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--- readme.renumf90 [2012/05/29 11:39] – ignacio
+++ readme.renumf90 [2012/05/29 11:50] – ignacio
@@ Line 57: / Line 57: @@
 FIELDS_PASSED TO OUTPUT
 p1 p2 .. pm
-<file>
+</file>
 fields p1-pn are passed to output without changes; can be empty
@@ Line 100: / Line 100: @@
 OPTIONAL
 o1 o2.. oq
-<file>
+</file>
 causes extra effects appended to the animal effect; current options include
 'pe' for permanent environment, 'mat' for maternal, and 'mped' for maternal
@@ Line 141: / Line 141: @@
 </file>
-<file>
 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
+----
 Sections starting from EFFECTS can be repeated any number of types.
@@ Line 218: / Line 229: @@
 skipped. 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:
  - the default size of character fields
+<file>
 	OPTION alpha size nn
+</file>
    where nn is the new size.
  - the size of th record length
+<file>
 	OPTION max_string_readline nn
+</file>
    where nn is the new size.
  - the maximun number of fields
+<file>
         OPTION max_field_readline nn
+</file>
    where nn is the number of fields.
@@ Line 239: / Line 257: @@
-Combining fields or interactions
+=====Combining fields or interactions======
-================================
 Several fields in the data file can be combined into one using a COMBINE keyword.
-	COMBINE a b c ....
+<file>
+COMBINE a b c ....
+</file>
 catenates b c ... into c. Keywords COMBINE need to be on top of the parameter
 file, but possibly after comments. There may be many combined fields.
 For example:
-	COMBINE 7 2 3 4
+</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).
@@ Line 256: / Line 277: @@
-Additive Pedigree File
+=====Additive Pedigree File======
-======================
 The additive pedigree file(s) renadd* has the following structure:
@@ Line 276: / Line 296: @@
-Extensions
+=====Extensions=======
-==========
 The program is being modified to support inbreeding, dominance, random
@@ Line 283: / Line 302: @@
-Example
+=====Example======
-========
+<file>
 data file - data.test
 ---------------------
@@ Line 294: / Line 313: @@
 aa  30 55 56 yy
 bb 1234567.890 66 67 zz
+</file>
+<file>
 pedigree file - test.ped
 ------------------------
@@ Line 302: / Line 323: @@
 cc qq 0
 dd 0 aa
+</file>
+</file>
 parameter file - testpar1
 -------------------------
@@ Line 347: / Line 370: @@
 RANDOM
 diagonal
+</file>
+</file>
 printout (temporary; the amount of details may change)
 ------------------------------------------------------
@@ Line 439: / Line 463: @@
  Wrote parameter file "renf90.par"
  Wrote renumbered data "renf90.dat"
+</file>
+<file>
 new parameter file - renf90.par
 -------------------------------
@@ Line 503: / Line 528: @@
 .000      0.1000
 .1000       1.000
+</file>
+<file>
 data file - renf90.dat
 ----------------------
@@ Line 514: / Line 540: @@
 55 2 3 5 56 2 2 aa 3
  1234567.890 66 3 1 3 67 3 3 bb 5
+</file>
+<file>
  Pedigree file (same format as from renum) - renadd02.ped
  --------------------------------------------------------
@@ Line 525: / Line 552: @@
 0 5 1 0 1 2 0 2 aa
 6 7 1 0 2 1 0 0 cc
+</file>
+<file>
 renumbering tables - renf90.tables
 ----------------------------------