Farbcodierung 95% Vertrauensellipsen für Zentroide

Ich habe Schwerpunkte für einen Gower-Ähnlichkeitsindex mit dem vegan{}-Paket in R gezeichnet und möchte die Ellipsenfüllungen basierend auf Faktoren in meinem ursprünglichen Datensatz farbcodieren. Die Zentroide sind für Month-Site-Kombinationen (und dies sind die einzigen Zentroide, die ich plotten möchte; siehe Datenbeispiel unten), aber ich möchte die Ellipsen nach Monat farbig codieren und dann in einem zweiten Diagramm nach Standort, um Unterschiede anzuzeigen zwischen Faktoren. Im Moment sieht der Code wie folgt:Farbcodierung 95% Vertrauensellipsen für Zentroide

dat.fac<-dat[,1:7] ##factors 

dat.mgower <- vegdist(decostand(dat[,8:34], "log"), "altGower") 
ord<-capscale(dat.mgower~1)  #Does the PCO 

plot(ord, display = "sites", type = "n") 

#for i in 
stats<-with(dat.fac, 
    ordiellipse(ord, Site_TP, kind="se", conf=0.95, 
    lwd=2, draw = "polygon",col="#0000ff22",border = "blue"))

Das MDS Grundstück mit den Schwerpunkten wie folgt aussieht: Centroids with Site_season titles

würde Ich mag Farbcode der Lage sein, die Füllungen der Zentroide bezogen auf a) Site und b) Saison (Mai vs. September). Ich habe versucht, col=c("#0000ff22","#CAFF7022",...) zu verwenden, aber das funktioniert nicht, da die Koordinaten für die Ellipsen in ord sind. Ich habe auch versucht

with(dat.fac,ordiellipse(ord, Site_TP[1:54], kind="se", conf=0.95, 
    lwd=2, draw = "polygon",col="#0000ff22",border = "blue"))

die erste Hälfte des ceentroids zu bekommen eine Farbe zu sein (die erste Hälfte alle aus dem gleichen Monat ist), aber dies führt zu dem Fehler „Fehler in cov.wt (X , W): 'x' darf nur endliche Werte enthalten. " Hilfe! Danke.

Die Daten wie folgt aussieht:

