From a169899e005a741005f097cefaee8154a3f161a5 Mon Sep 17 00:00:00 2001 From: Paul Bastide Date: Thu, 3 Oct 2019 11:36:11 -0700 Subject: [PATCH] Rebuild doc. --- docs/404.html | 135 ++++++++++++ docs/LICENSE-text.html | 40 ++-- docs/articles/index.html | 40 ++-- docs/articles/monkeys.html | 206 +++++++++--------- .../monkeys_files/figure-html/data-1.png | Bin 153351 -> 153363 bytes .../figure-html/unnamed-chunk-1-1.png | Bin 48481 -> 48493 bytes .../figure-html/unnamed-chunk-10-1.png | Bin 39839 -> 39851 bytes .../figure-html/unnamed-chunk-11-1.png | Bin 39839 -> 39851 bytes .../figure-html/unnamed-chunk-13-1.png | Bin 38422 -> 38434 bytes .../figure-html/unnamed-chunk-2-1.png | Bin 39724 -> 39736 bytes .../figure-html/unnamed-chunk-3-1.png | Bin 49874 -> 49886 bytes .../figure-html/unnamed-chunk-5-1.png | Bin 52137 -> 52149 bytes .../figure-html/unnamed-chunk-6-1.png | Bin 52215 -> 52227 bytes .../figure-html/unnamed-chunk-7-1.png | Bin 33228 -> 33240 bytes 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53 +++-- .../allocate_shifts_from_regimes.html | 53 +++-- .../allocate_subset_node.simulate.html | 51 +++-- docs/reference/check.selection.strength.html | 53 +++-- docs/reference/check_data.html | 53 +++-- docs/reference/check_dimensions.html | 51 +++-- docs/reference/check_parsimony.html | 53 +++-- docs/reference/check_parsimony_clusters.html | 53 +++-- docs/reference/check_range_alpha.html | 49 +++-- docs/reference/clusters_from_shifts.html | 53 +++-- docs/reference/compute_E.simple.html | 61 +++--- ...pute_actualization_matrix_ultrametric.html | 53 +++-- docs/reference/compute_betas_from_shifts.html | 53 +++-- docs/reference/compute_diff_exp.BM.html | 51 +++-- docs/reference/compute_dist_phy.html | 59 ++--- docs/reference/compute_expectations.BM.html | 51 +++-- docs/reference/compute_expectations.scOU.html | 51 +++-- docs/reference/compute_fixed_moments.html | 51 +++-- docs/reference/compute_gauss_lasso.html | 55 ++--- .../compute_log_likelihood.simple.html | 59 ++--- .../compute_mahalanobis_distance.simple.html | 57 ++--- .../compute_mean_variance.simple.html | 59 ++--- docs/reference/compute_residuals.simple.html | 51 +++-- docs/reference/compute_shifts_from_betas.html | 55 ++--- docs/reference/compute_state_filter.html | 53 +++-- .../compute_stationary_variance.html | 53 +++-- docs/reference/compute_sum_var_diff.html | 51 +++-- docs/reference/compute_times_ca.html | 59 ++--- .../compute_tree_correlations_matrix.BM.html | 51 +++-- ...compute_tree_correlations_matrix.scOU.html | 51 +++-- docs/reference/compute_var_M.BM.html | 53 +++-- docs/reference/compute_var_diff.BM.html | 51 +++-- .../compute_variance_covariance.BM.html | 51 +++-- .../compute_variance_covariance.OU.html | 51 +++-- ...compute_variance_covariance.OU.nonsym.html | 51 +++-- .../compute_variance_covariance.scOU.html | 51 +++-- docs/reference/correspondenceEdges.html | 51 +++-- docs/reference/enlight.html | 60 ++--- docs/reference/enumerate_parsimony-1.png | Bin 27086 -> 27098 bytes 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...egression_vectors.glmnet_multivariate.html | 53 +++-- docs/reference/find_rotation.html | 51 +++-- docs/reference/find_shift_values.html | 53 +++-- docs/reference/format_output.html | 53 +++-- docs/reference/get_criterion.html | 53 +++-- docs/reference/get_variance_node.html | 51 +++-- .../go_back_to_original_process.html | 51 +++-- docs/reference/imputed_traits.html | 60 ++--- docs/reference/incidence.matrix.full.html | 55 ++--- docs/reference/incidence.matrix.html | 55 ++--- ...ncidence_matrix_actualization_factors.html | 51 +++-- docs/reference/index.html | 40 ++-- docs/reference/init.EM.lasso.html | 70 +++--- .../init.allocate_regimes_from_shifts.html | 53 +++-- .../init.alpha.gamma.estimation.html | 59 ++--- .../init.compute_betas_from_shifts.html | 53 +++-- docs/reference/init.enumerate_parsimony.html | 53 +++-- .../reference/init.incidence.matrix.full.html | 53 +++-- docs/reference/init.incidence.matrix.html | 53 +++-- docs/reference/init.parsimonyCost.html | 55 ++--- docs/reference/init.parsimonyNumber.html | 53 +++-- docs/reference/init.simulate.BM.html | 53 +++-- docs/reference/init.simulate.OU.html | 53 +++-- docs/reference/init.simulate.StateAndExp.html | 53 +++-- docs/reference/is.in.ranges.html | 56 ++--- ...egression_K_fixed.glmnet_multivariate.html | 57 ++--- docs/reference/log_likelihood.html | 60 ++--- docs/reference/matrix_of_possibles.html | 53 +++-- .../merge_complementary_vectors.html | 53 +++-- docs/reference/merge_params_independent.html | 51 +++-- docs/reference/merge_rotations.html | 65 +++--- docs/reference/model_selection.html | 60 ++--- docs/reference/monkeys.html | 53 +++-- docs/reference/params_BM.html | 69 +++--- docs/reference/params_OU.html | 77 ++++--- docs/reference/params_process.PhyloEM.html | 53 +++-- docs/reference/params_process.character.html | 53 +++-- docs/reference/params_process.html | 60 ++--- docs/reference/parsimonyCost-1.png | Bin 28703 -> 28715 bytes docs/reference/parsimonyCost.html | 58 ++--- 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+++-- docs/reference/segmentation.BM.html | 53 +++-- .../segmentation.OU.specialCase.lasso.html | 55 ++--- ...gmentation.OU.specialCase.same_shifts.html | 53 +++-- docs/reference/shifts.list_to_matrix.html | 55 ++--- docs/reference/shifts.list_to_vector.html | 53 +++-- docs/reference/shifts.matrix_to_list.html | 53 +++-- docs/reference/shifts.vector_to_list.html | 53 +++-- docs/reference/shifts_to_simmap.html | 55 ++--- docs/reference/simul_process.html | 63 +++--- docs/reference/simulate_internal.html | 65 +++--- docs/reference/split_params_independent.html | 51 +++-- docs/reference/sum.partitions.cardFixed.html | 55 ++--- docs/reference/sum.partitions.html | 55 ++--- docs/reference/sum.prod.comb.html | 55 ++--- docs/reference/sum.simplex.html | 55 ++--- docs/reference/test.root.state.html | 55 ++--- docs/reference/transform_branch_length.html | 53 +++-- docs/reference/transform_shifts_values.html | 49 +++-- .../update.allocate_regimes_from_shifts.html | 53 +++-- .../update.compute_betas_from_shifts.html | 53 +++-- .../reference/update.enumerate_parsimony.html | 53 +++-- .../update.incidence.matrix.full.html | 53 +++-- docs/reference/update.incidence.matrix.html | 53 +++-- docs/reference/update.parsimonyCost.html | 53 +++-- docs/reference/update.parsimonyNumber.html | 53 +++-- .../update.partitionsNumber.gen.html | 53 +++-- docs/reference/wrapper_E_step.html | 48 ++-- 177 files changed, 4858 insertions(+), 3826 deletions(-) create mode 100644 docs/404.html diff --git a/docs/404.html b/docs/404.html new file mode 100644 index 0000000..194cdec --- /dev/null +++ b/docs/404.html @@ -0,0 +1,135 @@ + + + + + + + + +Page not found (404) • PhylogeneticEM + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + +
+ +
+
+
+

Page not found (404)

+
+ +Content not found. Please use links in the navbar. + +
+ +
+ + + +
+
+

Developed by Paul Bastide.

