Parameters and Configuration¶

Lasso.bag¶

mat¶

Type:	data.frame
Default:	`none`

independent variables

out.mat¶

Type:	data.frame
Default:	`none`

dependent variables, which contains one column or two columns

bootN¶

Type:	numeric
Default:	`1000`

the size of resampled sample, only valid when permutation set to TRUE

imputeN¶

Type:	numeric
Default:	`1000`

the initial permutation times, only valid when permutation set to TRUE

imputeN.max¶

Type:	numeric
Default:	`2000`

the max permutation times. Regardless of whether p has meet the requirement,, only valid when permutation set to TRUE

permut.increase¶

Type:	numeric
Default:	`1000`

if the initial imputeN times of permutation doesn’t meet the requirement, then we add ??permut.increase times of permutation?? to get more random/permutation values, only valid when permutation set to TRUE

boot.rep¶

Type:	bool
Default:	`TRUE`

whether :”sampling with return” or not, only valid when permutation set to TRUE

a.family¶

Type:	string
Default:	`none`

what kind of regression method to use, it should match the type of out.mat

parallel¶

Type:	bool
Default:	`FALSE`

whether the script run in parallel, you need to set n.cores in case this package conquers all your cpu resource

fit.pareto¶

Type:	string
Default:	`mle`

the method of fitting Generalized Pareto Distribution, alternative choice is “gd”, for gradient descend

permutation¶

Type:	string
Default:	`TRUE`

to decide whether to do permutation test, if set TRUE, no p value returns

n.cores¶

Type:	numeric
Default:	`1`

how many cores/process to be assigned for this function, in Windows, you have to set this to 1

rd.seed¶

Type:	numeric
Default:	`89757`

it is the random seed of this function, in case some of the experiments need to be reappeared

plot.freq¶

Type:	string/bool
Default:	`FALSE`

whether to show all the non-zero frequency in the final barplot or not. If “full”, all the features(including zero frequency) will be plotted. If “part”, all the non-zero features will be plotted. If “not”, will not print the plot.

plot.out¶

Type:	string/bool
Default:	`FALSE`

the path or file’s name to save the plot. If set to FALSE, no plot will be output. If you run this function in Linux command line, you don’t have to set this param for the plot.freq will output your plot to your current working directory with name “Rplot.pdf”.Default to FALSE

LessPermutation¶

X¶

Type:	vector
Default:	`none`

a union of input data, e.g. c(1,2,3,4,5,6).

x0¶

Type:	numeric
Default:	`none`

the observed value

fitting.method¶

Type:	string
Default:	`gd`

the fitting method of General Pareto Distribution(GPD)

search.step¶

Type:	numeric
Default:	`0.01`

the length of step (this param * length(X)) to find threshold, default 0.01

fit.cutoff¶

Type:	numeric
Default:	`0.05`

the cutoff of p value to judge whether it fits well to GPD, default 0.05

when.to.fit¶

Type:	numeric
Default:	`0.05`

a cutoff to tell how many sample values are bigger than the observed value then we don’t need to fit GPD. it is a portion.