structure(list(Core_num = structure(c(39L, 50L, 61L, 70L, 71L, 
72L, 73L, 74L, 75L, 76L, 85L, 86L, 87L, 88L, 89L, 90L, 91L, 92L, 
93L, 94L, 95L, 96L, 97L, 98L, 99L, 100L, 101L, 102L, 103L, 104L, 
105L, 106L, 107L, 108L, 112L, 113L, 115L, 116L, 117L, 118L, 119L, 
120L, 121L, 122L, 123L, 124L, 125L, 126L, 127L, 128L, 129L, 130L, 
131L, 132L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 17L, 18L, 
19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 
32L, 33L, 34L, 35L, 36L, 37L, 38L, 40L, 44L, 45L, 46L, 47L, 48L, 
49L, 51L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 62L, 63L, 
64L, 65L, 66L), .Label = c("152", "153", "154", "155", "156", 
"157", "158", "159", "160", "161", "162", "163", "164", "165", 
"166", "167", "168", "169", "170", "171", "172", "173", "174", 
"175", "176", "177", "178", "179", "180", "181", "182", "183", 
"184", "185", "186", "187", "188", "189", "19", "190", "191", 
"192", "193", "194", "195", "196", "197", "198", "199", "20", 
"200", "201", "202", "203", "204", "205", "206", "207", "208", 
"209", "21", "210", "211", "212", "213", "214", "215", "216", 
"217", "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", "L1", 
"L10", "L11", "L12", "L13", "L14", "L15", "L16", "L17", "L18", 
"L2", "L20", "L21", "L22", "L23", "L24", "L25", "L26", "L27", 
"L28", "L3", "L4", "L5", "L6", "L7", "L9"), class = "factor"), 
    Cage_num = c(47L, 46L, 45L, 2L, 24L, 1L, 23L, 25L, 3L, 61L, 
    5L, 6L, 27L, 49L, 4L, 7L, 48L, 29L, 28L, 26L, 8L, 10L, 51L, 
    50L, 9L, 11L, 30L, 33L, 31L, 32L, 52L, 53L, 54L, 55L, 18L, 
    60L, 41L, 38L, 63L, 19L, 16L, 17L, 40L, 44L, 43L, 21L, 20L, 
    22L, 39L, 62L, 65L, 66L, 42L, 64L, 9L, 54L, 31L, 52L, 10L, 
    53L, 33L, 32L, 8L, 11L, 55L, 30L, 66L, 64L, 21L, 20L, 43L, 
    42L, 44L, 65L, 63L, 18L, 16L, 22L, 62L, 61L, 38L, 19L, 60L, 
    17L, 39L, 40L, 41L, 3L, 24L, 25L, 2L, 23L, 1L, 46L, 47L, 
    45L, 5L, 28L, 48L, 6L, 51L, 50L, 4L, 7L, 29L, 49L, 26L, 27L 
    ), Treatment = structure(c(3L, 3L, 3L, 1L, 2L, 1L, 2L, 2L, 
    1L, 3L, 1L, 1L, 2L, 3L, 1L, 1L, 3L, 2L, 2L, 2L, 1L, 1L, 3L, 
    3L, 1L, 1L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 1L, 3L, 2L, 2L, 
    3L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 3L, 3L, 3L, 2L, 
    3L, 1L, 3L, 2L, 3L, 1L, 3L, 2L, 2L, 1L, 1L, 3L, 2L, 3L, 3L, 
    1L, 1L, 2L, 2L, 2L, 3L, 3L, 1L, 1L, 1L, 3L, 3L, 2L, 1L, 3L, 
    1L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 3L, 3L, 3L, 1L, 2L, 
    3L, 1L, 3L, 3L, 1L, 1L, 2L, 3L, 2L, 2L), .Label = c("C", 
    "CC", "NC"), class = "factor"), Site = structure(c(2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 7L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 1L, 8L, 8L, 1L, 1L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 
    8L, 8L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 6L, 6L, 6L, 6L, 
    6L, 7L, 7L, 6L, 6L, 6L, 6L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 
    8L, 8L, 8L, 8L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 
    6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L), .Label = c("M1", "M2", "R07", "R08_Feb", "R08_Jul", 
    "R09", "R10", "R11", "R11_5m"), class = "factor"), Days_Since_Removal = c(0, 
    0, 0, 0, 0, 0, 0, 0, 0, 291, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 291, 291, 291, 
    291, 291, 291, 291, 291, 291, 669, 669, 669, 669, 669, 291, 
    291, 669, 669, 669, 669, 86, 86, 86, 86, 86, 86, 86, 86, 
    86, 86, 86, 86, 806, 806, 806, 806, 806, 806, 806, 806, 428, 
    428, 428, 806, 428, 428, 428, 428, 428, 428, 428, 428, 428, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0), Time_point = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("May", 
    "September"), class = "factor"), Site_TP = structure(c(3L, 
    3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 10L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 14L, 14L, 1L, 1L, 14L, 14L, 14L, 14L, 
    14L, 14L, 14L, 14L, 14L, 14L, 10L, 10L, 10L, 10L, 10L, 10L, 
    10L, 10L, 10L, 8L, 8L, 8L, 8L, 8L, 10L, 10L, 8L, 8L, 8L, 
    8L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 
