10 Documenting the package and building
We finish by running commands that will document, build, and install the package. It may also be a good idea to check the package from within this file.
## ℹ Updating flowtrend documentation
## ℹ Loading flowtrend
## ℹ Re-compiling flowtrend (debug build)
##
## ✖ Estep.R:5: @param requires two parts: an argument name and a description.
## ✖ Estep.R:7: @param requires two parts: an argument name and a description.
## ✖ Estep.R:8: @param requires two parts: an argument name and a description.
## ✖ Estep.R:9: @param requires two parts: an argument name and a description.
## ✖ Estep.R:10: @param requires two parts: an argument name and a description.
## ✖ Estep.R:11: @param requires two parts: an argument name and a description.
## ✖ Estep.R:12: @param requires two parts: an argument name and a description.
## ✖ Estep.R:17: @return requires a value.
## ✖ Mstep_mu.R:7: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:8: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:9: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:10: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:11: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:12: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:13: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:14: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:15: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:16: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:17: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:18: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:19: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:20: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:21: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:22: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:23: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:24: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:25: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:26: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:27: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:28: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:29: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:30: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu.R:33: @return requires a value.
## ✖ Mstep_mu.R:36: @examples requires a value.
## ✖ Mstep_mu_cvxr.R:5: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu_cvxr.R:6: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu_cvxr.R:7: @param requires two parts: an argument name and a description.
