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--- readme.renumf90 [2012/05/28 01:02] – ignacio
+++ readme.renumf90 [2012/05/29 11:42] – ignacio
@@ Line 1: / Line 1: @@
-<file>
-=======================================================
+=======RENUMF90======
-RENUMF90 -  renumbering program for the BLUPF90 family
+renumbering program for the BLUPF90 family now works with SNP info\\
-            now works with SNP info
+Ignacy Misztal and Ignacio Aguilar, University of Georgia\\
-=======================================================
-Ignacy Misztal and Ignacio Aguilar, University of Georgia
 August 27, 2001 - Mar 17, 2011
-Summary
+=====Summary=====
-=======
 RENUMF90 is a renumbering program for the BLUPF90 family of programs. It
@@ Line 21: / Line 18: @@
 Warnings
-	- input files cannot contain character #.
+  * input files cannot contain character #.
-	- missing animals have code 0; 00 may be treated as a known animal
+  * missing animals have code 0; 00 may be treated as a known animal
-Structure of parameter file
+=====Structure of parameter file======
-===========================
 The parameter file contains keywords in capital followed by specifications
@@ Line 32: / Line 28: @@
 keywords need to occur sequentially, as shown below.
-Bugs
-====
+=====Bugs=====
 IDs starting with "-" may not work
-Fields in the parameter file
-=============================
+=====Fields in the parameter file=====
 # Parameter file for program renf90; it is translated to parameter
 # file for BLUPF90 family of programs.
-   Lines with # are treated as comments
+Lines with # are treated as comments
+<file>
 DATAFILE
 f1
+</file>
+The data file is f1
-   The data file is f1
+<file>
 TRAITS
 t1 t2 .. tn
+</file>
+t1-tn are positions of traits in datafile; n defines the number of traits
-   t1-tn are positions of traits in datafile; n defines the number of traits
+<file>
 FIELDS_PASSED TO OUTPUT
 p1 p2 .. pm
+<file>
-   fields p1-pn are passed to output without changes; can be empty
+fields p1-pn are passed to output without changes; can be empty
+<file>
 WEIGHT(S)
 w
-   w is  position of weight if present; can be empty
+</file>
+w is  position of weight if present; can be empty
+<file>
 RESIDUAL_VARIANCE
 r
-   r is matrix of residual (co)variances  of size n x n
+</file>
+r is matrix of residual (co)variances  of size n x n
+<file>
 EFFECT
 e1.. en type form
+</file>
+this line defines one group of effects; e1 .. en are positions of this
+effect for all traits; positions can be different for each trait for fixed
+effects; for random effects, only one position + 0 (misising) efefct are
+possible.
+  * type is 'cross' for crossclassified or 'cov' for covariables
+  * form is 'alpha' for alphanumeric or 'numer' for numeric
-   this line defines one group of effects; e1 .. en are positions of this
+<file>
-   effect for all traits; positions can be different for each trait for fixed
-   effects; for random effects, only one position + 0 (misising) efefct are
-   possible.
-   type is 'cross' for crossclassified or 'cov' for covariables
-   form is 'alpha' for alphanumeric or 'numer' for numeric
 NESTED
 d1 .. dn form
+</file>
-   optional for covariables only, specifies nesting; form is as above
+optional for covariables only, specifies nesting; form is as above
+<file>
 RANDOM
 rtype
+</file>
-   the RANDOM keyword occurs only if the current effect is random;
+the RANDOM keyword occurs only if the current effect is random;
-   rtype is 'diagonal', 'sire' or 'animal'
+rtype is 'diagonal', 'sire' or 'animal'
+<file>
 OPTIONAL
 o1 o2.. oq
+<file>
+causes extra effects appended to the animal effect; current options include
+'pe' for permanent environment, 'mat' for maternal, and 'mped' for maternal
+permanent environment
-   causes extra effects appended to the animal effect; current options include
+<file>
-   'pe' for permanent environment, 'mat' for maternal, and 'mped' for maternal
-   permanent environment
 FILE
 fped
+</file>
-   for animal and sire model only, fped specifies the pedigree file
+for animal and sire model only, fped specifies the pedigree file
+<file>
 FILE_POS
 an s d alt_dam yob
+</file>
-   for animal effect only; specifies positions in the pedigree file of animal
+for animal effect only; specifies positions in the pedigree file of animal
-   an, sire s, dam d, alternate_dam dam rec_dam , and year of birth yob; missing
+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
+alt_dam or yob can be replaced by 0; if this line is not given, defaults are
 2 3 0 0. 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
+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
+alt_dam field is not zero, it should include ID of real or recipient
-   dam.
