Merge branch 'master' into weave_doc

.travis.yml

@@ -6,7 +6,7 @@ julia: # WARNING: any change here must also be done in docs/make.jl
 # - release
   - 0.6
 env:
-  - DRAW_FIG="true"
+  - DRAW_FIG="false"
     DOCUMENTER_DEBUG="true"
 notifications:
   email: false

docs/readme.md

@@ -0,0 +1,59 @@
+# notes to maintain documentation
+
+- built with [Documenter](https://juliadocs.github.io/Documenter.jl)
+  using Paul Bastide's [fork](https://github.com/pbastide/Documenter.jl)
+  to have the flexibility to avoid committing new figures (see below)
+- deployed [here](http://crsl4.github.io/PhyloNetworks.jl/)
+  (go to `latest/` or `stable/`)
+  using github and files committed to the `gh-pages` branch.
+
+## how it works: overview
+
+- `.travis.yml` asks to run `docs/make.jl` after a successful test & build.
+- the julia script `docs/make.jl` has 3 steps:
+  1. run `docs/src/man/src/make_weave.jl` to
+     [Weave](http://weavejl.mpastell.com/stable/) the `.jmd` files
+     in `docs/src/man/src/*.jmd`: turns them into markdown files placed in
+     `docs/src/man/*.md`, that contain the input & output of julia code.
+  2. run `makedocs()` from `Documenter`: make the documentation
+  3. run `deploydocs(...)` also from Documenter. This step calls `mkdocs`,
+     which turns the markdown files in `docs/.../*.md` into html files.
+
+## about julia markdown
+
+- The `.jmd` files that are weaved into `.md` files
+  are listed in `docs/src/man/src/make_weave.jl`:
+  **add** to this list any new `.jmd` file that needs to be added to the manual.
+- `.jmd` is similar to `.Rmd`: we can choose which julia chunks to eval, echo,
+  show as in the REPL (`term=true`) etc.
+- the default chunk options are defined on line 3 of
+  `docs/src/man/src/make_weave.jl`: unlike in Rstudio,
+  the defaults here are `results="hidden"` and `eval=false`,
+  so that a `{julia}` chunk won't be evaluated. Just the input code will be shown.
+  To run the chunk and show both input and output, use:
+
+  `{julia; eval=true; results="markup"; term=true}`
+
+  for REPL display, or
+
+  `{julia; eval=true; results="markup";}`
+
+  to show output separately from input.
+
+## figures
+
+- all figures produced by the code are placed in `docs/assets/figures`.
+  `mkdocs` exports all files in `docs/assets` during the publishing;
+  they are tracked on the `gh-pages` branch (not on `master`).
+- the chunk label determines the name of any files
+  that the chunk will create if one or more figures are drawn.
+  Figures are tracked by git,
+  so it's best to control the name of the files being created. example:
+
+  `{julia; eval=true; label="truenet_opt"; fig_width=4; fig_height=4}`
+
+- `.travis.yml` defines an environment variable: `DRAW_FIG`.
+  If `"false"`, any figure produced during weaving of the jmd files
+  are suppressed from the commit (see Paul Bastide's `/src/Documenter.jl`
+  [here](https://github.com/pbastide/Documenter.jl/blob/master/src/Documenter.jl#L356)
+  for instance), to avoid tracking unimportant changes to `png` or `pdf` images.

src/readwrite.jl

@@ -1267,7 +1267,7 @@ function symmetricNet(n::Int, i::Int, j::Int, gamma::Real, ell::Real)
         clo = clo*"):$(ell)"
     end
     clobis = clo[1:(length(clo)-length("$(ell)"))]*"$(0.5*ell)"
-    tree = replace(tree, op, "(#H:$(0.5*ell)::$(gamma),"*op)
+    tree = replace(tree, op, "(#H:$(ell)::$(gamma),"*op)
     tree = replace(tree, clo, clobis*"):$(0.5*ell)")
     ## end hyb
     op = "A$(2^(i-1)+1):$(ell)"

src/traits.jl

@@ -1159,7 +1159,6 @@ function setGammas!(net::HybridNetwork, gammas::Vector)
             else
                 net.nodes_changed[i].edge[majorHybrid][2].gamma = 1 - gammas[i]
             end
-            net.nodes_changed[i].edge[minorHybrid][1].gamma = 1 - gammas[i]
         end
     end
     return nothing
@@ -1176,7 +1175,9 @@ end
 function maxLambda(times::Vector, V::MatrixTopologicalOrder)
     maskTips = indexin(V.tipNumbers, V.nodeNumbersTopOrder)
     maskNodes = indexin(V.internalNodeNumbers, V.nodeNumbersTopOrder)
-    return maximum(times[maskTips]) / maximum(times[maskNodes])
+    return minimum(times[maskTips]) / maximum(times[maskNodes])
+    # res = minimum(times[maskTips]) / maximum(times[maskNodes])
+    # res = res * (1 - 1/5/maximum(times[maskTips]))
 end
 
 function transform_matrix_lambda!{T <: AbstractFloat}(V::MatrixTopologicalOrder, lam::T,
@@ -1203,12 +1204,13 @@ function logLik_lam{T <: AbstractFloat}(lam::T,
                                         msng=trues(length(Y))::BitArray{1}, # Which tips are not missing ?
                                         ind=[0]::Vector{Int})
     # Transform V according to lambda
-    transform_matrix_lambda!(V, lam, gammas, times)
+    Vp = deepcopy(V)
+    transform_matrix_lambda!(Vp, lam, gammas, times)
     # Fit and take likelihood
-    fit_lam = phyloNetworklm_BM(X, Y, V; msng=msng, ind=ind)
+    fit_lam = phyloNetworklm_BM(X, Y, Vp; msng=msng, ind=ind)
     res = - loglikelihood(fit_lam)
     # Go back to original V
-    transform_matrix_lambda!(V, 1/lam, gammas, times)
+    # transform_matrix_lambda!(V, 1/lam, gammas, times)
     return res
 end