09c531 100644 --- a/docs/404.html +++ b/docs/404.html @@ -49,10 +49,10 @@ diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 6a35a3f..39bba0a 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -32,10 +32,10 @@
  • diff --git a/docs/LICENSE.html b/docs/LICENSE.html index ed71ae9..655cb99 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -32,10 +32,10 @@
  • diff --git a/docs/articles/tutorial.html b/docs/articles/01-tutorial.html similarity index 97% rename from docs/articles/tutorial.html rename to docs/articles/01-tutorial.html index b48793d..7c4b766 100644 --- a/docs/articles/tutorial.html +++ b/docs/articles/01-tutorial.html @@ -50,10 +50,10 @@
    • @@ -88,8 +88,8 @@

    Martin

    2024-05-08

    - Source: vignettes/tutorial.Rmd - + Source: vignettes/01-tutorial.Rmd + @@ -188,12 +188,12 @@

    A note about EIGENSTRAT format
    (prefix <- download_data(dirname = tempdir()))
-[1] "/var/folders/70/b_q2zdh116b9pfg29p03sx600000gn/T//RtmpNja4nr/snps/snps"
    +[1] "/var/folders/70/b_q2zdh116b9pfg29p03sx600000gn/T//RtmpzHxCwT/snps/snps"

    We can verify that there are indeed three files with this prefix:

    list.files(path = dirname(prefix), pattern = basename(prefix), full.names = TRUE)
-[1] "/var/folders/70/b_q2zdh116b9pfg29p03sx600000gn/T//RtmpNja4nr/snps/snps.geno"
-[2] "/var/folders/70/b_q2zdh116b9pfg29p03sx600000gn/T//RtmpNja4nr/snps/snps.ind" 
-[3] "/var/folders/70/b_q2zdh116b9pfg29p03sx600000gn/T//RtmpNja4nr/snps/snps.snp"
    +[1] "/var/folders/70/b_q2zdh116b9pfg29p03sx600000gn/T//RtmpzHxCwT/snps/snps.geno" +[2] "/var/folders/70/b_q2zdh116b9pfg29p03sx600000gn/T//RtmpzHxCwT/snps/snps.ind" +[3] "/var/folders/70/b_q2zdh116b9pfg29p03sx600000gn/T//RtmpzHxCwT/snps/snps.snp"

    Let’s look at their contents:

    @@ -288,9 +288,9 @@

    Internal representation of E #> EIGENSTRAT object #> ================= #> components: -#> ind file: /var/folders/70/b_q2zdh116b9pfg29p03sx600000gn/T//RtmpNja4nr/snps/snps.ind -#> snp file: /var/folders/70/b_q2zdh116b9pfg29p03sx600000gn/T//RtmpNja4nr/snps/snps.snp -#> geno file: /var/folders/70/b_q2zdh116b9pfg29p03sx600000gn/T//RtmpNja4nr/snps/snps.geno

    +#> ind file: /var/folders/70/b_q2zdh116b9pfg29p03sx600000gn/T//RtmpzHxCwT/snps/snps.ind +#> snp file: /var/folders/70/b_q2zdh116b9pfg29p03sx600000gn/T//RtmpzHxCwT/snps/snps.snp +#> geno file: /var/folders/70/b_q2zdh116b9pfg29p03sx600000gn/T//RtmpzHxCwT/snps/snps.geno

    This object encapsulates the paths to all three EIGENSTRAT components and makes it easy to pass the data to different admixr functions.

    @@ -461,7 +461,7 @@

    D statisticgeom_point() + geom_hline(yintercept = 0, linetype = 2) + geom_errorbar(aes(ymin = D - 2 * stderr, ymax = D + 2 * stderr)) -

    +

    (If you want to more know about data analysis using R, including plotting with ggplot2, I highly recommend this free book.)

    We can see that the \(D\) values for @@ -708,7 +708,7 @@

    f4-ratio statisticgeom_errorbar(aes(ymin = alpha - 2 * stderr, ymax = alpha + 2 * stderr)) + geom_hline(yintercept = 0, linetype = 2) + labs(y = "Neandertal ancestry proportion", x = "present-day individual") -

    +

    We can make several observations: