compute derived phenotypic variables
Arguments
- x
a dataframe
- sz
number of plants per plot
- btwn
spacing between ridges in metres
- within
spacing between plants in the same ridge in metres
- crop
one of
'pt'or'sp'
Examples
f <- system.file("uon-trial-1.csv", package = "pbwrangler")
df <- read_workbooks(dir = NULL, file_to_read = f) %>%
purrr::map(
.,
~ dplyr::mutate(
.,
space_between_ridges = "0.75m",
space_between_plants_in_ridges = "0.3m",
number_of_plants_per_plot = 10
)
)
#> 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
#> 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", "space_between_ridges", "space_between_plants_in_ridges", "number_of_plants_per_plot", "n_tubers", "pls", "pld")
#> 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", "space_between_ridges", "space_between_plants_in_ridges", "number_of_plants_per_plot", "n_tubers", "pls", "pld")
#> 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", "space_between_ridges", "space_between_plants_in_ridges", "number_of_plants_per_plot", "n_tubers", "pls", "pld")
#> Warning: Rows with out of scale values replaced with NA for variable nmtp: 54
#> Warning: Rows with out of scale values replaced with NA for variable ppe: 1 2 3 4 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: 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: Rows with extreme values replaced with NA for variable ttwp: 54
#> Warning: Rows with extreme values replaced with NA for variable ttyna: 54
#> Warning: Some columns with invalid names: c("unique", "entry", "growth_speed", "flowering_date", "flower_colour", "overall_impression", "late_blight_60_days", "obs", "photo", "space_between_ridges", "space_between_plants_in_ridges", "number_of_plants_per_plot", "n_tubers", "pls", "pld")
#> Warning: Some variables have been overwritten: c("atmw", "atw", "ppe", "mtyna", "ttyna")
#> Warning: Some columns with invalid names: c("unique", "entry", "growth_speed", "flowering_date", "flower_colour", "overall_impression", "late_blight_60_days", "obs", "photo", "space_between_ridges", "space_between_plants_in_ridges", "number_of_plants_per_plot", "n_tubers", "pls", "pld")
#> Warning: Rows with out of scale values replaced with NA for variable ppe: 1 2 3 4 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: 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
purrr::map(df_out, names_df)
#> $`UON-TRIAL-1`
#> [1] "atmw" "atw"
#> [3] "col" "entry"
#> [5] "flower_colour" "flowering"
#> [7] "flowering_date" "geno"
#> [9] "growth_speed" "late_blight_60_days"
#> [11] "mtwp" "mtyna"
#> [13] "n_tubers" "nmtp"
#> [15] "npe" "ntp"
#> [17] "number_of_plants_per_plot" "obs"
#> [19] "overall_impression" "pgh"
#> [21] "photo" "plant_unif"
#> [23] "plant_vigor" "pld"
#> [25] "plot" "pls"
#> [27] "ppe" "rep"
#> [29] "row" "se"
#> [31] "space_between_plants_in_ridges" "space_between_ridges"
#> [33] "tbfsh1" "tbskn1"
#> [35] "tntp" "ttwp"
#> [37] "ttyna" "tub_size"
#> [39] "tub_unif" "tuber_apper"
#> [41] "unique"
#>