## ✖ Mstep_mu_cvxr.R:8: @param requires two parts: an argument name and a description.
## ✖ Mstep_sigma.R:13: @examples requires a value.
## ✖ etilde_mat.R:5: @param requires two parts: an argument name and a description.
## ✖ flowtrend.R:8: @return requires a value.
## ✖ flowtrend.R:11: @examples requires a value.
## ✖ flowtrend_once.R:22: @param requires two parts: an argument name and a description.
## ✖ flowtrend_once.R:23: @param requires two parts: an argument name and a description.
## ✖ flowtrend_once.R:24: @param requires two parts: an argument name and a description.
## ✖ flowtrend_once.R:25: @param requires two parts: an argument name and a description.
## ✖ flowtrend_once.R:31: @examples requires a value.
## ✖ gen_diff_mat.R:12: @examples requires a value.
## ✖ get_AB_mats.R:5: @param requires two parts: an argument name and a description.
## ✖ get_C_mat.R:4: @param requires two parts: an argument name and a description.
## ✖ la_admm_oneclust.R:5: @param requires two parts: an argument name and a description.
## ✖ la_admm_oneclust.R:8: @return requires a value.
## ✖ la_admm_oneclust.R:10: @examples requires a value.
## ✖ make_cvscore_filename.R:4: @param requires two parts: an argument name and a description.
## ✖ make_cvscore_filename.R:5: @param requires two parts: an argument name and a description.
## ✖ make_cvscore_filename.R:6: @param requires two parts: an argument name and a description.
## ✖ make_cvscore_filename.R:16: @param requires two parts: an argument name and a description.
## ✖ make_cvscore_filename.R:17: @param requires two parts: an argument name and a description.
## ✖ make_cvscore_filename.R:18: @param requires two parts: an argument name and a description.
## ✖ make_cvscore_filename.R:30: @param requires two parts: an argument name and a description.
## ✖ make_cvscore_filename.R:31: @param requires two parts: an argument name and a description.
## ✖ make_cvscore_filename.R:42: @param requires two parts: an argument name and a description.
## ✖ match_clusters_gmm.R:108: @return requires a value.
## ✖ memlist_to_respmat.R:7: @return requires a value.
## ✖ objective.R:5: @param requires two parts: an argument name and a description.
## ✖ objective.R:6: @param requires two parts: an argument name and a description.
## ✖ objective.R:7: @param requires two parts: an argument name and a description.
## ✖ objective.R:8: @param requires two parts: an argument name and a description.
## ✖ objective.R:9: @param requires two parts: an argument name and a description.
## ✖ objective.R:10: @param requires two parts: an argument name and a description.
## ✖ objective.R:11: @param requires two parts: an argument name and a description.
## ✖ objective.R:12: @param requires two parts: an argument name and a description.
## ✖ objective.R:13: @param requires two parts: an argument name and a description.
## ✖ objective.R:14: @param requires two parts: an argument name and a description.
## ✖ objective.R:15: @param requires two parts: an argument name and a description.
## ✖ objective.R:16: @param requires two parts: an argument name and a description.
## ✖ objective.R:17: @param requires two parts: an argument name and a description.
## ✖ objective.R:18: @param requires two parts: an argument name and a description.
## ✖ objective.R:21: @return requires a value.
## ✖ objective.R:24: @examples requires a value.
## ✖ overfit_gmm.R:7: @return requires a value.
## ✖ plot_3d.R:15: @return requires a value.
## ✖ rand_old.R:118: @return Could not resolve link to topic "1:2,1:2" in the dependencies or base packages.
## ℹ If you haven't documented "1:2,1:2" yet, or just changed its name, this is normal. Once "1:2,1:2" is documented, this
## warning goes away.
## ℹ Make sure that the name of the topic is spelled correctly.
## ℹ Always list the linked package as a dependency.
## ℹ Alternatively, you can fully qualify the link with a package name.
## ✖ rand_old.R:118: @return Could not resolve link to topic ",3" in the dependencies or base packages.
## ℹ If you haven't documented ",3" yet, or just changed its name, this is normal. Once ",3" is documented, this warning goes
## away.
## ℹ Make sure that the name of the topic is spelled correctly.
## ℹ Always list the linked package as a dependency.
## ℹ Alternatively, you can fully qualify the link with a package name.
## ✖ rand_old.R:118: @return Could not resolve link to topic "3," in the dependencies or base packages.
## ℹ If you haven't documented "3," yet, or just changed its name, this is normal. Once "3," is documented, this warning goes
## away.
## ℹ Make sure that the name of the topic is spelled correctly.
## ℹ Always list the linked package as a dependency.
## ℹ Alternatively, you can fully qualify the link with a package name.
## ✖ rand_old.R:132: @param Could not resolve link to topic "1:2,1:2" in the dependencies or base packages.
## ℹ If you haven't documented "1:2,1:2" yet, or just changed its name, this is normal. Once "1:2,1:2" is documented, this