    15L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 11L, 11L, 11L, 9L, 11L, 
    11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 4L, 4L, 4L, 4L, 4L, 
    4L, 4L, 4L, 4L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L), .Label = c("M1_May", "M1_September", "M2_May", "M2_September", 
    "R07_May", "R08_Feb_May", "R08_Jul_May", "R09_May", "R09_September", 
    "R10_May", "R10_September", "R11_5m_May", "R11_5m_September", 
    "R11_May", "R11_September"), class = "factor"), Spionidae = c(0, 
    2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 19, 7, 2, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Nereididae = c(0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 7, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Syllidae = c(0, 0, 0, 0, 
    0, 0, 0, 0, 0, 2, 8, 0, 0, 0, 3, 1, 0, 0, 0, 4, 4, 0, 0, 
    0, 1, 0, 1, 4, 1, 0, 0, 1, 1, 2, 2, 0, 1, 0, 3, 0, 0, 0, 
    3, 1, 22, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 1, 5, 3, 0, 0, 0, 0, 9, 5, 0, 0, 
    0, 0, 29, 0, 7, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 1, 0, 0), Opheliidae = c(0, 2, 1, 1, 3, 
    0, 0, 1, 0, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 14, 0, 1, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 3, 0, 14, 1, 0, 1, 0, 0, 1, 1, 0, 2, 
    2, 3, 5, 0, 1, 0, 0, 10, 0, 4, 7, 0, 2, 1, 5, 0, 0, 3, 3, 
    0, 1, 5, 0, 8, 11, 0, 0, 13, 9, 5, 4, 6, 1, 19, 3, 2, 5, 
    1, 1, 0, 0, 3, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 
    0, 0, 0, 0, 0, 0, 0, 1, 1), Cossuridae = c(6, 29, 8, 7, 5, 
    0, 10, 31, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    4, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 4, 7, 6, 12, 0, 0, 19, 3, 4, 2, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0), Sternaspidae = c(0, 0, 0, 0, 0, 
    0, 0, 0, 6, 0, 0, 11, 5, 0, 1, 9, 1, 0, 7, 0, 0, 0, 13, 13, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 10, 0, 0, 0, 24, 1, 27, 
    5, 31, 5, 7, 4, 0, 2, 17), Sabellariidae = c(0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 10, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0), Sabellidae = c(1, 2, 1, 2, 0, 
    0, 3, 0, 2, 3, 2, 0, 0, 0, 0, 0, 2, 1, 0, 1, 0, 6, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 2, 0, 3, 0, 2, 0, 0, 0, 2, 0, 0, 0, 
    4, 16, 29, 0, 1, 0, 3, 2, 1, 7, 3, 24, 1, 1, 11, 1, 2, 1, 
    50, 0, 18, 27, 0, 0, 6, 1, 1, 43, 0, 4, 2, 1, 4, 153, 119, 
    2, 2, 2, 0, 0, 0, 0, 3, 0, 0, 4, 0, 0, 0, 0, 1, 0, 0, 0, 
    0, 4, 0, 0, 0, 2, 2, 1, 0, 0, 0), Capitellidae = c(1, 3, 
    3, 10, 7, 1, 10, 6, 17, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 3, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 4, 0, 0, 4, 0, 0, 0, 0, 
    0, 1, 0, 0, 0, 4, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 3, 1, 3, 
    1, 3, 14, 1, 0, 1, 3, 1, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, 0, 
    0, 0, 6, 6, 2, 1, 0, 4, 2, 2, 1, 0, 1, 0, 0, 4, 0, 0, 1, 
    1, 1, 0, 0, 0, 0, 0, 0, 0, 4, 1, 0), Dorvillidae = c(0, 0, 
    0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 0, 
    2, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 2, 0, 
    0, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Cirratulidae = c(0, 0, 
    0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 8, 0, 
    0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Oligochaeta = c(19, 35, 
    14, 41, 31, 12, 42, 38, 27, 16, 28, 2, 3, 2, 32, 0, 12, 12, 
    2, 7, 2, 4, 1, 20, 9, 14, 35, 5, 1, 0, 1, 4, 0, 6, 264, 48, 
    27, 8, 22, 0, 3, 133, 42, 5, 40, 21, 0, 2, 101, 4, 2, 0, 
    0, 11, 20, 4, 21, 22, 1, 9, 64, 5, 0, 38, 8, 20, 6, 5, 5, 
    35, 8, 7, 13, 9, 93, 20, 25, 12, 28, 63, 21, 71, 271, 4, 
    204, 8, 51, 14, 11, 10, 10, 1, 5, 4, 6, 4, 2, 3, 1, 0, 0, 
    1, 0, 1, 2, 9, 24, 1), Nemertea = c(0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0), Nematoda = c(2, 0, 0, 4, 5, 5, 0, 1, 13, 
    0, 0, 0, 1, 0, 0, 2, 0, 8, 3, 3, 2, 1, 4, 4, 0, 0, 18, 0, 
    1, 1, 1, 8, 2, 12, 1, 0, 4, 0, 1, 0, 0, 6, 0, 1, 4, 0, 0, 
    0, 1, 0, 0, 2, 6, 0, 0, 0, 1, 15, 0, 0, 20, 1, 0, 1, 2, 0, 