+
+ +
+

Site built with pkgdown 1.4.1.

+
+ +
+
+ + + + + + + + diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 5255e45..176b663 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ License • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,12 +34,15 @@ + + - + + + @@ -51,14 +59,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -171,6 +174,8 @@

Contents

+ + diff --git a/docs/reference/check_range_alpha.html b/docs/reference/check_range_alpha.html index 5f7aac1..d30f689 100644 --- a/docs/reference/check_range_alpha.html +++ b/docs/reference/check_range_alpha.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Check range of alpha — check_range_alpha • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -150,6 +157,8 @@

Contents

+ + diff --git a/docs/reference/clusters_from_shifts.html b/docs/reference/clusters_from_shifts.html index 2757cfa..64a9aad 100644 --- a/docs/reference/clusters_from_shifts.html +++ b/docs/reference/clusters_from_shifts.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Clustering associated to a shift allocation, assuming no homoplasy. — clusters_from_shifts • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -170,6 +173,8 @@

Contents

+ + diff --git a/docs/reference/compute_E.simple.html b/docs/reference/compute_E.simple.html index fdd7fe9..6375c55 100644 --- a/docs/reference/compute_E.simple.html +++ b/docs/reference/compute_E.simple.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ E step — compute_E.simple • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,15 +34,17 @@ - + + - + + + @@ -54,14 +61,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -191,6 +194,8 @@

Contents

+ + diff --git a/docs/reference/compute_actualization_matrix_ultrametric.html b/docs/reference/compute_actualization_matrix_ultrametric.html index c209f66..fe2a6df 100644 --- a/docs/reference/compute_actualization_matrix_ultrametric.html +++ b/docs/reference/compute_actualization_matrix_ultrametric.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Compute Matrix W of actualization (Ultrametric case) — compute_actualization_matrix_ultrametric • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -167,6 +170,8 @@

Contents

+ + diff --git a/docs/reference/compute_betas_from_shifts.html b/docs/reference/compute_betas_from_shifts.html index ef23658..fca1e71 100644 --- a/docs/reference/compute_betas_from_shifts.html +++ b/docs/reference/compute_betas_from_shifts.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Computation of the optimal values at nodes and tips. — compute_betas_from_shifts • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -163,6 +168,8 @@

Contents

+ + diff --git a/docs/reference/compute_diff_exp.BM.html b/docs/reference/compute_diff_exp.BM.html index 969b4fb..e398051 100644 --- a/docs/reference/compute_diff_exp.BM.html +++ b/docs/reference/compute_diff_exp.BM.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Compute differences of expectations between node and parent. — compute_diff_exp.BM • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -157,6 +162,8 @@

Contents

+ + diff --git a/docs/reference/compute_dist_phy.html b/docs/reference/compute_dist_phy.html index abc48cb..092643c 100644 --- a/docs/reference/compute_dist_phy.html +++ b/docs/reference/compute_dist_phy.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Phylogenetic Distances — compute_dist_phy • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -160,6 +163,8 @@

Contents

+ + diff --git a/docs/reference/compute_expectations.BM.html b/docs/reference/compute_expectations.BM.html index 4b6e0f6..a773749 100644 --- a/docs/reference/compute_expectations.BM.html +++ b/docs/reference/compute_expectations.BM.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Compute the expected states of a BM — compute_expectations.BM • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -170,6 +175,8 @@

Contents

+ + diff --git a/docs/reference/compute_expectations.scOU.html b/docs/reference/compute_expectations.scOU.html index 8590e20..2b074eb 100644 --- a/docs/reference/compute_expectations.scOU.html +++ b/docs/reference/compute_expectations.scOU.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Compute the expected states of a scOU — compute_expectations.scOU • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -171,6 +176,8 @@

Contents

+ + diff --git a/docs/reference/compute_fixed_moments.html b/docs/reference/compute_fixed_moments.html index 8c3843b..e087ab3 100644 --- a/docs/reference/compute_fixed_moments.html +++ b/docs/reference/compute_fixed_moments.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Compute fixed moments for E step. — compute_fixed_moments • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -154,6 +159,8 @@

Contents

+ + diff --git a/docs/reference/compute_gauss_lasso.html b/docs/reference/compute_gauss_lasso.html index 6f31a4f..ebc6da2 100644 --- a/docs/reference/compute_gauss_lasso.html +++ b/docs/reference/compute_gauss_lasso.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Do a lm on top of a lasso regression. — compute_gauss_lasso • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + + + @@ -57,14 +64,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -181,6 +184,8 @@

Contents

+ + diff --git a/docs/reference/compute_log_likelihood.simple.html b/docs/reference/compute_log_likelihood.simple.html index 94fffc1..9df3381 100644 --- a/docs/reference/compute_log_likelihood.simple.html +++ b/docs/reference/compute_log_likelihood.simple.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Log Likelihood — compute_log_likelihood.simple • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -180,6 +183,8 @@

Contents

+ + diff --git a/docs/reference/compute_mahalanobis_distance.simple.html b/docs/reference/compute_mahalanobis_distance.simple.html index 569ea17..eaffd52 100644 --- a/docs/reference/compute_mahalanobis_distance.simple.html +++ b/docs/reference/compute_mahalanobis_distance.simple.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Squared Mahalanobis Distance — compute_mahalanobis_distance.simple • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -176,6 +179,8 @@

Contents

+ + diff --git a/docs/reference/compute_mean_variance.simple.html b/docs/reference/compute_mean_variance.simple.html index dee9c20..a09f096 100644 --- a/docs/reference/compute_mean_variance.simple.html +++ b/docs/reference/compute_mean_variance.simple.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Compute moments of params_old — compute_mean_variance.simple • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -186,6 +189,8 @@

Contents

+ + diff --git a/docs/reference/compute_residuals.simple.html b/docs/reference/compute_residuals.simple.html index 30ff51f..d26ff9d 100644 --- a/docs/reference/compute_residuals.simple.html +++ b/docs/reference/compute_residuals.simple.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Residuals — compute_residuals.simple • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -166,6 +171,8 @@

Contents

+ + diff --git a/docs/reference/compute_shifts_from_betas.html b/docs/reference/compute_shifts_from_betas.html index 2fda83a..fd9b8a7 100644 --- a/docs/reference/compute_shifts_from_betas.html +++ b/docs/reference/compute_shifts_from_betas.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Computation of shifts from the vector of optimal values — compute_shifts_from_betas • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -163,6 +166,8 @@

Contents

+ + diff --git a/docs/reference/compute_state_filter.html b/docs/reference/compute_state_filter.html index a935fda..42f5d30 100644 --- a/docs/reference/compute_state_filter.html +++ b/docs/reference/compute_state_filter.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ List of potential daughter states when parent is in state k. — compute_state_filter • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -166,6 +169,8 @@