## warning goes away.
## ℹ Make sure that the name of the topic is spelled correctly.
## ℹ Always list the linked package as a dependency.
## ℹ Alternatively, you can fully qualify the link with a package name.
## ✖ rand_old.R:148: @param requires two parts: an argument name and a description.
## ✖ soft_gate_one_responsibility_matrix.R:7: @return requires a value.
## ✖ underfit_gmm.R:7: @return requires a value.
## ✖ In topic 'U_update_W.Rd': Skipping; no name and/or title.
## ✖ In topic 'U_update_Z.Rd': Skipping; no name and/or title.
## ✖ In topic 'myschur.Rd': Skipping; no name and/or title.
## Writing 'NAMESPACE'
## Writing 'Estep.Rd'
## Writing 'Mstep_mu.Rd'
## Writing 'Mstep_mu_cvxr.Rd'
## Writing 'Mstep_prob.Rd'
## Writing 'Mstep_sigma.Rd'
## Writing 'matrix_function_solve_triangular_sylvester_barebonesC2.Rd'
## Writing 'prox_dp.Rd'
## Writing 'W_update_fused.Rd'
## Writing 'projCmat.Rd'
## Writing 'admm_oneclust.Rd'
## Writing 'aug_lagr.Rd'
## Writing 'calc_max_lambda.Rd'
## Writing 'check_converge.Rd'
## Writing 'check_converge_rel.Rd'
## Writing 'create_destin.Rd'
## Writing 'create_oracle.Rd'
## Writing 'cv_aggregate.Rd'
## Writing 'cv_aggregate_res.Rd'
## Writing 'cv_flowtrend.Rd'
## Writing 'cv_makebest.Rd'
## Writing 'load_all_objectives.Rd'
## Writing 'load_all_refit_objectives.Rd'
## Writing 'keep_only_best.Rd'
## Writing 'keep_only_best_refit.Rd'
## Writing 'cv_summary.Rd'
## Writing 'dt2ylist.Rd'
## Writing 'etilde_mat.Rd'
## Writing 'flowtrend-package.Rd'
## Writing 'flowtrend.Rd'
## Writing 'flowtrend_once.Rd'
## Writing 'form_symmetric_kl_distmat.Rd'
## Writing 'gen_diff_mat.Rd'
## Writing 'gen_tf_mat.Rd'
## Writing 'gen_tf_mat_equalspace.Rd'
## Writing 'gendat_1d.Rd'
## Writing 'gendat_2d.Rd'
## Writing 'gendat_3d.Rd'
## Writing 'get_AB_mats.Rd'
## Writing 'get_C_mat.Rd'
## Writing 'get_best_match_from_kl.Rd'
## Writing 'get_max_lambda.Rd'
## Writing 'init_mn.Rd'
## Writing 'init_sigma.Rd'
## Writing 'interpolate_mn.Rd'
## Writing 'interpolate_prob.Rd'
## Writing 'la_admm_oneclust.Rd'
## Writing 'loglik_tt.Rd'
## Writing 'logspace.Rd'
## Writing 'make_cv_folds.Rd'
## Writing 'make_cv_folds_in_blocks.Rd'
## Writing 'make_cvscore_filename.Rd'
## Writing 'make_best_cvscore_filename.Rd'
## Writing 'make_refit_filename.Rd'
## Writing 'make_best_refit_filename.Rd'
## Writing 'make_iilist.Rd'
## Writing 'make_iimat.Rd'
## Writing 'make_iimat_small.Rd'
## Writing 'match_clusters_gmm.Rd'
## Writing 'symmetric_kl_between_gaussians.Rd'
## Writing 'one_symmetric_kl.Rd'
## Writing 'gmm_each.Rd'
## Writing 'memlist_to_respmat.Rd'
## Writing 'my_mfrow.Rd'
## Writing 'objective.Rd'
## Writing 'objective_per_cluster.Rd'
## Writing 'one_job.Rd'
## Writing 'one_job_refit.Rd'
## Writing 'overfit_gmm.Rd'
## Writing 'parse_args.Rd'
## Writing 'plot_1d.Rd'
## Writing 'plot_1d_add_model.Rd'
## Writing 'plot_1d_with_membership.Rd'
## Writing 'plot_2d.Rd'
## Writing 'plot_3d.Rd'
## Writing 'plot_prob.Rd'
## Writing 'predict_flowtrend.Rd'
## Writing 'print_progress.Rd'
## Writing 'rand_old.Rd'
## Writing 'rand.Rd'
## Writing 'make_contingency_table.Rd'
## Writing 'get_rand_from_table.Rd'
## Writing 'rand_from_mems.Rd'
## Writing 'reorder_clust.Rd'
## Writing 'reorder_gmm_fit.Rd'
## Writing 'reorder_kl.Rd'
## Writing 'soft_gate_one_responsibility_matrix.Rd'
## Writing 'softmax.Rd'
## Writing 'symmetric_kl.Rd'
## Writing 'underfit_gmm.Rd'
## Writing 'pipe.Rd'## Note to self: the fancier readme and pkgdown features don't seem to work
## during the knitting; need to be done manually afterwards, which is fine.
if(FALSE){
## Temporarily here; This tricks litr::render(minimal_eval=TRUE) into running this code.
litr::add_readme("../setup/readme-for-r-package.Rmd") ## adds readme to R package
litr::add_pkgdown("../setup/_pkgdown.yml") ## adds pkgdown site
}