+dam.
+<file>
 SNP_FILE
 fsnp
+</file>
-   optional; fsnp specifies files with ID and SNP information; if present, the
+optional; fsnp specifies files with ID and SNP information; if present, the
-   relationship matrix will be constructed as in Aguilar et al. (2010) and will
+relationship matrix will be constructed as in Aguilar et al. (2010) and will
-   include the genomic information; file fsnp should start with ID with the
+include the genomic information; file fsnp should start with ID with the
-   same format as fped and SNP info needs to start from a fixed column and
+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
+include digits 0, 1, 2 and 5; ID and SNP info need to be separated by
-   at leats one space; see info for program PreGSf90
+at leats one space; see info for program PreGSf90
+<file>
 PED_DEPTH
 p
+</file>
-   optional for animal effect only; p specifies the depth of pedigree search;
-   the default is 3; all pedigrees are loaded if p=0.
+optional for animal effect only; p specifies the depth of pedigree search;
+the default is 3; all pedigrees are loaded if p=0.
+<file>
 GEN_INT
 min avg max
+</file>
+optional; specifies minimum, average and maximum generation interval;
+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.
-   optional; specifies minimum, average and maximum generation interval;
+<file>
-   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.
 REC_SEX
 i
+</file>
+optional; if only one sex has records, specifies which parent it is; used for
+pedigree checks.
-   optional; if only one sex has records, specifies which parent it is; used for
+<file>
-   pedigree checks.
 UPG_TYPE
 t
+</file>
-   optional;
+optional;
-   if t is 'yob', the asignment is based on year of birth; the
+if t is 'yob', the asignment is based on year of birth; the
-   subsequent line should contain list of years to separate different UPG;
+subsequent line should contain list of years to separate different UPG;
-   if t is 'in_pedigrees', the value of a missing parent should be -x, where x is
+if t is 'in_pedigrees', the value of a missing parent should be -x, where x is
-   UPG number that this missing parent should be allocated to; in this option,
+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
+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.
+contain either the ID of a real parent, or a negative UPG number.
-   if t is 'internal',  allocation is by a user-written function
+if t is 'internal',  allocation is by a user-written function
-   custom_upg(year_of_birth,sex,ID, parent_code).
+custom_upg(year_of_birth,sex,ID, parent_code).
+<file>
 RANDOM_REGRESSION
 r_type
+</file>
+Specifies that random regressions should be applied to the animal and
+corresponding effects (mat, pe and mpe), this keyword also could be
+applied to set covariables for fixed effects; r_type is 'data' if covariables for
+random regressions are in the data, or "legendre' if legendre plynomials are
+to be generated from a single data variable; not yet implemented
-   Specifies that random regressions should be applied to the animal and
+<file>
-   corresponding effects (mat, pe and mpe), this keyword also could be
-   applied to set covariables for fixed effects; r_type is 'data' if covariables for
-   random regressions are in the data, or "legendre' if legendre plynomials are
-   to be generated from a single data variable; not yet implemented
 RR_POSITION
 r1 .. rq
-   for random regressions, r1-rq specifies positions of covariables if
+</file>
-   r_type='data', or r1 is order of legendre polynomial and r2 is position of
+for random regressions, r1-rq specifies positions of covariables if
-   covariable if r_type='legendre'; not yet implemented
+r_type='data', or r1 is order of legendre polynomial and r2 is position of
+covariable if r_type='legendre'; not yet implemented
+</file>
+<file>
 (CO)VARIANCES
 g
+</file>
-   g are (co)variances for the animal effect; the dimensions of g should
+//g// are (co)variances for the animal effect; the dimensions of g should
-   account for the maternal effect if present
+account for the maternal effect if present
+<file>
 (CO)VARIANCES_PE
 gpe
+</file>
+//gpe// are (co)variances for the PE effect if present
-   gpe are (co)variances for the PE effect if present
+<file>
 (CO)VARIANCES_MPE
 gmpe
+</file>
-   gmpe are (co)variances for the MPE effect if present
+//gmpe// are (co)variances for the MPE effect if present