Contents

+ + diff --git a/docs/reference/compute_stationary_variance.html b/docs/reference/compute_stationary_variance.html index 641d0be..a7ef1d4 100644 --- a/docs/reference/compute_stationary_variance.html +++ b/docs/reference/compute_stationary_variance.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Compute the stationary variance matrix — compute_stationary_variance • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -157,6 +162,8 @@

Contents

+ + diff --git a/docs/reference/compute_sum_var_diff.html b/docs/reference/compute_sum_var_diff.html index 2141153..f34ea33 100644 --- a/docs/reference/compute_sum_var_diff.html +++ b/docs/reference/compute_sum_var_diff.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Compute weighted sum of var_diff — compute_sum_var_diff • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,15 +34,17 @@ - + + - + + + @@ -54,14 +61,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -154,6 +159,8 @@

Contents

+ + diff --git a/docs/reference/compute_times_ca.html b/docs/reference/compute_times_ca.html index 751e4a4..583b33b 100644 --- a/docs/reference/compute_times_ca.html +++ b/docs/reference/compute_times_ca.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Common Ancestors Times — compute_times_ca • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -160,6 +163,8 @@

Contents

+ + diff --git a/docs/reference/compute_tree_correlations_matrix.BM.html b/docs/reference/compute_tree_correlations_matrix.BM.html index eed2fce..bf628e1 100644 --- a/docs/reference/compute_tree_correlations_matrix.BM.html +++ b/docs/reference/compute_tree_correlations_matrix.BM.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Matrix of tree-induced correlations for the BM — compute_tree_correlations_matrix.BM • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,15 +34,17 @@ - + + - + + + @@ -54,14 +61,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -151,6 +156,8 @@

Contents

+ + diff --git a/docs/reference/compute_tree_correlations_matrix.scOU.html b/docs/reference/compute_tree_correlations_matrix.scOU.html index fb9614a..51e8829 100644 --- a/docs/reference/compute_tree_correlations_matrix.scOU.html +++ b/docs/reference/compute_tree_correlations_matrix.scOU.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Matrix of tree-induced correlations for the scOU — compute_tree_correlations_matrix.scOU • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -165,6 +170,8 @@

Contents

+ + diff --git a/docs/reference/compute_var_M.BM.html b/docs/reference/compute_var_M.BM.html index 7a82803..94e9a1a 100644 --- a/docs/reference/compute_var_M.BM.html +++ b/docs/reference/compute_var_M.BM.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Computation of the variance. — compute_var_M.BM • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,15 +34,17 @@ - + + - + + + @@ -54,14 +61,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -169,6 +172,8 @@

Contents

+ + diff --git a/docs/reference/compute_var_diff.BM.html b/docs/reference/compute_var_diff.BM.html index c8cad01..eae410a 100644 --- a/docs/reference/compute_var_diff.BM.html +++ b/docs/reference/compute_var_diff.BM.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Compute variances of differences between nodes and parents. — compute_var_diff.BM • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -157,6 +162,8 @@

Contents

+ + diff --git a/docs/reference/compute_variance_covariance.BM.html b/docs/reference/compute_variance_covariance.BM.html index 342f574..33555a1 100644 --- a/docs/reference/compute_variance_covariance.BM.html +++ b/docs/reference/compute_variance_covariance.BM.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Complete variance covariance matrix for BM — compute_variance_covariance.BM • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -157,6 +162,8 @@

Contents

+ + diff --git a/docs/reference/compute_variance_covariance.OU.html b/docs/reference/compute_variance_covariance.OU.html index 1e36d4a..afe1d18 100644 --- a/docs/reference/compute_variance_covariance.OU.html +++ b/docs/reference/compute_variance_covariance.OU.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Complete variance covariance matrix for OU — compute_variance_covariance.OU • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -158,6 +163,8 @@

Contents

+ + diff --git a/docs/reference/compute_variance_covariance.OU.nonsym.html b/docs/reference/compute_variance_covariance.OU.nonsym.html index 3a1702b..2805c03 100644 --- a/docs/reference/compute_variance_covariance.OU.nonsym.html +++ b/docs/reference/compute_variance_covariance.OU.nonsym.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Complete variance covariance matrix for OU — compute_variance_covariance.OU.nonsym • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -158,6 +163,8 @@

Contents

+ + diff --git a/docs/reference/compute_variance_covariance.scOU.html b/docs/reference/compute_variance_covariance.scOU.html index 4166747..debfdf5 100644 --- a/docs/reference/compute_variance_covariance.scOU.html +++ b/docs/reference/compute_variance_covariance.scOU.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Complete variance covariance matrix for scOU — compute_variance_covariance.scOU • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -163,6 +168,8 @@

Contents

+ + diff --git a/docs/reference/correspondenceEdges.html b/docs/reference/correspondenceEdges.html index 23bee37..e7fb1fe 100644 --- a/docs/reference/correspondenceEdges.html +++ b/docs/reference/correspondenceEdges.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Correspondence between edges numbers — correspondenceEdges • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -160,6 +165,8 @@

Contents

+ + diff --git a/docs/reference/enlight.html b/docs/reference/enlight.html index 0b95f82..1b33ceb 100644 --- a/docs/reference/enlight.html +++ b/docs/reference/enlight.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Make the result lighter — enlight • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -183,6 +183,8 @@

Contents

+ + diff --git a/docs/reference/enumerate_parsimony-1.png b/docs/reference/enumerate_parsimony-1.png index 8caee7e275c948d72ecbaf4b754b75d3a9bb6956..8c57f9ce8879cbc0e024861a8c20fa9228daf531 100644 GIT binary patch delta 51 zcmX?ineoy4SeRqD-*2{J HnUV?s^pX-I delta 39 vcmcb0nep6Z#tA9{yqV6<0iMpz3IRp=X_+~x8y%QfSOOCMy4SeRqD-*2{J HiJJ)k*1r*l delta 39 vcmZ3on`y>wrU@znyqV6<0iMpz3IRp=X_+~x8y%QfSOOCM - + @@ -9,21 +9,25 @@ Enumerate all the possible regime allocations, given a clustering of the tips. — enumerate_parsimony • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -31,9 +35,9 @@ + - @@ -41,8 +45,10 @@ + - + + + @@ -58,14 +65,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -211,6 +212,8 @@

Contents

+ + diff --git a/docs/reference/enumerate_tips_under_edges.html b/docs/reference/enumerate_tips_under_edges.html index 3b23000..055e04f 100644 --- a/docs/reference/enumerate_tips_under_edges.html +++ b/docs/reference/enumerate_tips_under_edges.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Tips descendants of nodes. — enumerate_tips_under_edges • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -158,6 +161,8 @@

Contents

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+

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -242,6 +244,8 @@

Contents

+ + diff --git a/docs/reference/equivalent_shifts_edges.html b/docs/reference/equivalent_shifts_edges.html index 3f4363f..92ccece 100644 --- a/docs/reference/equivalent_shifts_edges.html +++ b/docs/reference/equivalent_shifts_edges.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Find all the equivalent shift edges allocations. — equivalent_shifts_edges • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -180,6 +181,8 @@

Contents

+ + diff --git a/docs/reference/equivalent_shifts_values.html b/docs/reference/equivalent_shifts_values.html index 68cbf98..d12c696 100644 --- a/docs/reference/equivalent_shifts_values.html +++ b/docs/reference/equivalent_shifts_values.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Find values given edges. OU stationary case. Ultrametric tree. — equivalent_shifts_values • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -187,6 +190,8 @@