    0, 0, 0, 1, 16, 5, 1, 1, 0, 0, 35, 3, 1, 0, 1, 0, 0, 0, 0, 
    0, 0, 0, 1, 0, 1, 0, 1, 16, 2, 1, 0, 18, 0, 0, 0, 0, 0, 0, 
    0, 1, 0, 0), Platyhelminthes = c(0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0), Sipuncula = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    2, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 25, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 
    0, 0, 0, 0), Ostracoda = c(0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 
    0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 7, 1, 0, 0, 0, 0, 0, 0, 0, 0, 5, 
    7, 0, 2, 11, 5, 5, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0), Decapoda = c(0, 0, 0, 4, 0, 0, 2, 0, 0, 0, 0, 0, 
    1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 
    0, 0, 0, 0, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 
    0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 
    0, 1, 1, 0, 0, 4, 0, 1, 1, 0, 0, 1, 0, 2, 1, 0, 0, 1, 0, 
    0, 0, 17, 0, 0, 0, 0, 2, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 2, 
    0), Amphipoda = c(1, 1, 5, 17, 8, 75, 22, 0, 34, 4, 38, 0, 
    27, 24, 89, 2, 1, 5, 3, 42, 88, 3, 1, 21, 6, 1, 6, 60, 6, 
    11, 0, 4, 11, 17, 15, 0, 13, 5, 44, 9, 0, 0, 0, 11, 20, 28, 
    8, 45, 0, 0, 18, 2, 14, 8, 3, 0, 2, 6, 6, 0, 2, 14, 2, 2, 
    6, 3, 37, 37, 5, 20, 63, 12, 10, 49, 6, 3, 150, 83, 7, 3, 
    5, 20, 15, 4, 19, 1, 6, 0, 3, 0, 0, 0, 14, 0, 1, 2, 3, 0, 
    0, 0, 1, 16, 3, 3, 0, 3, 1, 1), Isopoda = c(0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0), Copepoda = c(0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 2, 0, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 7, 0, 0, 1, 0, 0, 0, 
    1, 0, 8, 1, 0, 2, 5, 1, 5, 2, 2, 0, 2, 4, 1, 0, 0, 0, 0, 
    0, 1, 1, 0, 0, 1, 0, 0, 0, 5, 3, 0, 0, 0, 1, 0, 0, 0, 0, 
    0, 0, 1, 0, 0, 0), Tanaidacea = c(0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 6, 0, 1, 0, 0, 0, 0, 3, 
    0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 3, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 
    0, 2, 0, 1, 1, 6, 2, 0, 1, 0, 2, 1, 3, 1, 0, 0, 0, 0, 2, 
    0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0), HYRDOZOA = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0), ANTHOZOA = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0), Cnidarian_larvae = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0), Tunicata = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), 
    Mollusca = c(0L, 0L, 0L, 4L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
    0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
    0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 
    0L, 0L, 2L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
    1L, 14L, 2L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 
    1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 4L, 
    0L, 3L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
    0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L)), .Names = c("Core_num", 
"Cage_num", "Treatment", "Site", "Days_Since_Removal", "Time_point", 
"Site_TP", "Spionidae", "Nereididae", "Syllidae", "Opheliidae", 
"Cossuridae", "Sternaspidae", "Sabellariidae", "Sabellidae", 
"Capitellidae", "Dorvillidae", "Cirratulidae", "Oligochaeta", 
"Nemertea", "Nematoda", "Platyhelminthes", "Sipuncula", "Ostracoda", 
"Decapoda", "Amphipoda", "Isopoda", "Copepoda", "Tanaidacea", 
"HYRDOZOA", "ANTHOZOA", "Cnidarian_larvae", "Tunicata", "Mollusca" 
), row.names = c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 19L, 
20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 32L, 
33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 46L, 47L, 49L, 
50L, 51L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 
63L, 64L, 65L, 66L, 67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 
76L, 83L, 84L, 85L, 86L, 87L, 88L, 89L, 90L, 91L, 92L, 93L, 94L, 
95L, 96L, 97L, 98L, 99L, 100L, 101L, 102L, 103L, 104L, 105L, 
109L, 110L, 111L, 112L, 113L, 114L, 115L, 116L, 117L, 118L, 119L, 
120L, 121L, 122L, 123L, 124L, 125L, 126L, 127L, 128L, 129L), class = "data.frame")

