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Identify the Experimental Design

The function check_design_met helps us to check the quality of the data and also to identify the experimental design of the trials. This works as a quality check or quality control before we fit any model.

library(agriutilities)
library(agridat)
data(besag.met)
dat <- besag.met
results <- check_design_met(
  data = dat,
  genotype = "gen",
  trial = "county",
  traits = "yield",
  rep = "rep",
  block = "block",
  col = "col",
  row = "row"
)
print(results)
#> ---------------------------------------------------------------------
#> Summary Traits by Trial:
#> ---------------------------------------------------------------------
#> # A tibble: 6 × 11
#>   county traits   Min  Mean Median   Max    SD    CV     n n_miss miss_perc
#>   <fct>  <chr>  <dbl> <dbl>  <dbl> <dbl> <dbl> <dbl> <int>  <int>     <dbl>
#> 1 C1     yield   87.9 149.   151.   200.  17.7 0.119   198      6    0.0303
#> 2 C2     yield   24.4  56.1   52.1  125.  18.4 0.328   198      6    0.0303
#> 3 C3     yield   28.2  87.9   89.2  137.  19.7 0.225   198      6    0.0303
#> 4 C4     yield  103.  145.   143.   190.  17.1 0.118   198      6    0.0303
#> 5 C5     yield   66.9 115.   116.   152.  16.4 0.142   198      6    0.0303
#> 6 C6     yield   29.2  87.6   87.8  148.  26.6 0.304   198      6    0.0303
#> 
#> ---------------------------------------------------------------------
#> Experimental Design Detected:
#> ---------------------------------------------------------------------
#>   county exp_design
#> 1     C1    row_col
#> 2     C2    row_col
#> 3     C3    row_col
#> 4     C4    row_col
#> 5     C5    row_col
#> 6     C6    row_col
#> 
#> ---------------------------------------------------------------------
#> Summary Experimental Design:
#> ---------------------------------------------------------------------
#> # A tibble: 6 × 9
#>   county     n n_gen n_rep n_block n_col n_row num_of_reps num_of_gen
#>   <fct>  <int> <int> <int>   <int> <int> <int> <fct>       <fct>     
#> 1 C1       198    64     3       8    11    18 3_9         63_1      
#> 2 C2       198    64     3       8    11    18 3_9         63_1      
#> 3 C3       198    64     3       8    11    18 3_9         63_1      
#> 4 C4       198    64     3       8    11    18 3_9         63_1      
#> 5 C5       198    64     3       8    11    18 3_9         63_1      
#> 6 C6       198    64     3       8    11    18 3_9         63_1      
#> 
#> ---------------------------------------------------------------------
#> Connectivity Matrix:
#> ---------------------------------------------------------------------
#>    C1 C2 C3 C4 C5 C6
#> C1 64 64 64 64 64 64
#> C2 64 64 64 64 64 64
#> C3 64 64 64 64 64 64
#> C4 64 64 64 64 64 64
#> C5 64 64 64 64 64 64
#> C6 64 64 64 64 64 64
#> 
#> ---------------------------------------------------------------------
#> Filters Applied:
#> ---------------------------------------------------------------------
#> List of 1
#>  $ yield:List of 4
#>   ..$ missing_50%     : chr(0) 
#>   ..$ no_variation    : chr(0) 
#>   ..$ row_col_dup     : chr(0) 
#>   ..$ trials_to_remove: chr(0)

Single Trial Analysis

The results of the previous function are used in single_trial_analysis() to fit single trial models.

