bestpred.par

! bestpred.par -- Parameter file for maindcr program
!                for best prediction of lactation
!                yields and persistency of MFPS.
!
! Each parameter is preceded by a description of what
! that parameter does, as well as a list of allowed
! values. As a general rule, the program DOES NOT
! check your inputs for correctness. Be careful.
!
! IMPORTANT NOTE: If you are getting strange error messages
! when you run the maindcr program check the maindcr.par
! file to make sure that it has valid <eol> characters in
! it. Some editors do not set them correctly, particularly
! on the last line of the file.
!
! "bestpred" is the namelist that contains all of the
! parameters defined in this file; it's a Fortran thing.
! Please don't change it.
!
&bestpred
  !
  ! laclen specifies the length of the lactation for
  ! which calculations are being made. The default is
  ! 305. A negative value will be set to 305.
  !
  laclen = 305
  !
  ! maxlen specifies the longest possible lactation
  ! length. maxlen MUST be >= laclen. A negative value will
  ! be set to 305; if maxlen < laclen then maxlen will be
  ! set to laclen.
  !
  maxlen = 365
  !
  ! dailyfreq specifies the frequency with which actual
  ! daily yields are calculated. The default is 6 (actual yields
  ! calculated every 6 days). A value of 0 indicates that no daily
  ! values should be calculated. A negative value will be set to
  ! the default of 6. Note that computing time increases as
  ! dailyfreq decreases towards 1, that is, a dailyfreq of 1 will
  ! require much more processing time than a dailyfreq of 6.
  !
  dailyfreq = 1
  !
  ! plotfreq specifies the frequency with which yields are plotted
  ! by the inbuilt plotting routine.
  !
  plotfreq = 6
  !
  ! 0 doesn't adjust for 3X milking,
  ! 1 uses old factors, 2 new factors,
  ! 3 uses phased-in factors over time
  !
  use3X = 3
  !
  ! 1 does only ST to save CPU time; 3 does MT M,F,P;
  ! 4 does MT M,F,P,S. Single trait best prediction
  ! is the fastest, may be moot on modern hardware.
  !
  mtrait = 3
  !
  ! Individual Source 14 records contain an mtrait
  ! switch. When set to a valid non-zero value of
  ! mtrait (1, 3, or 4) GLOBALmtrait overrides the
  ! individual switches and uses the same computat-
  ! ion method for all records read from the same
  ! file. Only used when source = 14.
  !
  GLOBALmtrait = 3
  !
  ! GRAFplot contains 0/1/2 flags indicating which
  ! lactation curves should be plotted; 1 = plot ME,
  ! 2 = plot actual, 0 = don't plot. The elements
  ! of GRAFplot are 1 = Milk, 2 = Fat, 3 = Protein,
  ! and 4 = SCS. ONscreen overrides GRAFplot -- if
  ! terminal output is turned off, graphs will not
  ! be drawn even if GRAFplot is turned on. GRAFplot
  ! also controls which traits are writter to the
  ! CURVEfile output file.
  !
  GRAFplot(1) = 0
  GRAFplot(2) = 0
  GRAFplot(3) = 0
  GRAFplot(4) = 0
  !
  ! UNITSin and UNITSout specify, respectively, the
  ! units in which yields are inout (UNITSin) and the
  ! the units in which output should be written
  ! (UNITSout). Note that these apply only to MFP,
  ! not S. Values may be 'P' for pounds or 'K' for
  ! kilograms, and UNITSin and UNITSout may be set
  ! to different units. If an invalid value is pro-
  ! vided a default of 'P' is used.
  !
  UNITSin = 'P'
  UNITSout = 'P'
  !
  ! PERSfloor and PERSceiling provide minimum and
  ! maximum values for persistencies calculated
  ! from Source 14 records. Values smaller than
  ! the floor and larger than the ceiling are
  ! rounded up or down, as appropriate. These
  ! options affect ONLY Source 14 records. If you
  ! set a floor or ceiling whose absolute value
  ! is greater than 9.99 then you will also need
  ! to modify the format used to write the contents
  ! of OUTfile in the maindcr.f90 program.
  !
  PERSfloor = -9.99
  PERSceiling = 9.99
  !
  ! DO NOT change "source" unless you really know what
  ! you're doing. Settings of interest:
  !   10 inputs test day data in format 4 as defined in
  !      the document "Listing of Format 4 -- Cow/Doe
  !      Lactation Data utilizing multiple test day
  !      segments" (http://aipl.arsusda.gov/formats/fmt4.html)
  !      from the file format4.dat.
  !   11 uses testing plans coded by user from the file
  !      DCRexample.dat.
  !   12 inputs USDA master file records from the file
  !      input.dcr.
  !   14 inputs TD data in DRMS format from the file
  !      INfile and writes results to the file OUTfile.