Contents

+ + diff --git a/docs/reference/estimate.alpha.html b/docs/reference/estimate.alpha.html index 5942177..15d80d7 100644 --- a/docs/reference/estimate.alpha.html +++ b/docs/reference/estimate.alpha.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Function to estimate alpha — estimate.alpha • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + + + @@ -57,14 +64,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -190,6 +193,8 @@

Contents

+ + diff --git a/docs/reference/estimateEM.html b/docs/reference/estimateEM.html index dc3e1b4..d41fb80 100644 --- a/docs/reference/estimateEM.html +++ b/docs/reference/estimateEM.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Perform One EM — estimateEM • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -442,6 +440,8 @@

Contents

+ + diff --git a/docs/reference/extract.enumerate_parsimony.html b/docs/reference/extract.enumerate_parsimony.html index dce419b..2f4bef6 100644 --- a/docs/reference/extract.enumerate_parsimony.html +++ b/docs/reference/extract.enumerate_parsimony.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Extract the result of <code>enumerate_parsimony</code> at a node. — extract.enumerate_parsimony • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -177,6 +180,8 @@

Contents

+ + diff --git a/docs/reference/extract.equivalent_shifts.html b/docs/reference/extract.equivalent_shifts.html index 832905b..fd0a0b6 100644 --- a/docs/reference/extract.equivalent_shifts.html +++ b/docs/reference/extract.equivalent_shifts.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Extract the shifts values for one trait. — extract.equivalent_shifts • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -178,6 +181,8 @@

Contents

+ + diff --git a/docs/reference/extract.html b/docs/reference/extract.html index 29f052c..617a1fa 100644 --- a/docs/reference/extract.html +++ b/docs/reference/extract.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Extraction function — extract • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,15 +34,17 @@ - + + - + + + @@ -54,14 +61,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -163,6 +166,8 @@

Contents

+ + diff --git a/docs/reference/extract.parsimonyCost.html b/docs/reference/extract.parsimonyCost.html index bc86ad4..27d672f 100644 --- a/docs/reference/extract.parsimonyCost.html +++ b/docs/reference/extract.parsimonyCost.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Extraction of the actual number of solutions. — extract.parsimonyCost • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -170,6 +173,8 @@

Contents

+ + diff --git a/docs/reference/extract.parsimonyNumber.html b/docs/reference/extract.parsimonyNumber.html index 099fdb9..ade2ef0 100644 --- a/docs/reference/extract.parsimonyNumber.html +++ b/docs/reference/extract.parsimonyNumber.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Extraction of the actual number of solutions. — extract.parsimonyNumber • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -185,6 +186,8 @@

Contents

+ + diff --git a/docs/reference/extract.partitionsNumber.html b/docs/reference/extract.partitionsNumber.html index fb04e47..1e6d14d 100644 --- a/docs/reference/extract.partitionsNumber.html +++ b/docs/reference/extract.partitionsNumber.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Extract from object <code>partitionsNumber</code> — extract.partitionsNumber • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -183,6 +186,8 @@

Contents

+ + diff --git a/docs/reference/extract.simul_process.html b/docs/reference/extract.simul_process.html index 927b050..d2f891e 100644 --- a/docs/reference/extract.simul_process.html +++ b/docs/reference/extract.simul_process.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Extraction of simulated traits — extract.simul_process • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -182,6 +183,8 @@

Contents

+ + diff --git a/docs/reference/extract.variance_covariance.html b/docs/reference/extract.variance_covariance.html index 4eeb79e..8d2402c 100644 --- a/docs/reference/extract.variance_covariance.html +++ b/docs/reference/extract.variance_covariance.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Extract sub-matrices of variance. — extract.variance_covariance • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,15 +34,17 @@ - + + - + + + @@ -54,14 +61,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -166,6 +171,8 @@

Contents

+ + diff --git a/docs/reference/find_grid_alpha.html b/docs/reference/find_grid_alpha.html index 0941f4e..25a0287 100644 --- a/docs/reference/find_grid_alpha.html +++ b/docs/reference/find_grid_alpha.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Find a reasonable grid for alpha — find_grid_alpha • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + + + @@ -57,14 +64,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -209,6 +210,8 @@

Contents

+ + diff --git a/docs/reference/find_independent_regression_vectors.glmnet_multivariate.html b/docs/reference/find_independent_regression_vectors.glmnet_multivariate.html index 4401da8..0e8f469 100644 --- a/docs/reference/find_independent_regression_vectors.glmnet_multivariate.html +++ b/docs/reference/find_independent_regression_vectors.glmnet_multivariate.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Given a regularization path, find K selected independent variables. — find_independent_regression_vectors.glmnet_multivariate • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -168,6 +171,8 @@

Contents

+ + diff --git a/docs/reference/find_rotation.html b/docs/reference/find_rotation.html index 78a2d3b..d8ea6e8 100644 --- a/docs/reference/find_rotation.html +++ b/docs/reference/find_rotation.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Test for rotation invariant datasets — find_rotation • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -160,6 +165,8 @@

Contents

+ + diff --git a/docs/reference/find_shift_values.html b/docs/reference/find_shift_values.html index b47214b..6aa9dcc 100644 --- a/docs/reference/find_shift_values.html +++ b/docs/reference/find_shift_values.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Find values given edges. OU stationary case. Ultrametric tree. — find_shift_values • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + + + @@ -57,14 +64,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -172,6 +175,8 @@

Contents

+ + diff --git a/docs/reference/format_output.html b/docs/reference/format_output.html index 5b2229c..2c0039c 100644 --- a/docs/reference/format_output.html +++ b/docs/reference/format_output.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Run the EM for several values of K — format_output • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -195,6 +198,8 @@

Contents

+ + diff --git a/docs/reference/get_criterion.html b/docs/reference/get_criterion.html index c962d32..f5abe23 100644 --- a/docs/reference/get_criterion.html +++ b/docs/reference/get_criterion.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Get Model Selection Criterion — get_criterion • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -167,6 +170,8 @@

Contents

+ + diff --git a/docs/reference/get_variance_node.html b/docs/reference/get_variance_node.html index b6f24af..080235f 100644 --- a/docs/reference/get_variance_node.html +++ b/docs/reference/get_variance_node.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Get variance matrix of a node — get_variance_node • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -157,6 +162,8 @@

Contents

+ + diff --git a/docs/reference/go_back_to_original_process.html b/docs/reference/go_back_to_original_process.html index 5ee040d..2d5e1ac 100644 --- a/docs/reference/go_back_to_original_process.html +++ b/docs/reference/go_back_to_original_process.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Scale the parameters back to the original process — go_back_to_original_process • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -168,6 +173,8 @@

Contents

+ + diff --git a/docs/reference/imputed_traits.html b/docs/reference/imputed_traits.html index 15ae403..fe104ad 100644 --- a/docs/reference/imputed_traits.html +++ b/docs/reference/imputed_traits.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Ancestral State Reconstruction — imputed_traits • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -216,6 +218,8 @@

Contents

+ + diff --git a/docs/reference/incidence.matrix.full.html b/docs/reference/incidence.matrix.full.html index a92b59f..3b947a9 100644 --- a/docs/reference/incidence.matrix.full.html +++ b/docs/reference/incidence.matrix.full.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Incidence matrix of a tree. — incidence.matrix.full • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -160,6 +163,8 @@

Contents

+ + diff --git a/docs/reference/incidence.matrix.html b/docs/reference/incidence.matrix.html index 59cf16c..6c350fd 100644 --- a/docs/reference/incidence.matrix.html +++ b/docs/reference/incidence.matrix.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Incidence matrix of a tree. — incidence.matrix • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -160,6 +163,8 @@

