readme.renumf90
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readme.renumf90 [2012/05/29 12:09] – [Fields in the parameter file] ignacio | readme.renumf90 [2012/05/29 12:35] – [Fields in the parameter file] ignacio | ||
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e1.. en type form | e1.. en type form | ||
</ | </ | ||
- | this line defines one group of effects; e1 .. en are positions of this | + | this line defines one group of effects; e1 .. en are positions of this effect for all traits; |
- | effect for all traits; positions can be different for each trait for fixed | + | |
- | effects; for random effects, only one position + 0 (misising) efefct are | + | positions can be different for each trait for fixed effects; |
+ | |||
+ | for random effects, only one position + 0 (misising) efefct are | ||
possible. | possible. | ||
* type is ' | * type is ' | ||
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d1 .. dn form | d1 .. dn form | ||
</ | </ | ||
- | optional for covariables only, specifies nesting; form is as above | + | optional for covariables only, specifies nesting; |
+ | |||
+ | form is as above | ||
| | ||
< | < | ||
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the RANDOM keyword occurs only if the current effect is random; | the RANDOM keyword occurs only if the current effect is random; | ||
- | rtype is ' | + | rtype is: |
+ | * ' | ||
+ | * ' | ||
+ | * ' | ||
< | < | ||
Line 101: | Line 108: | ||
o1 o2.. oq | o1 o2.. oq | ||
</ | </ | ||
- | causes extra effects appended to the animal effect; current options include | + | causes extra effects appended to the animal effect; |
- | ' | + | |
- | permanent environment | + | current options include: |
+ | | ||
+ | * ' | ||
+ | * 'mpe' for maternal permanent environment | ||
< | < | ||
Line 110: | Line 120: | ||
</ | </ | ||
- | for animal and sire model only, fped specifies the pedigree file | + | for animal and sire model only |
+ | |||
+ | //fped// specifies the pedigree file | ||
< | < | ||
Line 117: | Line 129: | ||
</ | </ | ||
- | for animal effect only; specifies positions in the pedigree file of animal | + | for animal effect only; |
- | an, sire s, dam d, alternate_dam dam rec_dam , and year of birth yob; missing | + | |
- | alt_dam or yob can be replaced by 0; if this line is not given, defaults are | + | specifies positions in the pedigree file of animal an, sire s, dam d, alternate_dam dam rec_dam , and year of birth yob\\ |
- | 1 2 3 0 0. If maternal effect is specified, the maternal effect is due to | + | missing alt_dam or yob can be replaced by 0 |
- | position of d if alt_dam field is 0, or otherwise is due to alt_dam; | + | |
- | alt_dam field is not zero, it should include ID of real or recipient | + | if this line is not given, defaults are 1 2 3 0 0. |
- | dam. | + | |
+ | If maternal effect is specified, the maternal effect is due to position of d if alt_dam field is 0, or otherwise is due to alt_dam; | ||
+ | |||
+ | If alt_dam field is not zero, it should include ID of real or recipient dam. | ||
< | < | ||
Line 130: | Line 145: | ||
</ | </ | ||
- | optional; fsnp specifies files with ID and SNP information; | + | optional;\\ |
- | relationship matrix will be constructed as in Aguilar et al. (2010) and will | + | //fsnp// specifies files with ID and SNP information; |
- | include the genomic information; | + | |
- | same format as fped and SNP info needs to start from a fixed column and | + | if present, the relationship matrix will be constructed as in Aguilar et al. (2010) and will |
- | include digits 0, 1, 2 and 5; ID and SNP info need to be separated by | + | include the genomic information; |
- | at leats one space; see info for program PreGSf90 | + | |
+ | file //fsnp// should start with ID with the same format as fped and SNP info needs to start from a fixed column and | ||
+ | include digits 0, 1, 2 and 5; | ||
+ | |||
+ | |||
+ | ID and SNP info need to be separated by at leats one space; see info for program | ||
< | < | ||
Line 142: | Line 162: | ||
</ | </ | ||
- | optional for animal effect only; p specifies the depth of pedigree search; | + | optional |
- | the default is 3; all pedigrees are loaded if p=0. | + | |
+ | for animal effect only; | ||
+ | |||
+ | //p// specifies the depth of pedigree search; | ||
+ | |||
+ | the default is 3 | ||
+ | |||
+ | all pedigrees are loaded if p=0. | ||
< | < | ||
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min avg max | min avg max | ||
</ | </ | ||
- | optional; specifies minimum, average and maximum generation interval; | + | optional |
+ | |||
+ | specifies minimum, average and maximum generation interval | ||
applicable only if year of birth present; minimum and maximum used for | applicable only if year of birth present; minimum and maximum used for | ||
- | pedigree checks; average used to predict year of birth of parent with missing | + | pedigree checks |
+ | |||
+ | average used to predict year of birth of parent with missing | ||
pedigree. | pedigree. | ||
Line 158: | Line 190: | ||
i | i | ||
</ | </ | ||
- | optional; if only one sex has records, specifies which parent it is; used for | + | optional\\ |
- | pedigree checks. | + | if only one sex has records, specifies which parent it is |
+ | |||
+ | used for pedigree checks. | ||
< | < | ||
Line 165: | Line 199: | ||
t | t | ||
</ | </ | ||
- | optional; | + | optional\\ |
- | if t is ' | + | |
- | subsequent line should contain list of years to separate different UPG; | + | |