  !   15 As source 10, but also reads average 305-d MFPS
  !      yields from the file format4.means. EXPERIMENTAL!
  !   24 reads filenames for format 14 files from a text
  !      named "pcdart_files.txt".
  !
  source = 10
  !
  ! breed11 specifies the breed to be used for running the
  ! testing plans coded in DCRexample.dat. It is used only
  ! when source == 11. Breeds are as follows: 1=AY, 2=BS,
  ! 3=GU, 4=HO, 5=JE, 6=MS. The default is 4 (Holstein).
  !
  breed11 = 4
  !
  ! breedUNK specifies the breed to be used when an unknown
  ! breed code is found in a cow ID. Breeds are as follows:
  ! 1=AY, 2=BS, 3=GU, 4=HO, 5=JE, 6=MS. The default is 4
  ! (Holstein).
  !
  breedUNK = 4
  !
  ! If WRITEcurve is set to 1 then daily BP, YD yields,
  ! and standard curves will be written to the file
  ! CURVEfile. Note that CURVEfile is limited to 64
  ! characters. The cow ID will be appended to CURVEfile
  ! to create the final output file name. If an invalid
  ! value is provided for WRITEcurve a default of 0 is used.
  ! If CURVEsmall is set to 1 then only actual yield data
  ! are written to CURVEfile. If CURVEsingle is set to
  ! 1 then a separate CURVEfile is written out for each
  ! animal in the dataset.
  !
  WRITEcurve = 1
  CURVEfile = 'cowcurve'
  CURVEsmall = 0
  CURVEsingle = 1
  !
  ! If WRITEdata is set to 1 then daily BP, YD yields,
  ! and standard curves will be written to the file
  ! DATAfile. Note that DATAfile is limited to 64
  ! characters. The cow ID will be appended to DATAfile
  ! to create the final output file name. If an invalid
  ! value is provided for WRITEdata a default of 0 is used.
  !
  WRITEdata = 1
  DATAfile = 'cowdata'
  !
  ! INfile and OUTfile specify the names to be used when
  ! reading and writing Source 14 input and output files.
  ! Note that filenames are limited to 64 characters.
  !
  INfile = 'pcdart.bpi'
  OUTfile = 'pcdart.bpo'
  !
  ! maxprnt is the number of graphs to display. Set maxprnt
  ! to 1 and DEBUGmsgs to 1 to display the input variables.
  !
  maxprnt = 0
  !
  ! ONscreen is used to toggle output to the screen/terminal
  ! on (1) and off (0). ONscreen overrides maxprnt -- if
  ! console output is turned off only debugging messages will
  ! print to the terminal even if maxprnt is not 0.
  !
  ONscreen = 1
  !
  ! obs is the maximum number of records to read (DO NOT
  ! CHANGE, default = 99999999).
  !
  obs = 99999999
  !
  ! maxshow is the maximum number of cow records to display
  ! (DO NOT CHANGE, default = 5).
  !
  maxshow = 1
  !
  ! maxtd is the maximum number of test days in a lactation
  ! (DO NOT CHANGE, default = 50).
  !
  maxtd = 50
  !
  ! INTmethod specifies the interpolation method used for
  ! lactation curves for MFP (DO NOT CHANGE, default = 'L').
  !
  INTmethod = 'W'
  !
  ! INTmethodSCS specifies the interpolation method used for
  ! lactation curves for SCS (DO NOT CHANGE, default = 'L').
  !
  INTmethodSCS = 'G'
  ! The following parms are for controlling debugging messages
  ! and the like. You'll  probably never need to touch them.
  !
  ! When DEBUGparms is set the parameters read from this file
  ! will be written to the screen.
  DEBUGparms = 0
  ! DEBUGmsgs overrides ONscreen -- debugging messages will print
  ! even if screen output has been deactivated.
  DEBUGmsgs  = 0
  !
  ! The elements of dim0 are the DIM midpoints for persistency chosen
  ! such that yield and persistency for each trait are phenotypically
  ! independent.
  !
  ! These are the 2007 default values (smooth curves).
  dim0(1) = 115
  dim0(2) = 115
  dim0(3) = 150
  dim0(4) = 155
  dim0(5) = 161
  dim0(6) = 152
  dim0(7) = 159
  dim0(8) = 148
  !
  ! Set dim0flag to 1 to estimate new tipping points,Note that this
  ! slows down processing considerably and you don't want to estimate
  ! on-the-fly unless you have to.
  dim0flag = 0
  !
  ! The name of the file to which logging messages are written.
  ! Limited to 64 characters.
  !
  LOGon   = 0
  LOGfile = 'example'
  LOGfreq = 0
  !
  ! region and season specify defaults for analyses that
  ! use region- and/or season-specific lactation curves.
  !
  region = 1
  season = 1
/