Contents

+ + diff --git a/docs/reference/incidence_matrix_actualization_factors.html b/docs/reference/incidence_matrix_actualization_factors.html index 73e379e..3c72664 100644 --- a/docs/reference/incidence_matrix_actualization_factors.html +++ b/docs/reference/incidence_matrix_actualization_factors.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Compute the actualizations factors to apply to the incidence matrix. — incidence_matrix_actualization_factors • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -167,6 +172,8 @@

Contents

+ + diff --git a/docs/reference/index.html b/docs/reference/index.html index 03461b0..1aceb18 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Function reference • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,12 +34,15 @@ + + - + + + @@ -51,14 +59,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -530,6 +540,8 @@

Contents

+ + diff --git a/docs/reference/init.EM.lasso.html b/docs/reference/init.EM.lasso.html index 672d4b7..271b0f5 100644 --- a/docs/reference/init.EM.lasso.html +++ b/docs/reference/init.EM.lasso.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Initialization of the shifts using Lasso. — init.EM.lasso • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + + + @@ -60,14 +67,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -196,6 +198,8 @@

Contents

+ + diff --git a/docs/reference/init.allocate_regimes_from_shifts.html b/docs/reference/init.allocate_regimes_from_shifts.html index 3ccd9bf..2386355 100644 --- a/docs/reference/init.allocate_regimes_from_shifts.html +++ b/docs/reference/init.allocate_regimes_from_shifts.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Initialization for the allocation of shifts. — init.allocate_regimes_from_shifts • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -160,6 +163,8 @@

Contents

+ + diff --git a/docs/reference/init.alpha.gamma.estimation.html b/docs/reference/init.alpha.gamma.estimation.html index d228b0e..4930d58 100644 --- a/docs/reference/init.alpha.gamma.estimation.html +++ b/docs/reference/init.alpha.gamma.estimation.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Initialization the selection strength alpha using robust estimation — init.alpha.gamma.estimation • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + + + @@ -57,14 +64,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -183,6 +186,8 @@

Contents

+ + diff --git a/docs/reference/init.compute_betas_from_shifts.html b/docs/reference/init.compute_betas_from_shifts.html index 9287040..2b18539 100644 --- a/docs/reference/init.compute_betas_from_shifts.html +++ b/docs/reference/init.compute_betas_from_shifts.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Initialization for the computation of the optimal values — init.compute_betas_from_shifts • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -164,6 +167,8 @@

Contents

+ + diff --git a/docs/reference/init.enumerate_parsimony.html b/docs/reference/init.enumerate_parsimony.html index e3204cd..6344f5d 100644 --- a/docs/reference/init.enumerate_parsimony.html +++ b/docs/reference/init.enumerate_parsimony.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Initialization for the enumeration of parsimonious solutions. — init.enumerate_parsimony • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -165,6 +168,8 @@

Contents

+ + diff --git a/docs/reference/init.incidence.matrix.full.html b/docs/reference/init.incidence.matrix.full.html index edaf8c8..aba1cac 100644 --- a/docs/reference/init.incidence.matrix.full.html +++ b/docs/reference/init.incidence.matrix.full.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Initialization for incidence matrix (full tree) — init.incidence.matrix.full • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -163,6 +166,8 @@

Contents

+ + diff --git a/docs/reference/init.incidence.matrix.html b/docs/reference/init.incidence.matrix.html index dd3110e..cce9772 100644 --- a/docs/reference/init.incidence.matrix.html +++ b/docs/reference/init.incidence.matrix.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Initialization for incidence matrix — init.incidence.matrix • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -163,6 +166,8 @@

Contents

+ + diff --git a/docs/reference/init.parsimonyCost.html b/docs/reference/init.parsimonyCost.html index d9e65fa..19ce900 100644 --- a/docs/reference/init.parsimonyCost.html +++ b/docs/reference/init.parsimonyCost.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Initialization for parsimonyCost. — init.parsimonyCost • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -164,6 +167,8 @@

Contents

+ + diff --git a/docs/reference/init.parsimonyNumber.html b/docs/reference/init.parsimonyNumber.html index e9db3b7..8d85e5c 100644 --- a/docs/reference/init.parsimonyNumber.html +++ b/docs/reference/init.parsimonyNumber.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Initialization for parsimonyNumber. — init.parsimonyNumber • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -163,6 +166,8 @@

Contents

+ + diff --git a/docs/reference/init.simulate.BM.html b/docs/reference/init.simulate.BM.html index 0735d7a..bed31e7 100644 --- a/docs/reference/init.simulate.BM.html +++ b/docs/reference/init.simulate.BM.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Initialize BM — init.simulate.BM • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,15 +34,17 @@ - + + - + + + @@ -54,14 +61,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -160,6 +165,8 @@

Contents

+ + diff --git a/docs/reference/init.simulate.OU.html b/docs/reference/init.simulate.OU.html index 4965966..d266914 100644 --- a/docs/reference/init.simulate.OU.html +++ b/docs/reference/init.simulate.OU.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Initialize state and expectation matrices — init.simulate.OU • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,15 +34,17 @@ - + + - + + + @@ -54,14 +61,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -164,6 +169,8 @@

Contents

+ + diff --git a/docs/reference/init.simulate.StateAndExp.html b/docs/reference/init.simulate.StateAndExp.html index 528ce5f..4e754e7 100644 --- a/docs/reference/init.simulate.StateAndExp.html +++ b/docs/reference/init.simulate.StateAndExp.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Initialize state and expectation matrices — init.simulate.StateAndExp • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,15 +34,17 @@ - + + - + + + @@ -54,14 +61,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -164,6 +169,8 @@

Contents

+ + diff --git a/docs/reference/is.in.ranges.html b/docs/reference/is.in.ranges.html index 639872f..7378ea1 100644 --- a/docs/reference/is.in.ranges.html +++ b/docs/reference/is.in.ranges.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Check whether parameters are in ranges. — is.in.ranges • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -209,6 +213,8 @@

Contents

+ + diff --git a/docs/reference/lasso_regression_K_fixed.glmnet_multivariate.html b/docs/reference/lasso_regression_K_fixed.glmnet_multivariate.html index 1be176b..3249562 100644 --- a/docs/reference/lasso_regression_K_fixed.glmnet_multivariate.html +++ b/docs/reference/lasso_regression_K_fixed.glmnet_multivariate.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Do a lasso regression with the number of non-zero variables fixed. — lasso_regression_K_fixed.glmnet_multivariate • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + + + @@ -59,14 +66,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -178,6 +181,8 @@

Contents

+ + diff --git a/docs/reference/log_likelihood.html b/docs/reference/log_likelihood.html index db93310..374bd7a 100644 --- a/docs/reference/log_likelihood.html +++ b/docs/reference/log_likelihood.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Log Likelihood of a fitted object — log_likelihood • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,15 +34,17 @@ - + + - + + + @@ -54,14 +61,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -188,6 +190,8 @@

Contents

+ + diff --git a/docs/reference/matrix_of_possibles.html b/docs/reference/matrix_of_possibles.html index 141aaa7..f10d69a 100644 --- a/docs/reference/matrix_of_possibles.html +++ b/docs/reference/matrix_of_possibles.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Compute parent matrix from possibles daughter matrices. — matrix_of_possibles • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -161,6 +164,8 @@