- | if t is ' | + | * if t is ' |
- | UPG number that this missing parent should be allocated to; in this option, | + | |
- | all known parents should have pedigree lines, i.e., each parent field should | + | |
- | contain either the ID of a real parent, or a negative UPG number. | + | |
- | if t is ' | + | * if t is ' |
- | custom_upg(year_of_birth, | + | |
< | < | ||
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</ | </ | ||
Specifies that random regressions should be applied to the animal and | Specifies that random regressions should be applied to the animal and | ||
- | corresponding effects (mat, pe and mpe), this keyword also could be | + | corresponding effects (mat, pe and mpe) |
- | applied to set covariables for fixed effects; r_type | + | |
- | random regressions are in the data, or " | + | this keyword also could be applied to set covariables for fixed effects; |
- | to be generated from a single data variable; not yet implemented | + | |
+ | //r_type// could be: | ||
+ | * ' | ||
+ | * " | ||
< | < | ||
Line 191: | Line 223: | ||
r1 .. rq | r1 .. rq | ||
</ | </ | ||
- | for random regressions, | + | for random regressions, |
- | r_type=' | + | |
- | covariable if r_type=' | + | * //r1-rq// specifies positions of covariables if r_type=' |
- | </ | + | * //r1// is order of legendre polynomial and //r2// is position of covariable if r_type=' |
< | < | ||
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</ | </ | ||
- | //g// are (co)variances for the animal effect; the dimensions of g should | + | //g// are (co)variances for the animal effect |
- | account for the maternal | + | |
+ | the dimensions of g should account for random correlated | ||
< | < | ||
Line 217: | Line 250: | ||
- | ---- | + | =====Extra comments===== |
Sections starting from EFFECTS can be repeated any number of types. | Sections starting from EFFECTS can be repeated any number of types. | ||
+ | |||
If (Co)variances for any effect are missing, they are substituted with matrices containing 1.0 | If (Co)variances for any effect are missing, they are substituted with matrices containing 1.0 | ||
on diagonals and 0.1 on off-diagonals. | on diagonals and 0.1 on off-diagonals. | ||
Line 228: | Line 262: | ||
The sequence of keywords should be as above although optional fields can be | The sequence of keywords should be as above although optional fields can be | ||
- | skipped. Keywords out of order may not be recognized. | + | skipped. |
- | =====OPTIONS===== | + | Keywords out of order may not be recognized. |
+ | |||
+ | =====Options===== | ||
The following options can added at the end of the parameter file to redefine | The following options can added at the end of the parameter file to redefine | ||
- | parameter | + | parameters |
- the default size of character fields | - the default size of character fields | ||
Line 238: | Line 274: | ||
OPTION alpha size nn | OPTION alpha size nn | ||
</ | </ | ||
- | where nn is the new size. | + | where //nn// is the new size. |
- the size of th record length | - the size of th record length | ||
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OPTION max_string_readline nn | OPTION max_string_readline nn | ||
</ | </ | ||
- | where nn is the new size. | + | where //nn// is the new size. |
- the maximun number of fields | - the maximun number of fields | ||
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OPTION max_field_readline nn | OPTION max_field_readline nn | ||
</ | </ | ||
- | where nn is the number of fields. | + | where //nn// is the number of fields. |
- | The end of the parameter file for RENUMF90 can contain many lines beginning with OPTION. | + | The end of the parameter file for '' |
- | All of these lines are passed to parameter file renf90.par to be used by | + | |
- | application programs. | + | All of these lines are passed to parameter file renf90.par to be used by application programs. |
=====Combining fields or interactions====== | =====Combining fields or interactions====== | ||
- | Several fields in the data file can be combined into one using a COMBINE keyword. | + | Several fields in the data file can be combined into one using a '' |
< | < | ||
COMBINE a b c .... | COMBINE a b c .... | ||
</ | </ | ||
- | catenates b c ... into c. Keywords COMBINE need to be on top of the parameter | + | catenates |
- | file, but possibly after comments. There may be many combined fields. | + | Keywords COMBINE need to be on top of the parameter file, but possibly after comments. |
+ | |||
+ | There may be many combined fields. | ||
For example: | For example: | ||
- | </file> | + | < |
COMBINE 7 2 3 4 | COMBINE 7 2 3 4 | ||
</ | </ | ||
- | combines content of fields 2 3 4 into field 7; the data file is not changed, | + | |
- | only the program treats field 7 as fields 2 3 4 put together (without spaces). | + | combines content of fields 2 3 4 into field 7; |
- | The combined fields can be treated as " | + | |
- | and if their total length is <9. Otherwise, they need to be used as " | + | the data file is not changed, only the program treats field 7 as fields 2 3 4 put together (without spaces). |
- | Please note that the maximum size of the combined variable is limited by the | + | |
- | largest size of the " | + | |
+ | The combined fields can be treated as " | ||
+ | |||
+ | Please note that the maximum size of the combined variable is limited by the largest size of the " | ||
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani