Refresh package doc, some advances on vignette

[morpheus.git] / pkg / man / morpheus-package.Rd

diff --git a/pkg/man/morpheus-package.Rd b/pkg/man/morpheus-package.Rd
index e8181aa..a66684f 100644 (file)
--- a/pkg/man/morpheus-package.Rd
+++ b/pkg/man/morpheus-package.Rd
@@ -14,22 +14,23 @@
 \details{
        The package devtools should be useful in development stage, since we rely on testthat for
        unit tests, and roxygen2 for documentation. knitr is used to generate the package vignette.
+       jointDiag allows to solve a joint diagonalization problem, providing a more robust
+       solution compared to a single diagonalization.
        Concerning the other suggested packages:
        \itemize{
                \item{tensor is used for comparing to some reference functions initially coded in R;
                        it should not be required in further package versions;}
-               \item{jointDiag allows to solve a joint diagonalization problem, providing a more
-                       robust solution compared to a single diagonalization;}
                \item{parallel (generally) permits to run the bootstrap method faster.}
        }
 
-       The three main functions are located in R/main.R:
+       The two main functions are located in R/computeMu.R and R/optimParams.R:
        \itemize{
-               \item{getParamsDirs_ref: reference method to estimate parameters directions;}
-               \item{getParamsDirs: method of choice to estimate parameters directions, using a
-                       spectral decomposition of inputs/outputs;}
-               \item{getBootstrapParams: run getParamsDirs on B bootstrap replicates.}
+               \item{computeMu(): estimation of parameters directions;}
+               \item{optimParams(): builds an object \code{o} to estimate all other parameters
+                       when calling \code{o$run()}, starting from the directions obtained by previous function}
        }
+       See also \code{multiRun()}, which is a flexible method to run Monte-Carlo or bootstrap
+       estimations using different models in various contexts.
 }
 
 \author{