4.4 Screen Output

Output may be written to STDOUT, which is typically the console from which the program is run. If you are running the standalone executable bestpred then you'll see a banner that includes the version number of BESTPRED and contact information in the unlikely event that you need support.

[jcole@aipl366 bestpred]$ ./bestpred
--------------------------------------------------------------------------------
BESTPRED version 2.0b10
    Released: 08/08/2008
    Support : John B. Cole (john.cole@ars.usda.gov)
    Website : http://www.aipl.arusda.gov/software/bestpred/
--------------------------------------------------------------------------------

Following the banner is a header that includes the source of the data being processed, information about any requested plots, and single- versus multiple-trait methodology. It also prints breed- and parity-specific mature equivalent mean and SD of milk, fat, protein, and SCS, as well as the tipping points used for calculating persistency.

Reading example data from DCRexample.txt
Lactation yields are MATURE (adjusted for age, etc.) and ACTUAL (unadjusted) values
Plotted lactation curves are a mix of MATURE (adjusted for age, etc.) and ACTUAL (unadjusted) values
Multi-trait methods include data for   Milk    Fat   Prot
New 3X factors phased in over time
DCRs were not adjusted for bumpiness
=====================================================================
Breed H Lact  Mean, St.Dev.   Max.DCR   Lactation Corr.        mid-DIM
ME.Milk   2+  25658.   2946.    104.4   1.00  0.67  0.85 -0.08    161.
ME..Fat   2+    935.    119.    104.6   0.67  1.00  0.77 -0.14    159.
ME.Prot   2+    771.     97.    104.4   0.85  0.77  1.00 -0.10    166.
ME..SCS   2+    679.    295.    104.2  -0.08 -0.14 -0.10  1.00    155.
ME.Milk   1   22270.   2287.    104.0   1.00  0.67  0.85 -0.08    115.
ME..Fat   1     802.     90.    104.2   0.67  1.00  0.77 -0.14    115.
ME.Prot   1     652.     74.    104.0   0.85  0.77  1.00 -0.10    150.
ME..SCS   1     563.    267.    106.0  -0.08 -0.14 -0.10  1.00    155.
 =====================================================================
 Compute DCR, predict yield of cow ---, graph contemps ...
 Supervised =S    ampm1of2=A  2of3=B  1of3=C ver=V  LER=L dup=D
 OwnerSample=O  OSampm1of2=P  2of3=Q  1of3=R  ownerLER=U, bad=X
 Capital letters if milk was sampled, small if milk-only

If one or more elements of the GRAFplot array are set to a value of 1 or 2 then corresponding maxlen-d graphs will be printed to the screenm. You can request a mixture of ME and actual plots in the same run, but you can request only one plot per trait. The x- and y-axes correspond to DIM and yield, respectively. Units for M, F, and P are determined by UNITSout. The cow's lactation curve is represented by dashes (-), the standard (herd) curve by periods (.), and test days by lower- and upper-case letters (depending on the testing plan). Vertical lines of periods (.), vertical bars (|), and colons (:) represent lactation length to date, 305 DIM, and maxlen DIM, respectively. Fat and protein percent and SCS are printed immediately under the graph below their corresponding test days. Plots are of ME or actual values, depending on the values in GRAFplot, and the header will indicate if the plot contains ME or actual values. For example, the follwoing plots include ME milk and actual fat percent.

Milk lactation curve (ME) for cow HOUSA.EX.COW.    ,  fresh 1999 04 01
  90       S                                  |       .         :
  85      ----                                |       .         :
  80    --    ------                          |       .         :
  75  S- .......S...-S----S         S         |       .         :
  70  -..              ....----               |       .         :
  65 -.                      ..--------       S       .         :
  60                           S  .....-----------    .         :
  55 .                                  ..... |   -----         :
  50                                     S   ......   .-----    :
  45                                          |    ......   -----
  40                                          |       .  .......:
  35                                          |       .         .
    0   30   60   90  120  150  180  210  240  270  300  330  360
 Fat% 3.4 3.5     3.7 3.2 3.9 3.2     3.9 3.3 3.6
 Pro% 3.0 3.1     3.3 2.9 3.4 2.9     3.4 3.0 3.2
 SCS  4.6 3.7     2.8 1.9 1.4 1.3     1.7 2.5 3.5

Fat  lactation curve (Actual) for cow HOUSA.EX.COW.    ,  fresh 1999 04 01
3.2       S                                  |       .         :
3.1                                          |       .         :
3.0       -                                  |       .         :
2.9     -- ---           S         S         |       .         :
2.8   --      ---                            |       .         :
2.7  -         S ---     -                   |       .         :
2.6 -S..........    ----- --                 |       .         :
2.5  .          ....S       -      -         |       .         :
2.4 .                ....    ------ --       S       .         :
2.3                      .....        -      |       .         :
2.2                           ....     -   -----     .         :
2.1                               ....  ---  |  ---- .         :
2.0                           S       .....  |      ----       :
1.9                                        .....     .  ----   :
1.8                                          |  .... .      ----
1.7                                     S    |      .....      :
1.6                                          |       .   ......:
1.5                                          |       .         .
    0   30   60   90  120  150  180  210  240  270  300  330  360
 Fat% 3.4 3.5     3.7 3.2 3.9 3.2     3.9 3.3 3.6
 Pro% 3.0 3.1     3.3 2.9 3.4 2.9     3.4 3.0 3.2
 SCS  5.6 4.5     3.4 2.3 1.7 1.6     2.1 3.0 4.2

The number of tests, 305-d yield, 365-d yield, laclen-d yield, lactation-to-date yield, contemporary average yield, DCR, method of calculation (ST or MT), persistency of yield on a 305-d basis, and reliability of persistency is also output for each trait. Yields for M, F, and P are presented in UNITSout units, pounds in this case. Somatic cell scores are multiplied by 100. Mature equivalent values are presented first, followed by actual values. Note that a cow's lactation curve and the contemporary curve may be coincident in a plot when dailyfreq is set to a large value; examination of the actual data shows that they are not identical lines, but overlap due to the low resolution of the plot. See Section 4.6 for details on plotting high-resolution curves.

The plotfreq variable specifies the interval between days plotted. The default of 6 (a point is plotted every 6 days) provides reasonable output on an 80-column display. Setting plotfreq to a smaller value may result in plots that wrap and are unreadable on a terminal.

                                         Cntmp   Adjust   Persistency   Data
             255-d  305-d  365-d  305-d  305-d   Factors  Esti- Relia-  Collectn
 TRAIT Tests Yield  Yield  Yield  Yield  Mean   Age,  3X  mate  bility  Rating
 ME.Milk   9 18824. 21753. 24744. 21753. 20000. 1.00 1.00 -0.06  85.%   102. MT
 ME..Fat   9   669.   778.   893.   778.   700. 1.00 1.00  0.04  84.%   102. MT
 ME.Prot   9   595.   692.   796.   692.   600. 1.01 1.00 -0.31  84.%   102. MT
 ME..SCS   9   215.   221.   230.   221.   308. 0.83 1.00 -0.58  72.%   101. ST
    Milk   9 18805. 21731. 24720. 21731. 19980. 1.00 1.00 -0.06  85.%   102. MT
     Fat   9   666.   774.   889.   774.   697. 1.00 1.00  0.04  84.%   102. MT
    Prot   9   590.   687.   790.   687.   595. 1.01 1.00 -0.31  84.%   102. MT
     SCS   9   260.   268.   278.   268.   373. 0.83 1.00 -0.58  72.%   101. ST

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