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--- readme.renumf90 [2012/05/29 11:50] – ignacio
+++ readme.renumf90 [2012/05/29 12:28] – [Extra comments] ignacio
@@ Line 25: / Line 25: @@
 The parameter file contains keywords in capital followed by specifications
-of a given effect/data item. The keywords need to be typed exactly. Specific
+of a given effect/data item.\\ The keywords need to be typed exactly.\\ Specific
 keywords need to occur sequentially, as shown below.
@@ Line 42: / Line 42: @@
 Lines with # are treated as comments
 <file>
 DATAFILE
 f1
@@ Line 48: / Line 48: @@
 The data file is f1
 <file>
 TRAITS
 t1 t2 .. tn
@@ Line 66: / Line 66: @@
 w is  position of weight if present; can be empty
 <file>
 RESIDUAL_VARIANCE
 r
@@ Line 76: / Line 76: @@
 e1.. en type form
 </file>
-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
+positions can be different for each trait for fixed effects;\\
-effects; for random effects, only one position + 0 (misising) efefct are
+for random effects, only one position + 0 (misising) efefct are
 possible.
   * type is 'cross' for crossclassified or 'cov' for covariables
@@ Line 87: / Line 87: @@
 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>
@@ Line 97: / Line 98: @@
 rtype is 'diagonal', 'sire' or 'animal'
 <file>
 OPTIONAL
 o1 o2.. oq
 </file>
-causes extra effects appended to the animal effect; current options include
+causes extra effects appended to the animal effect;\\
-'pe' for permanent environment, 'mat' for maternal, and 'mped' for maternal
+current options include
-permanent environment
+  * 'pe' for permanent environment
+  * 'mat' for maternal
+  * 'mpe' for maternal permanent environment
 <file>
 FILE
 fped
@@ Line 117: / Line 120: @@
 </file>
-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
+specifies positions in the pedigree file of animal an, sire s, dam d, alternate_dam dam rec_dam , and year of birth yob\\
-alt_dam or yob can be replaced by 0; if this line is not given, defaults are
+missing alt_dam or yob can be replaced by 0\\
-2 3 0 0. If maternal effect is specified, the maternal effect is due to
+if this line is not given, defaults are 1 2 3 0 0.\\
-position of d if alt_dam field is 0, or otherwise is due to alt_dam; If
+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.
-alt_dam field is not zero, it should include ID of real or recipient
-dam.
 <file>
 SNP_FILE
 fsnp
 </file>
-optional; fsnp specifies files with ID and SNP information; if present, the
+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; file fsnp should start with ID with the
+if present, the relationship matrix will be constructed as in Aguilar et al. (2010) and will
-same format as fped and SNP info needs to start from a fixed column and
+include the genomic information;\\
-include digits 0, 1, 2 and 5; ID and SNP info need to be separated by
+file fsnp should start with ID with the same format as fped and SNP info needs to start from a fixed column and
-at leats one space; see info for program PreGSf90
+include digits 0, 1, 2 and 5;\\
-<file>
+ID and SNP info need to be separated by at leats one space; see info for program [[readme.pregsf90|PreGSf90]]
+<file>
 PED_DEPTH
 p
 </file>
-optional for animal effect only; p specifies the depth of pedigree search;
+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;
+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 checks;\\
+average used to predict year of birth of parent with missing
 pedigree.
 <file>
 REC_SEX
 i
 </file>
-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.
 <file>
 UPG_TYPE
 t
 </file>
-optional;
+optional\\
-if t is 'yob', the asignment is based on year of birth; the
+  * if t is 'yob', the assignment 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, 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.
