Parameter file elements - Revision history

127.0.0.1: /* grm name> */

2022-08-31T23:44:20Z

grm name>

← Older revision		Revision as of 23:44, 31 August 2022
Line 346:		Line 346:
	{{!}}-		{{!}}-
	{{!}}'''method'''		{{!}}'''method'''
	{{!}}'''method''':'''YA'''		{{!}}'''method''':'''vr1'''
	{{!}}optional		{{!}}optional
	{{!}}alternative words		{{!}}alternative words
	{{!}}'''VR<nowiki>\|</nowiki>YA'''		{{!}}'''vr1<nowiki>\|</nowiki>vr2'''
	{{!}}'''VR'''		{{!}}'''vr1'''
	{{!}}content determines the method to be used for building a grm from genotypes		{{!}}content determines the method to be used for building a grm from genotypes
	*'''VR''': VanRaden Method 1 is used		*'''vr1''': VanRaden Method 1 is used
	*'''YA''': VanRaden Method 2(method Yang) is used		*'''vr2''': VanRaden Method 2(method Yang) is used
	{{!}}-		{{!}}-
	{{!}}'''outfile'''		{{!}}'''outfile'''

2022-06-07T04:54:27Z

mcemreml>

← Older revision		Revision as of 04:54, 7 June 2022
Line 1,358:		Line 1,358:
	{{!}}numeric value		{{!}}numeric value
	{{!}}real number		{{!}}real number
	{{!}}-6.907755		{{!}} -6.907755
	{{!}}provides the convergence threshold		{{!}}provides the convergence threshold
	{{!}}-		{{!}}-

2022-06-07T04:52:56Z

mcemreml>

← Older revision		Revision as of 04:52, 7 June 2022
Line 1,327:		Line 1,327:
	jobs: mcemreml,..		jobs: mcemreml,..
	<mcemreml>		<mcemreml>
	~~emrounds~~: 500		rounds: 500
	sampler: mysampler		sampler: mysampler
			solver: mysolver
	</mcemreml>		</mcemreml>
	..		..
Line 1,344:		Line 1,345:
	*key strings		*key strings
	{{tablekeys2\|		{{tablekeys2\|
	{{!}}'''~~emrounds~~'''		{{!}}'''rounds'''
	{{!}}'''~~emrounds~~''': ''~~500~~''		{{!}}'''rounds''': ''1000''
	{{!}}~~compulsory~~		{{!}}optional
	{{!}}numeric value		{{!}}numeric value
	{{!}}positive integer		{{!}}positive integer
	{{!}}~~none~~		{{!}}500
	{{!}}provides the number of mcemreml-rounds to run		{{!}}provides maximum the number of mcemreml-rounds to run
			{{!}}-
			{{!}}'''conv'''
			{{!}}'''conv''': ''-16.21''
			{{!}}optional
			{{!}}numeric value
			{{!}}real number
			{{!}}-6.907755
			{{!}}provides the convergence threshold
	{{!}}-		{{!}}-
	{{!}}'''sampler'''		{{!}}'''sampler'''
Line 1,359:		Line 1,368:
	{{!}}none		{{!}}none
	{{!}}''sampler name'' must be the name of a previously defined sampler		{{!}}''sampler name'' must be the name of a previously defined sampler
			{{!}}-
			{{!}}'''solver'''
			{{!}}'''solver''': ''mysolver''
			{{!}}compulsory
			{{!}}word
			{{!}}''solver name''
			{{!}}none
			{{!}}''solver name'' must be the name of a previously defined solver
	}}		}}