Contents

+ + diff --git a/docs/reference/merge_complementary_vectors.html b/docs/reference/merge_complementary_vectors.html index 47ef89e..077400c 100644 --- a/docs/reference/merge_complementary_vectors.html +++ b/docs/reference/merge_complementary_vectors.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Merge several complementary vectors into one. — merge_complementary_vectors • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -165,6 +168,8 @@

Contents

+ + diff --git a/docs/reference/merge_params_independent.html b/docs/reference/merge_params_independent.html index 65452f6..34870db 100644 --- a/docs/reference/merge_params_independent.html +++ b/docs/reference/merge_params_independent.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Merge a list of independent parameters into into one parameter — merge_params_independent • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -154,6 +159,8 @@

Contents

+ + diff --git a/docs/reference/merge_rotations.html b/docs/reference/merge_rotations.html index db93df1..f462e26 100644 --- a/docs/reference/merge_rotations.html +++ b/docs/reference/merge_rotations.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Merge fits from independent runs of PhyloEM. — merge_rotations • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + + + @@ -58,14 +65,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -207,6 +210,8 @@

Contents

+ + diff --git a/docs/reference/model_selection.html b/docs/reference/model_selection.html index db1576b..2d84eda 100644 --- a/docs/reference/model_selection.html +++ b/docs/reference/model_selection.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Model Selection of a fitted object — model_selection • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -205,6 +207,8 @@

Contents

+ + diff --git a/docs/reference/monkeys.html b/docs/reference/monkeys.html index b7fd37e..259f2d1 100644 --- a/docs/reference/monkeys.html +++ b/docs/reference/monkeys.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ New World Monkeys dataset — monkeys • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -156,6 +161,8 @@

Contents

+ + diff --git a/docs/reference/params_BM.html b/docs/reference/params_BM.html index 7a231e3..bfcb822 100644 --- a/docs/reference/params_BM.html +++ b/docs/reference/params_BM.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Create an object <code>params_process</code> for a BM — params_BM • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -227,6 +230,8 @@

Contents

+ + diff --git a/docs/reference/params_OU.html b/docs/reference/params_OU.html index 30f901d..41ba7ca 100644 --- a/docs/reference/params_OU.html +++ b/docs/reference/params_OU.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Create an object <code>params_process</code> for an OU — params_OU • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -239,6 +242,8 @@

Contents

+ + diff --git a/docs/reference/params_process.PhyloEM.html b/docs/reference/params_process.PhyloEM.html index f81c7d3..3b52e2c 100644 --- a/docs/reference/params_process.PhyloEM.html +++ b/docs/reference/params_process.PhyloEM.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Parameter estimates — params_process.PhyloEM • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -194,6 +197,8 @@

Contents

+ + diff --git a/docs/reference/params_process.character.html b/docs/reference/params_process.character.html index 2d89f5a..1dd1bc3 100644 --- a/docs/reference/params_process.character.html +++ b/docs/reference/params_process.character.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Create an object <code>params_process</code> — params_process.character • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -164,6 +167,8 @@

Contents

+ + diff --git a/docs/reference/params_process.html b/docs/reference/params_process.html index 6916a05..102cfc7 100644 --- a/docs/reference/params_process.html +++ b/docs/reference/params_process.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Create an object params_process — params_process • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -188,6 +190,8 @@

Contents

+ + diff --git a/docs/reference/parsimonyCost-1.png b/docs/reference/parsimonyCost-1.png index 85b83a2cea85e374731c5faaee92c9e64cadb833..90ec9bba81ad6c97fb398108ebffcdce559fa23a 100644 GIT binary patch delta 51 zcmbRLfN}K$#tAAil9|rV0ol&(&iOg{MZpD$$*JzCd8tL2$wBT;8%>y4SeRqD-*2{J Hd72FX=lT*h delta 39 vcmZ4efN}l<#tA9{yqV6<0iMpz3IRp=X_+~x8y%QfSOOCM - + @@ -8,21 +8,25 @@ Minimal number of shifts needed to get a clustering. — parsimonyCost • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + + + @@ -58,14 +65,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -188,6 +190,8 @@

Contents

+ + diff --git a/docs/reference/parsimonyNumber-1.png b/docs/reference/parsimonyNumber-1.png index 7f3cf01eac045d6cf628837410f035e467254a70..eab3751a25203e9be7b146909adab9a3a4d03cfa 100644 GIT binary patch delta 51 zcmaF#kn!C^#tAAil9|rV0ol&(&iOg{MZpD$$*JzCd8tL2$wBT;8%>y4SeRqD-*2{J HS&;((0ooFR delta 39 vcmaF&knzz&#tA9{yqV6<0iMpz3IRp=X_+~x8y%QfSOOCM - + @@ -8,21 +8,25 @@ Number of equivalent parsimonious allocations. — parsimonyNumber • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -200,6 +201,8 @@

Contents

+ + diff --git a/docs/reference/partitionsNumber-1.png b/docs/reference/partitionsNumber-1.png index 451148139807f924253ec9a118af3816f71b6644..6990fb1119948b8416821b9de695bea4e1210429 100644 GIT binary patch delta 51 zcmX?jpYiN{#tAAil9|rV0ol&(&iOg{MZpD$$*JzCd8tL2$wBT;8%>y4SeRqD-*2{J HY0m}#^aBza delta 39 vcmX?mpYh;*#tA9{yqV6<0iMpz3IRp=X_+~x8y%QfSOOCM - + @@ -8,21 +8,25 @@ Number of different models — partitionsNumber • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -193,6 +195,8 @@

Contents

+ + diff --git a/docs/reference/penalty_BaraudGiraudHuet_likelihood.html b/docs/reference/penalty_BaraudGiraudHuet_likelihood.html index 23103ad..af2061b 100644 --- a/docs/reference/penalty_BaraudGiraudHuet_likelihood.html +++ b/docs/reference/penalty_BaraudGiraudHuet_likelihood.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Penalty function type Baraud Giraud Huet. — penalty_BaraudGiraudHuet_likelihood • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + + + @@ -58,14 +65,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -187,6 +188,8 @@

Contents

+ + diff --git a/docs/reference/penalty_BirgeMassart_shape1.html b/docs/reference/penalty_BirgeMassart_shape1.html index 0b20ee0..4373dbc 100644 --- a/docs/reference/penalty_BirgeMassart_shape1.html +++ b/docs/reference/penalty_BirgeMassart_shape1.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Penalty function type Birgé-Massart 1 — penalty_BirgeMassart_shape1 • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -182,6 +183,8 @@

Contents

+ + diff --git a/docs/reference/penalty_BirgeMassart_shape2.html b/docs/reference/penalty_BirgeMassart_shape2.html index af14dbd..bb3f15a 100644 --- a/docs/reference/penalty_BirgeMassart_shape2.html +++ b/docs/reference/penalty_BirgeMassart_shape2.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Penalty function type Birgé-Massart 2 — penalty_BirgeMassart_shape2 • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -182,6 +183,8 @@

Contents

+ + diff --git a/docs/reference/penalty_pBIC.html b/docs/reference/penalty_pBIC.html index 49bdf74..124e8bb 100644 --- a/docs/reference/penalty_pBIC.html +++ b/docs/reference/penalty_pBIC.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Penalty function type pBIC — penalty_pBIC • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,15 +34,17 @@ - + + - + + + @@ -54,14 +61,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -171,6 +174,8 @@

Contents

+ + diff --git a/docs/reference/plot.PhyloEM.html b/docs/reference/plot.PhyloEM.html index f60c0ac..fce6884 100644 --- a/docs/reference/plot.PhyloEM.html +++ b/docs/reference/plot.PhyloEM.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Plot for class <code>PhyloEM</code> — plot.PhyloEM • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -321,6 +331,8 @@