obj <- single_trial_analysis(results, progress = FALSE)
print(obj)
#> ---------------------------------------------------------------------
#> Summary Fitted Models:
#> ---------------------------------------------------------------------
#>     trait  trial heritability        CV    VarGen    VarErr  design
#>    <char> <char>        <num>     <num>     <num>     <num>  <char>
#> 1:  yield     C1         0.73  6.022489  87.39848  82.86095 row_col
#> 2:  yield     C2         0.37 17.104998  25.80684 108.68546 row_col
#> 3:  yield     C3         0.64 12.357202  83.57907 118.55567 row_col
#> 4:  yield     C4         0.41  8.179408  35.75568 136.21218 row_col
#> 5:  yield     C5         0.80  7.037586 103.79822  66.97523 row_col
#> 6:  yield     C6         0.49 16.632367  71.92232 207.53073 row_col
#> 
#> ---------------------------------------------------------------------
#> Outliers Removed:
#> ---------------------------------------------------------------------
#>     trait  trial genotype    id outlier
#>    <char> <fctr>   <fctr> <int>  <lgcl>
#> 1:  yield     C1      G60    50    TRUE
#> 
#> ---------------------------------------------------------------------
#> First Predicted Values and Standard Errors (BLUEs/BLUPs):
#> ---------------------------------------------------------------------
#>     trait genotype  trial    BLUEs  seBLUEs    BLUPs  seBLUPs         wt
#>    <char>   <fctr> <fctr>    <num>    <num>    <num>    <num>      <num>
#> 1:  yield      G01     C1 141.4161 6.078858 143.5308 5.249771 0.02706176
#> 2:  yield      G02     C1 157.8110 5.979708 155.8037 5.194547 0.02796663
#> 3:  yield      G03     C1 127.3836 6.091534 133.0256 5.269999 0.02694925
#> 4:  yield      G04     C1 154.8445 6.093866 153.8364 5.270427 0.02692863
#> 5:  yield      G05     C1 163.8950 6.132141 161.1831 5.271809 0.02659352
#> 6:  yield      G06     C1 128.5168 6.087902 133.6857 5.247130 0.02698141

Multi-Environmental Trial Analysis

The results of the previous function are used in met_analysis() to fit multi-environmental trial models.

met_results <- met_analysis(obj)
print(met_results)
#> Online License checked out Mon Jun 17 09:29:11 2024
#> Fitting MET model for yield.
#> ---------------------------------------------------------------------
#> Trial Effects (BLUEs):
#> ---------------------------------------------------------------------
#>   trait trial predicted.value std.error    status
#> 1 yield    C1       149.74946  1.358117 Estimable
#> 2 yield    C2        65.99561  1.141995 Estimable
#> 3 yield    C3        90.60825  1.449096 Estimable
#> 4 yield    C4       148.12392  1.202934 Estimable
#> 5 yield    C5       121.77612  1.429239 Estimable
#> 6 yield    C6        88.31194  1.532688 Estimable
#> 
#> ---------------------------------------------------------------------
#> Heritability:
#> ---------------------------------------------------------------------
#>   trait        h2
#> 1 yield 0.8239191
#> 
#> ---------------------------------------------------------------------
#> First Overall Predicted Values and Standard Errors (BLUPs):
#> ---------------------------------------------------------------------
#>   trait genotype predicted.value std.error    status
#> 1 yield      G01        110.4297  2.528111 Estimable
#> 2 yield      G02        110.8617  2.537200 Estimable
#> 3 yield      G03        102.6812  2.541066 Estimable
#> 4 yield      G04        115.4946  2.533730 Estimable
#> 5 yield      G05        120.6600  2.548344 Estimable
#> 6 yield      G06        108.8297  2.555281 Estimable
#> 
#> ---------------------------------------------------------------------
#> Variance-Covariance Matrix:
#> ---------------------------------------------------------------------
#> 
#> Correlation Matrix ('us'): yield
#>      C1   C2   C3   C4   C5   C6
#> C1 1.00 0.57 0.58 0.65 0.95 0.43
#> C2 0.57 1.00 0.55 0.70 0.52 0.76
#> C3 0.58 0.55 1.00 0.95 0.72 0.27
#> C4 0.65 0.70 0.95 1.00 0.75 0.47
#> C5 0.95 0.52 0.72 0.75 1.00 0.33
#> C6 0.43 0.76 0.27 0.47 0.33 1.00
#> 
#> Covariance Matrix ('us'): yield
#>       C1    C2    C3    C4     C5    C6
#> C1 80.57 27.36 46.81 31.67  85.61 31.17
#> C2 27.36 28.90 26.44 20.41  27.99 33.51
#> C3 46.81 26.44 79.66 45.84  64.54 19.81
#> C4 31.67 20.41 45.84 29.28  40.79 20.76
#> C5 85.61 27.99 64.54 40.79 100.60 27.13
#> C6 31.17 33.51 19.81 20.76  27.13 66.66
#> 
#> ---------------------------------------------------------------------
#> First Stability Coefficients:
#> ---------------------------------------------------------------------
#>   trait genotype superiority   static    wricke predicted.value
#> 1 yield      G57    22.67503 32.45871 13.962970        92.45997
#> 2 yield      G29    17.27533 34.41794  4.343501        99.38429
#> 3 yield      G34    17.26249 33.29276  8.514332        99.74688
#> 4 yield      G59    16.94882 34.39425  4.798863        99.87221
#> 5 yield      G31    16.23001 31.89042 11.722935       101.66382
#> 6 yield      G10    15.75253 32.02994 11.499867       102.39802