Description Usage Arguments Details Value Examples

This is a function for a matrix decomposition method incorporating sparse and supervised modeling for a multiblock multivariable data analysis

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
msma(X, ...)
## Default S3 method:
msma(X, Y = NULL, Z = NULL, comp = 2, lambdaX = NULL,
lambdaY = NULL, eta = 1, type = "lasso", inX = NULL, inY = NULL,
muX = 0, muY = 0, defmethod = "canonical", scaling = TRUE,
verbose = FALSE, ...)
## S3 method for class 'msma'
print(x, ...)
## S3 method for class 'msma'
plot(x, ...)
``` |

`X` |
a (list of) matrix, explanatory variable(s) which is required. |

`...` |
further arguments passed to or from other methods. |

`Y` |
a (list of) matrix, objective variable(s). This is optional. If no input for Y, then the PCA method is implemented. |

`Z` |
a vector, response variable(s). This is optional. The length is the number of subjects. If no input for Z, then the unsupervised PLS/PCA is implemented. |

`comp` |
numeric scalar for the number of components to be considered. |

`lambdaX` |
numeric vector of regularized parameters for X with length equal to the number of blocks. If omitted, no regularization is conducted. |

`lambdaY` |
numeric vector of regularized parameters for Y with length equal to the number of blocks. If omitted, no regularization is conducted. |

`eta` |
numeric scalar, the parameter indexing the penalty family. This version has only the choice 1. |

`type` |
a character, the penalty family. This version has only the choice "lasso". |

`inX` |
a (list of) numeric vector to specify the variables of X which are always in the model. |

`inY` |
a (list of) numeric vector to specify the variables of Y which are always in the model. |

`muX` |
a numeric scalar for the weight of X for the supervised. 0<=muX<=1. |

`muY` |
a numeric scalar for the weight of Y for the supervised. 0<=muY<=1. |

`defmethod` |
a character, the deflation method, this version has only the choice "canonical". |

`scaling` |
a logical, whether the scaling data is done, the default is TRUE. |

`verbose` |
information |

`x` |
an object of class " |

`msma`

requires at least one input X as the matrix or the list. In this case, the (multiblock) principal components analysis is conducted. If Y is also specified, the partial least squares with X as explanatory variables and Y as objective variables. This function scaled each data matrix to mean 0 and variance 1 in the default. The block structure can be represented as the list. If Z is also specified, the supervised version is implemented and the degree is controlled by muX or muY where 0<=muX<=1, 0<=muY<=1, and 0<=muX+muY<1. If the positive lambdaX or lambdaY is specified, the sparse estimation based on L1 penalty is implemented.

`dmode` |
Which modes "PLS" or "PCA" |

`X` |
Scaled X which has a list form. |

`Y` |
Scaled Y which has a list form. |

`Xscale` |
Scaling information for X. The means and standard deviations for each block of X are returned. |

`Yscale` |
Scaling information for Y. The means and standard deviations for each block of Y are returned. |

`comp` |
the number of components |

`wbX` |
block loading for X. The list has same length as that of the input list X (the number of blocks) and consists of the matrix with the number of variables in the row and the number of components in the column. |

`sbX` |
block score for X. The list has same length as that of the input list X (the number of blocks) and consists of the matrix with the number of subjects in the row and the number of components in the column. |

`wbY` |
block loading for Y. The list has same length as that of the input list Y (the number of blocks) and consists of the matrix with the number of variables in the row and the number of components in the column. |

`sbY` |
block score for Y. The list has same length as that of the input list Y (the number of blocks) and consists of the matrix with the number of subjects in the row and the number of components in the column. |

`ssX` |
super score for X. The matrix has the number of subjects in the row and the number of components in the column. |

`wsX` |
super loading for X. The matrix has the number of blocks in the row and the number of components in the column. |

`ssY` |
super score for Y. The matrix has the number of subjects in the row and the number of components in the column. |

`wsY` |
super loading for Y. The matrix has the number of blocks in the row and the number of components in the column. |

`nzwbX` |
number of nonzeros in block loading for X |

`nzwbY` |
number of nonzeros in block loading for Y |

`selectXnames` |
names of selected variables for X. This returns the names of X |

`selectYnames` |
names of selected variables for Y. This returns the names of Y |

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | ```
##### data #####
tmpdata = simdata(n = 50, rho = 0.8, Yps = c(10, 12, 15), Xps = 20, seed=1)
X = tmpdata$X; Y = tmpdata$Y
##### One Component #####
fit1 = msma(X, Y, comp=1, lambdaX=2, lambdaY=1:3)
fit1
##### Two Component #####
fit2 = msma(X, Y, comp=2, lambdaX=2, lambdaY=1:3)
fit2
##### Matrix data #####
sigma = matrix(0.8, 10, 10)
diag(sigma) = 1
X2 = rmvnorm(50, rep(0, 10), sigma)
Y2 = rmvnorm(50, rep(0, 10), sigma)
fit3 = msma(X2, Y2, comp=1, lambdaX=2, lambdaY=2)
fit3
##### Sparse Principal Component Analysis #####
fit5 = msma(X2, comp=5, lambdaX=2.5)
summary(fit5)
``` |

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