Contents

+ + diff --git a/docs/reference/plot.enumerate_parsimony.html b/docs/reference/plot.enumerate_parsimony.html index eb3c343..85dd990 100644 --- a/docs/reference/plot.enumerate_parsimony.html +++ b/docs/reference/plot.enumerate_parsimony.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Plot all the equivalent solutions. — plot.enumerate_parsimony • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -183,6 +184,8 @@

Contents

+ + diff --git a/docs/reference/plot.equivalent_shifts.html b/docs/reference/plot.equivalent_shifts.html index d8a758f..672deb7 100644 --- a/docs/reference/plot.equivalent_shifts.html +++ b/docs/reference/plot.equivalent_shifts.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Plot all the equivalent solutions. — plot.equivalent_shifts • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -214,6 +215,8 @@

Contents

+ + diff --git a/docs/reference/plot.params_process.html b/docs/reference/plot.params_process.html index d08b85d..2506b7f 100644 --- a/docs/reference/plot.params_process.html +++ b/docs/reference/plot.params_process.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Plot for class <code>simul_process</code> — plot.params_process • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -312,6 +317,8 @@

Contents

+ + diff --git a/docs/reference/plot_criterion.html b/docs/reference/plot_criterion.html index d9e8347..dcdb2cb 100644 --- a/docs/reference/plot_criterion.html +++ b/docs/reference/plot_criterion.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Plot Model Selection Criterion — plot_criterion • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -172,6 +177,8 @@

Contents

+ + diff --git a/docs/reference/prod.index.html b/docs/reference/prod.index.html index 6f6879b..ec86cf5 100644 --- a/docs/reference/prod.index.html +++ b/docs/reference/prod.index.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Product of elements of a matrix — prod.index • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,15 +34,17 @@ - + + - + + + @@ -54,14 +61,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -165,6 +168,8 @@

Contents

+ + diff --git a/docs/reference/qr.solve_exact.html b/docs/reference/qr.solve_exact.html index 68000bd..8e7c0bf 100644 --- a/docs/reference/qr.solve_exact.html +++ b/docs/reference/qr.solve_exact.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ exact qr.solve — qr.solve_exact • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -158,6 +165,8 @@

Contents

+ + diff --git a/docs/reference/recursionDown.html b/docs/reference/recursionDown.html index f7b18ec..269ea33 100644 --- a/docs/reference/recursionDown.html +++ b/docs/reference/recursionDown.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Generic recursion down the tree. — recursionDown • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -172,6 +175,8 @@

Contents

+ + diff --git a/docs/reference/residuals.PhyloEM.html b/docs/reference/residuals.PhyloEM.html index 0eafcdf..eac5b6b 100644 --- a/docs/reference/residuals.PhyloEM.html +++ b/docs/reference/residuals.PhyloEM.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Residuals of a fitted object — residuals.PhyloEM • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,15 +34,17 @@ - + + - + + + @@ -54,14 +61,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -166,6 +169,8 @@

Contents

+ + diff --git a/docs/reference/sample_edges_intervals.html b/docs/reference/sample_edges_intervals.html index 90be3e5..8c42db2 100644 --- a/docs/reference/sample_edges_intervals.html +++ b/docs/reference/sample_edges_intervals.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Sample equally spaced edges. — sample_edges_intervals • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -163,6 +166,8 @@

Contents

+ + diff --git a/docs/reference/sample_shifts_edges.html b/docs/reference/sample_shifts_edges.html index 6dd5227..7a6a4a7 100644 --- a/docs/reference/sample_shifts_edges.html +++ b/docs/reference/sample_shifts_edges.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Sample shifts edges in a parsimonious way. — sample_shifts_edges • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -167,6 +170,8 @@

Contents

+ + diff --git a/docs/reference/scale_params.html b/docs/reference/scale_params.html index ba41b09..41ea064 100644 --- a/docs/reference/scale_params.html +++ b/docs/reference/scale_params.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Scale variance and selection strength from a linear transform — scale_params • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,15 +34,17 @@ - + + - + + + @@ -54,14 +61,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -155,6 +160,8 @@

Contents

+ + diff --git a/docs/reference/segmentation.BM.html b/docs/reference/segmentation.BM.html index 34b57f5..786ec73 100644 --- a/docs/reference/segmentation.BM.html +++ b/docs/reference/segmentation.BM.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Segmentation in the BM case — segmentation.BM • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,15 +34,17 @@ - + + - + + + @@ -54,14 +61,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -167,6 +170,8 @@

Contents

+ + diff --git a/docs/reference/segmentation.OU.specialCase.lasso.html b/docs/reference/segmentation.OU.specialCase.lasso.html index 9355dd2..ab57bd4 100644 --- a/docs/reference/segmentation.OU.specialCase.lasso.html +++ b/docs/reference/segmentation.OU.specialCase.lasso.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Segmentation in the OU special case, using lasso regression — segmentation.OU.specialCase.lasso • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -177,6 +180,8 @@

Contents

+ + diff --git a/docs/reference/segmentation.OU.specialCase.same_shifts.html b/docs/reference/segmentation.OU.specialCase.same_shifts.html index eaf1617..af6808a 100644 --- a/docs/reference/segmentation.OU.specialCase.same_shifts.html +++ b/docs/reference/segmentation.OU.specialCase.same_shifts.html @@ -1,6 +1,6 @@ - + @@ -9,21 +9,25 @@ Segmentation in the OU special case, conserving the same shifts position. — segmentation.OU.specialCase.same_shifts • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -31,9 +35,9 @@ + - @@ -41,8 +45,10 @@ + - + + + @@ -58,14 +65,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -178,6 +181,8 @@

Contents

+ + diff --git a/docs/reference/shifts.list_to_matrix.html b/docs/reference/shifts.list_to_matrix.html index e761e5f..7e16e21 100644 --- a/docs/reference/shifts.list_to_matrix.html +++ b/docs/reference/shifts.list_to_matrix.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Compute the matrix of shifts. — shifts.list_to_matrix • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -168,6 +171,8 @@

Contents

+ + diff --git a/docs/reference/shifts.list_to_vector.html b/docs/reference/shifts.list_to_vector.html index bdd122c..046cd77 100644 --- a/docs/reference/shifts.list_to_vector.html +++ b/docs/reference/shifts.list_to_vector.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Compute the vector of shifts. — shifts.list_to_vector • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -164,6 +167,8 @@

Contents

+ + diff --git a/docs/reference/shifts.matrix_to_list.html b/docs/reference/shifts.matrix_to_list.html index 35bef1e..0f6edf0 100644 --- a/docs/reference/shifts.matrix_to_list.html +++ b/docs/reference/shifts.matrix_to_list.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Compute the list of shifts. — shifts.matrix_to_list • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -158,6 +161,8 @@

Contents

+ + diff --git a/docs/reference/shifts.vector_to_list.html b/docs/reference/shifts.vector_to_list.html index 9e9d02a..f129208 100644 --- a/docs/reference/shifts.vector_to_list.html +++ b/docs/reference/shifts.vector_to_list.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Compute the list of shifts. — shifts.vector_to_list • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -158,6 +161,8 @@

Contents

+ + diff --git a/docs/reference/shifts_to_simmap.html b/docs/reference/shifts_to_simmap.html index f33ef7e..d064ce5 100644 --- a/docs/reference/shifts_to_simmap.html +++ b/docs/reference/shifts_to_simmap.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Simmap format mapping from list of edges — shifts_to_simmap • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -162,6 +165,8 @@

