diff --git a/docs/articles/index.html b/docs/articles/index.html index 4f1a4ad2..41604d03 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -23,7 +23,8 @@ - + + @@ -51,10 +52,28 @@ -
+

-BUG FIX

+BUG FIX
  • Bootstrapping algorithm for bruvo.boot function was not shuffling the repeat lengths for each locus resulting in potentially erroneous bootstrap support values. This has been fixed by implementing an internal S4 class that will allow direct bootstrapping of the data and repeat lengths together.
  • An occasional error, “INTEGER() can only be applied to a ‘integer’, not a ‘NULL’” in bruvo.boot or bruvo.dist fixed.
    • @@ -863,9 +928,9 @@

  • Changes to bruvo.boot allow for ever so slightly faster bootstrapping.

-
+

-MISC

+MISC
  • Permutations for I_A and \bar{r}_d are now visualized as a progress bar as opposed to dots.
@@ -874,18 +939,18 @@

poppr 1.0.4

-
+

-BUG FIX

+BUG FIX

  • A previous error where bootstrap values greater than 100 were reported from bruvo.boot on UPGMA trees has been fixed.
  • Fixed correction of negative branch lengths using Kuhner and Felsenstein

(1994) normalization for NJ trees.

-
+

-MISC

+MISC
  • github repository for poppr has changed from github.com/poppr/poppr to github.com/grunwaldlab/poppr
@@ -902,9 +967,9 @@

  • Utilized rmultinom function to increase speed of bootstrap sampling methods for shufflepop and ia.

    • -
    +

    -NEW FEATURES

    +NEW FEATURES
    • Function informloci will remove phylogenetically uninformative loci.
    @@ -944,9 +1009,9 @@

  • Expanded installation section to include installation instructions from github.

    • -
    +

    -MISC

    +MISC
    • internal permutation algorithm no longer lists permutations in reverse order
    @@ -971,9 +1036,9 @@

  • Input values that are not multiples of the specified repeat length for Bruvo’s distance are now rounded (as opposed to being forced as integers).

    • -
    +

    -MISC

    +MISC
    • Vignette updated for aesthetics and to reflect algorithmic changes.
    @@ -982,9 +1047,9 @@

    poppr 1.0.0

    -
    +

    -MISC

    +MISC

    • Poppr has been confirmed to work on Linux, Mac, and Windows systems with R 3.0.0.
    • Vignette poppr_manual now has cross-references to different sections.
      • @@ -1002,9 +1067,9 @@

      poppr 0.4.1

      -
      +

      -NEW FEATURES

      +NEW FEATURES

      • getfile has a new argument, “combine”, which will automatically add the path to the list of files, so they can be read without switching working directory.
        • @@ -1035,9 +1100,9 @@

        read.genalex can now correctly recognize regional formatting without an extra column.

    -
    +

    -NEW FEATURES

    +NEW FEATURES
    • read.genalex will now be able to take in a file that is formatted with both regional and geographic data.
      • @@ -1080,17 +1145,17 @@

      poppr 0.3

      -
      +

      -NEW FUNCTIONS

      +NEW FUNCTIONS

      • poppr.msn will draw a minimum spanning network for any distance matrix derived from your data set.
    -
    +

    -NEW FEATURES

    +NEW FEATURES
    • vignette now has sections describing poppr.msn, diss.dist, greycurve, and a section discussing how to export graphics.
    @@ -1108,9 +1173,9 @@

    poppr 0.2.2

    -
    +

    -NEW FEATURES

    +NEW FEATURES

    • index of association distributions will now feature a rug plot at the bottom as a better way to visualize the distribution of the index of association from the shuffled data sets.
    @@ -1119,9 +1184,9 @@

    poppr 0.2.1

    -
    +

    -NEW FUNCTIONS

    +NEW FUNCTIONS

    • diss.dist will produce a distance matrix based on discreet distances.
      • @@ -1129,9 +1194,9 @@

      greycurve will produce a grey scale adjusted to user-supplied parameters. This will be useful for future minimum spanning network functions.

    -
    +

    -NEW FEATURES

    +NEW FEATURES
    • bruvo.msn can now adjust the edge grey level to be weighted toward either closely or distantly weighted individuals.
      • @@ -1151,9 +1216,9 @@

      poppr 0.2

      -
      +

      -NEW FEATURES

      +NEW FEATURES

      • Added NEWS file and will now be incrementing version number (3/15/2013)
      @@ -1173,6 +1238,7 @@

      Contents

        +
      • 2.6.0
      • 2.5.0
      • 2.4.1
      • 2.4.0
        • diff --git a/docs/pkgdown.css b/docs/pkgdown.css index 9c437c74..209ce57f 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -34,6 +34,10 @@ img.icon { float: right; } +img { + max-width: 100%; +} + /* Section anchors ---------------------------------*/ a.anchor { @@ -133,9 +137,14 @@ pre, code { color: #333; } -pre img { +pre .img { + margin: 5px 0; +} + +pre .img img { background-color: #fff; display: block; + height: auto; } code a, pre a { diff --git a/docs/pkgdown.js b/docs/pkgdown.js index c8b38c49..4b817132 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -5,4 +5,41 @@ $(function() { offset: 60 }); + var cur_path = paths(location.pathname); + $("#navbar ul li a").each(function(index, value) { + if (value.text == "Home") + return; + if (value.getAttribute("href") === "#") + return; + + var path = paths(value.pathname); + if (is_prefix(cur_path, path)) { + // Add class to parent
      • , and enclosing
      • if in dropdown + var menu_anchor = $(value); + menu_anchor.parent().addClass("active"); + menu_anchor.closest("li.dropdown").addClass("active"); + } + }); }); + +function paths(pathname) { + var pieces = pathname.split("/"); + pieces.shift(); // always starts with / + + var end = pieces[pieces.length - 1]; + if (end === "index.html" || end === "") + pieces.pop(); + return(pieces); +} + +function is_prefix(needle, haystack) { + if (needle.length > haystack.lengh) + return(false); + + for (var i = 0; i < haystack.length; i++) { + if (needle[i] != haystack[i]) + return(false); + } + + return(true); +} diff --git a/docs/reference/Aeut.html b/docs/reference/Aeut.html index 2409b433..9441127b 100644 --- a/docs/reference/Aeut.html +++ b/docs/reference/Aeut.html @@ -23,7 +23,8 @@ - + + @@ -51,10 +52,28 @@ diff --git a/docs/reference/MLG-accessors.html b/docs/reference/MLG-accessors.html index 327196db..365ec6e4 100644 --- a/docs/reference/MLG-accessors.html +++ b/docs/reference/MLG-accessors.html @@ -23,7 +23,8 @@ - + + @@ -51,10 +52,28 @@ # NOT RUN { +# These examples will simply show you what you can do with these +set.seed(5000) +(x <- sample(10, 20, replace = TRUE)) +(m <- new("MLG", x)) + +# Visibility ------------------------------ +visible(m) # original +visible(m) <- "contracted" +m # shows contracted MLGS + +# Conversion to data frame ---------------- +MLG2df(m) # Grab the internal data frame + +# Distance function handling -------------- +distname(m) # nei.dist +distargs(m) # list() +distalgo(m) # farthest +cutoff(m) + +distname(m) <- substitute("diss.dist") +distargs(m) <- list(percent = TRUE) +distalgo(m) <- "average" +cutoff(m)["contracted"] <- 0.2 + +# }