-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 '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
+corresponding effects (mat, pe and mpe),\\
-applied to set covariables for fixed effects; r_type is 'data' if covariables for
+this keyword also could be applied to set covariables for fixed effects;\\
-random regressions are in the data, or "legendre' if legendre plynomials are
+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
 <file>
 RR_POSITION
 r1 .. rq
@@ Line 195: / Line 198: @@
 </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;\\
-account for the maternal effect if present
+the dimensions of g should account for the maternal effect if present
 <file>
 (CO)VARIANCES_PE
 gpe
@@ Line 209: / Line 212: @@
 //gpe// are (co)variances for the PE effect if present
 <file>
 (CO)VARIANCES_MPE
 gmpe
@@ Line 216: / Line 219: @@
-----
+=====Extra comments=====
 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
 on diagonals and 0.1 on off-diagonals.
@@ Line 227: / Line 231: @@
 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
-parameter used to read the input file:
+parameters used to read the input file:
  - the default size of character fields
@@ Line 237: / Line 243: @@
 	OPTION alpha size nn
 </file>
-   where nn is the new size.
+where //nn// is the new size.
  - the size of th record length
@@ Line 243: / Line 249: @@
 	OPTION max_string_readline nn
 </file>
-   where nn is the new size.
+where //nn// is the new size.
  - the maximun number of fields
@@ Line 249: / Line 255: @@
         OPTION max_field_readline nn
 </file>
-   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 ''RENUMF90'' can contain many lines beginning with OPTION.
-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======
-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'' keyword.
 <file>
 COMBINE a b c ....
 </file>
-catenates b c ... into c. Keywords COMBINE need to be on top of the parameter
+catenates //b c// ... into //a//.\\
-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:
-</file>
+<file>
 COMBINE 7 2 3 4
 </file>
-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 "numeric", if they are composed of numbers
-and if their total length is <9. Otherwise, they need to be used as "alpha".
+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 "alpha" field.
+The combined fields can be treated as "numeric", if they are composed of numbers and if their total length is <9. Otherwise, they need to be used as "alpha".\\
+Please note that the maximum size of the combined variable is limited by the largest size of the "alpha" field.
@@ Line 303: / Line 314: @@
 =====Example======
+**__data file__** - ''data.test''
 <file>
-data file - data.test
----------------------
 aa 34.5 11 12 zz
 bb 21.333 22 23 xx
@@ Line 315: / Line 327: @@
 </file>
+**__pedigree file__** - ''test.ped''
 <file>
-pedigree file - test.ped
-------------------------
 qq 0 0
 aa 0 0
@@ Line 325: / Line 337: @@
 </file>
-</file>
-parameter file - testpar1
+**__parameter file__** - ''testpar1''
--------------------------
+<file>
 # Parameter file for program renf90; it is translated to parameter
 # file for BLUPF90 family f programs.
@@ Line 372: / Line 384: @@
 </file>
-</file>
+**__printout__** \\
-printout (temporary; the amount of details may change)
+\\
-------------------------------------------------------
+(temporary; the amount of details may change)
+<file>
  RENUMF90 version 1.93
  name of parameter file? testpar1
@@ Line 465: / Line 478: @@
 </file>
+**__new parameter file__** - ''renf90.par''
 <file>
-new parameter file - renf90.par
--------------------------------
 # BLUPF90 parameter file created by RENF90
 DATAFILE
@@ Line 531: / Line 543: @@
+**__data file__** - ''renf90.dat''
 <file>
-data file - renf90.dat
-----------------------
 .5 11 1 3 5 12 1 3 aa 1
 .333 22 2 1 3 23 2 1 bb 3
@@ Line 542: / Line 554: @@
 </file>
+**__Pedigree file__** - ''renadd02.ped''
 <file>
- Pedigree file (same format as from renum) - renadd02.ped
- --------------------------------------------------------
 6 3 1 0 2 2 0 0 bb
 0 0 1 0 0 0 2 0 qq
@@ Line 554: / Line 566: @@
 </file>
+**''renumbering tables''** - ''renf90.tables''
 <file>
-renumbering tables - renf90.tables
-----------------------------------
  Effect group 1 of column 1 with 4 levels
  Value    #    consecutive number