Contents

+ + diff --git a/docs/reference/simul_process.html b/docs/reference/simul_process.html index a914b08..ba51532 100644 --- a/docs/reference/simul_process.html +++ b/docs/reference/simul_process.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Simulate a Stochastic Process on a tree — simul_process • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,15 +34,17 @@ - + + - + + + @@ -54,14 +61,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -213,6 +216,8 @@

Contents

+ + diff --git a/docs/reference/simulate_internal.html b/docs/reference/simulate_internal.html index c78d62f..b2641a7 100644 --- a/docs/reference/simulate_internal.html +++ b/docs/reference/simulate_internal.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Simulate a Stochastic Process on a tree — simulate_internal • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,15 +34,17 @@ - + + - + + + @@ -54,14 +61,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -229,6 +236,8 @@

Contents

+ + diff --git a/docs/reference/split_params_independent.html b/docs/reference/split_params_independent.html index bf05aae..0f8a1d5 100644 --- a/docs/reference/split_params_independent.html +++ b/docs/reference/split_params_independent.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Split independent parameters into a list of parameters — split_params_independent • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -154,6 +159,8 @@

Contents

+ + diff --git a/docs/reference/sum.partitions.cardFixed.html b/docs/reference/sum.partitions.cardFixed.html index 3a1ab5a..a66e354 100644 --- a/docs/reference/sum.partitions.cardFixed.html +++ b/docs/reference/sum.partitions.cardFixed.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Sum on subsets of a given cardinal. — sum.partitions.cardFixed • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -179,6 +182,8 @@

Contents

+ + diff --git a/docs/reference/sum.partitions.html b/docs/reference/sum.partitions.html index 6f96d39..2f088a4 100644 --- a/docs/reference/sum.partitions.html +++ b/docs/reference/sum.partitions.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Sum on all subsets. — sum.partitions • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,15 +34,17 @@ - + + - + + + @@ -54,14 +61,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -177,6 +180,8 @@

Contents

+ + diff --git a/docs/reference/sum.prod.comb.html b/docs/reference/sum.prod.comb.html index 6417985..15cb6c5 100644 --- a/docs/reference/sum.prod.comb.html +++ b/docs/reference/sum.prod.comb.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Sum on a simplex — sum.prod.comb • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -179,6 +182,8 @@

Contents

+ + diff --git a/docs/reference/sum.simplex.html b/docs/reference/sum.simplex.html index b38088c..b74db76 100644 --- a/docs/reference/sum.simplex.html +++ b/docs/reference/sum.simplex.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Sum on a simplex — sum.simplex • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -170,6 +173,8 @@

Contents

+ + diff --git a/docs/reference/test.root.state.html b/docs/reference/test.root.state.html index 60d2513..979becb 100644 --- a/docs/reference/test.root.state.html +++ b/docs/reference/test.root.state.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Test state of root. — test.root.state • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -169,6 +172,8 @@

Contents

+ + diff --git a/docs/reference/transform_branch_length.html b/docs/reference/transform_branch_length.html index 1ec07b1..c4c46eb 100644 --- a/docs/reference/transform_branch_length.html +++ b/docs/reference/transform_branch_length.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Transform branch length for a re-scaled BM — transform_branch_length • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -159,6 +164,8 @@

Contents

+ + diff --git a/docs/reference/transform_shifts_values.html b/docs/reference/transform_shifts_values.html index 722e20f..25ac568 100644 --- a/docs/reference/transform_shifts_values.html +++ b/docs/reference/transform_shifts_values.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Transform the shift values — transform_shifts_values • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + + + @@ -57,14 +64,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -163,6 +170,8 @@

Contents

+ + diff --git a/docs/reference/update.allocate_regimes_from_shifts.html b/docs/reference/update.allocate_regimes_from_shifts.html index 3158a01..44362a4 100644 --- a/docs/reference/update.allocate_regimes_from_shifts.html +++ b/docs/reference/update.allocate_regimes_from_shifts.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Update function for regime allocation. — update.allocate_regimes_from_shifts • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -168,6 +171,8 @@

Contents

+ + diff --git a/docs/reference/update.compute_betas_from_shifts.html b/docs/reference/update.compute_betas_from_shifts.html index a491c01..15cf099 100644 --- a/docs/reference/update.compute_betas_from_shifts.html +++ b/docs/reference/update.compute_betas_from_shifts.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Update function for optimal value computation — update.compute_betas_from_shifts • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -167,6 +170,8 @@

Contents

+ + diff --git a/docs/reference/update.enumerate_parsimony.html b/docs/reference/update.enumerate_parsimony.html index 5afe895..c4f7fec 100644 --- a/docs/reference/update.enumerate_parsimony.html +++ b/docs/reference/update.enumerate_parsimony.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Actualization of the enumeration. — update.enumerate_parsimony • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -173,6 +176,8 @@

Contents

+ + diff --git a/docs/reference/update.incidence.matrix.full.html b/docs/reference/update.incidence.matrix.full.html index b2e3e46..12f351a 100644 --- a/docs/reference/update.incidence.matrix.full.html +++ b/docs/reference/update.incidence.matrix.full.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Update function for incidence matrix — update.incidence.matrix.full • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -162,6 +165,8 @@

Contents

+ + diff --git a/docs/reference/update.incidence.matrix.html b/docs/reference/update.incidence.matrix.html index 729bc15..dd067ec 100644 --- a/docs/reference/update.incidence.matrix.html +++ b/docs/reference/update.incidence.matrix.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Update function for incidence matrix — update.incidence.matrix • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,8 +43,10 @@ + - + + + @@ -56,14 +63,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -162,6 +165,8 @@

Contents

+ + diff --git a/docs/reference/update.parsimonyCost.html b/docs/reference/update.parsimonyCost.html index 21854dc..a6be185 100644 --- a/docs/reference/update.parsimonyCost.html +++ b/docs/reference/update.parsimonyCost.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Actualization for parsimonyCost. — update.parsimonyCost • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -161,6 +164,8 @@

Contents

+ + diff --git a/docs/reference/update.parsimonyNumber.html b/docs/reference/update.parsimonyNumber.html index 52e21ba..dc3250b 100644 --- a/docs/reference/update.parsimonyNumber.html +++ b/docs/reference/update.parsimonyNumber.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Actualization for parsimonyNumber. — update.parsimonyNumber • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -168,6 +171,8 @@

Contents

+ + diff --git a/docs/reference/update.partitionsNumber.gen.html b/docs/reference/update.partitionsNumber.gen.html index 5a610bc..d797477 100644 --- a/docs/reference/update.partitionsNumber.gen.html +++ b/docs/reference/update.partitionsNumber.gen.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Update formula in the general case — update.partitionsNumber.gen • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -164,6 +167,8 @@

Contents

+ + diff --git a/docs/reference/wrapper_E_step.html b/docs/reference/wrapper_E_step.html index e6d79fd..e3403c5 100644 --- a/docs/reference/wrapper_E_step.html +++ b/docs/reference/wrapper_E_step.html @@ -1,6 +1,6 @@ - + @@ -8,21 +8,25 @@ Wrapper for E step in EM — wrapper_E_step • PhylogeneticEM + - + - - + + + - + + - + - - + + + @@ -30,16 +34,18 @@ - + + - + + + @@ -55,14 +62,15 @@ +

Developed by Paul Bastide.

-

Site built with pkgdown.

+

Site built with pkgdown 1.4.1.

@@ -138,6 +146,8 @@

Contents

+ +