compute derived phenotypic variables
Arguments
- x
a dataframe
- sz
size of farm, here taken to be 10000 sq metres
- btwn
spacing between ridges in metres
- within
spacing between plants in the same ridge in metres
Examples
f <- system.file("uon-trial-1.csv", package = "pbwrangler")
df <- read_workbooks(dir = NULL, file_to_read = f)
#> Rows: 108 Columns: 32
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (8): unique, geno, flowering_date, flower_colour, flesh_colour, skin_co...
#> dbl (24): plot, entry, row, col, rep, ntp, npe, growth_speed, pgh, plant_uni...
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
df_out <- pre_process_trials(df) |> process_trials() %>%
purrr::map(., run_data_processes)
#> Warning: NAs introduced by coercion
#> Warning: NAs introduced by coercion
#> Warning: NAs introduced by coercion
#> Warning: NAs introduced by coercion
#> Warning: NAs introduced by coercion
#> Warning: NAs introduced by coercion
#> Warning: NAs introduced by coercion
#> Warning: NAs introduced by coercion
#> Joining with `by = join_by(old_family_code)`
#> Warning: Some columns with invalid names: c("unique", "entry", "growth_speed", "flowering_date", "flower_colour", "overall_impression", "flesh_colour", "skin_colour", "late_blight_60_days", "obs", "photo", "n_tubers")
#> Warning: Some columns with invalid names: c("unique", "entry", "growth_speed", "flowering_date", "flower_colour", "overall_impression", "flesh_colour", "skin_colour", "late_blight_60_days", "obs", "photo", "n_tubers")
#> Warning: Some columns with invalid names: c("unique", "entry", "growth_speed", "flowering_date", "flower_colour", "overall_impression", "flesh_colour", "skin_colour", "late_blight_60_days", "obs", "photo", "n_tubers")
#> Warning: Rows with out of scale values replaced with NA for variable nmtp: 54
#> Warning: Rows with extreme values replaced with NA for variable atmw: 54
#> Warning: Rows with extreme values replaced with NA for variable mtwp: 54
#> Warning: Rows with extreme values replaced with NA for variable mtyna: 54
#> Warning: pt crop detected
#> Warning: Some columns with invalid names: c("unique", "entry", "growth_speed", "flowering_date", "flower_colour", "overall_impression", "late_blight_60_days", "obs", "photo", "n_tubers")
#> Warning: Some variables have been overwritten: c("atmw", "ppe", "mtyna")
#> Warning: pt crop detected
#> Warning: Some columns with invalid names: c("unique", "entry", "growth_speed", "flowering_date", "flower_colour", "overall_impression", "late_blight_60_days", "obs", "photo", "n_tubers")
#> Warning: Rows with out of scale values replaced with NA for variable tbfsh1: 1 2 3 4 5 6 19 20 21 22 23 24 37 38 39 40 41 42 55 56 57 58 59 60 73 74 75 76 77 78 91 92 93 94 95 96
#> Warning: Rows with out of scale values replaced with NA for variable tbskn1: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108
#> Warning: pt crop detected
#> Warning: Some columns with invalid names: c("unique", "entry", "growth_speed", "flowering_date", "flower_colour", "overall_impression", "late_blight_60_days", "obs", "photo", "n_tubers")
#> Warning: Some variables have been overwritten: c("atmw", "ppe", "mtyna")
#> Warning: pt crop detected
#> Warning: Some columns with invalid names: c("unique", "entry", "growth_speed", "flowering_date", "flower_colour", "overall_impression", "late_blight_60_days", "obs", "photo", "n_tubers")
purrr::map(df_out, names_df)
#> $`UON-TRIAL-1`
#> [1] "atmw" "col" "entry"
#> [4] "flower_colour" "flowering" "flowering_date"
#> [7] "geno" "growth_speed" "late_blight_60_days"
#> [10] "mtwp" "mtyna" "n_tubers"
#> [13] "nmtp" "npe" "ntp"
#> [16] "obs" "overall_impression" "pgh"
#> [19] "photo" "plant_unif" "plant_vigor"
#> [22] "plot" "ppe" "rep"
#> [25] "row" "se" "tbfsh1"
#> [28] "tbskn1" "tub_size" "tub_unif"
#> [31] "tuber_apper" "unique"
#>