2022-05-25T10:29:02Z

airemlc>

← Older revision		Revision as of 10:29, 25 May 2022
Line 1,312:		Line 1,312:
	{{!}}csv word-list		{{!}}csv word-list
	{{!}}any real number		{{!}}any real number
	{{!}}'''writeai,residuals'''		{{!}}'''writeai,residuals,solutions'''
	{{!}}		{{!}}
	*'''writeai''': write ai matrix and gradient vector to files ai_ai.csv and ai_ja.csv.		*'''writeai''': write ai matrix and gradient vector to files ai_ai.csv and ai_ja.csv.
	*'''residuals''': after convergence write the residuals to file aic_residuals.csv		*'''residuals''': after convergence write the residuals to file aic_residuals.csv
			*'''solutions''': after convergence write the MME solutions to file results.csv
	}}		}}

2022-05-16T05:46:21Z

airemlc>

← Older revision		Revision as of 05:46, 16 May 2022
Line 1,298:		Line 1,298:
	{{!}}''-16.1181''		{{!}}''-16.1181''
	{{!}}provides the convergence threshold for convergence criterion '''cd'''		{{!}}provides the convergence threshold for convergence criterion '''cd'''
			{{!}}-
			{{!}}'''nscale'''
			{{!}}'''nscale''': ''0.5''
			{{!}}optional
			{{!}}numeric value
			{{!}}any real number
			{{!}}''1.0''
			{{!}}scales the length of the Newton step.
	{{!}}-		{{!}}-
	{{!}}'''switch'''		{{!}}'''switch'''

2022-05-15T23:32:38Z

airemlc>

← Older revision		Revision as of 23:32, 15 May 2022
Line 1,267:		Line 1,267:
	{{!}}word		{{!}}word
	{{!}}'''cd<nowiki>\|</nowiki>ng<nowiki>\|</nowiki>ll<nowiki>\|</nowiki>any<nowiki>\|</nowiki>all'''		{{!}}'''cd<nowiki>\|</nowiki>ng<nowiki>\|</nowiki>ll<nowiki>\|</nowiki>any<nowiki>\|</nowiki>all'''
	{{!}}'''ll'''		{{!}}'''cd'''
	{{!}}provides the convergence criterion to use		{{!}}provides the convergence criterion to use
	* ll: log of relative change in log-likelihood		* ll: log of relative change in log-likelihood

2022-05-08T13:31:28Z

airemlc>

← Older revision		Revision as of 13:31, 8 May 2022
Line 1,306:		Line 1,306:
	{{!}}'''writeai,residuals'''		{{!}}'''writeai,residuals'''
	{{!}}		{{!}}
	*'''writeai''': write ai matrix and gradient vector to files ~~aic_ai~~.csv and ~~aic_ja~~.csv.		*'''writeai''': write ai matrix and gradient vector to files ai_ai.csv and ai_ja.csv.
	*'''residuals''': after convergence write the residuals to file aic_residuals.csv		*'''residuals''': after convergence write the residuals to file aic_residuals.csv
	}}		}}

2022-05-08T12:23:45Z

airemlc>

@@ Line 1,298: / Line 1,298: @@
 {{!}}''-16.1181''
 {{!}}provides the convergence threshold for convergence criterion '''cd'''
 }}

2022-05-08T03:27:44Z

maskmatrix attributes="array">

← Older revision		Revision as of 03:27, 8 May 2022
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	{{!}}'''sigma'''		{{!}}'''sigma'''
	{{!}}optional		{{!}}optional
	{{!}}hosts the content of a single $$\Sigma$$ matrix. Is mutually exclusive with key string '''~~file~~: '''.		{{!}}hosts the content of a single indicator matrix of the same dimensions as the respective $$\Sigma$$ matrix. Is mutually exclusive with key string '''maskfile: '''.
	}}		}}

2022-05-08T03:26:43Z

← Older revision		Revision as of 03:26, 8 May 2022
Line 520:		Line 520:
	{{!}}prior degree of freedom when doing Gibbs sampling		{{!}}prior degree of freedom when doing Gibbs sampling
	{{!}}-		{{!}}-
			{{!}}'''maskfile'''
	{{!}}'''maskfile''': ''mymatrixmask.csv''		{{!}}'''maskfile''': ''mymatrixmask.csv''
	{{!}}optional		{{!}}optional