Quelle

2012-08-17 Margaret

Sie möchten also die Farbe der Hülle des Rumpfes ändern?Außerdem verstehe ich deine Handlung nicht genau mit diesem Code. –

Ja. Und der Code sollte nur die Ellipsen zeigen, nicht die Zentroide. Das sind die Teile, für die ich die Füllung ändern möchte. – Margaret

Idealerweise könnte die Funktion der x- und y-Koordinaten in den Ellipsen verwendet zurückzukehren. Hier ist eine einfache Modifikation von ordiellipse() die xy jedem Listenelement der Funktionsausgabe ergänzt:

ordiellipse2 <- 
function (ord, groups, display = "sites", kind = c("sd", "se"), 
     conf, draw = c("lines", "polygon", "none"), 
     w = weights(ord, display), col = NULL, alpha = 127, 
     show.groups, label = FALSE, ...) 
{ 
    weights.default <- function(object, ...) NULL 
    kind <- match.arg(kind) 
    draw <- match.arg(draw) 
    pts <- scores(ord, display = display, ...) 
    ## ordiellipse only works with 2D data (2 columns) 
    pts <- as.matrix(pts) 
    if (ncol(pts) > 2) 
     pts <- pts[ , 1:2, drop = FALSE] 
    if (ncol(pts) < 2) 
     stop("ordiellipse needs two dimensions") 
    w <- eval(w) 
    if (length(w) == 1) 
     w <- rep(1, nrow(pts)) 
    if (is.null(w)) 
     w <- rep(1, nrow(pts)) 
    ## make semitransparent fill 
    if (draw == "polygon" && !is.null(col)) 
     col <- rgb(t(col2rgb(col)), alpha = alpha, maxColorValue = 255) 
    if (!missing(show.groups)) { 
     take <- groups %in% show.groups 
     pts <- pts[take, , drop = FALSE] 
     groups <- groups[take] 
     w <- w[take] 
    } 
    out <- seq(along = groups) 
    inds <- names(table(groups)) 
    res <- list() 
    if (label) 
     cntrs <- names <- NULL 
    ## Remove NA scores 
    kk <- complete.cases(pts) 
    for (is in inds) { 
     gr <- out[groups == is & kk] 
     if (length(gr) > 2) { 
      X <- pts[gr, ] 
      W <- w[gr] 
      mat <- cov.wt(X, W) 
      if (kind == "se") 
       mat$cov <- mat$cov/mat$n.obs 
      if (missing(conf)) 
       t <- 1 
      else t <- sqrt(qchisq(conf, 2)) 
      xy <- vegan:::veganCovEllipse(mat$cov, mat$center, t) 
      if (draw == "lines") 
       vegan:::ordiArgAbsorber(xy, FUN = lines, 
         col = if(is.null(col)) par("fg") else col, 
         ...) 

      else if (draw == "polygon") 
       vegan:::ordiArgAbsorber(xy[, 1], xy[, 2], col = col, FUN = polygon, 
         ...) 

      if (label && draw != "none") { 
       cntrs <- rbind(cntrs, mat$center) 
       names <- c(names, is) 
      } 
      mat$scale <- t 
      mat$xy <- xy # this is the only substantive change I made 
      res[[is]] <- mat 
     } 
    } 
    if (label && draw != "none") { 
     if (draw == "lines") 
      vegan:::ordiArgAbsorber(cntrs[,1], cntrs[,2], labels=names, col = col, 
        FUN = text, ...) 
    else 
     vegan:::ordiArgAbsorber(cntrs, labels = names, col = NULL, 
       FUN = ordilabel, ...) 
    } 
    class(res) <- "ordiellipse" 
    invisible(res) 
}

Jetzt können Sie erstellen Ihre stats Objekt, pro Ihr Beispiel, aber angeben draw = "none", because you'll want to play with stats` auf eigene Faust die volle Kontrolle zu haben, die Ellipse Plotten (keine Notwendigkeit graphische Argumente angeben):

stats<-with(dat.fac, ordiellipse2(ord, Site_TP, kind = "se", conf = 0.95, draw = "none"))

Hinweis nun, dass die Statistiken die gleiche Form haben, aber es ist ein Element xy für jede Ellipse:

names(stats[[1]]) 
[1] "cov" "center" "n.obs" "wt"  "scale" "xy"

Sie können diese in einer Schleife zeichnen Sie die polygon() Funktion, aber besser wäre alles in einem einzigen matrix oder data.frame die xy-Koordinaten, zu platzieren, so dass Sie nur einen einzigen Anruf zu polygon(), aber mit vektorisiert Argumente machen wie col, lwd. Ich extrahiere die xy Matrizen unter Verwendung , dann kollabieren sie zusammen als data.frame. Key ist die Trennung der einzelnen Ellipsen mit NA s, so dass die Polygonzeichnungs weiß, wo man aufhört und die nächste beginnt:

xy.mat <- t(as.data.frame(lapply(stats, function(x){ 
      t(rbind(x$xy, NA)) 
     })))

Plotten einfach wird:

plot(ord, display = "sites", type = "n") 
polygon(xy.mat[, 1], xy.mat[, 2], col = c(rep("#0000ff20", 5), rep("#ff000030", 5)), border = c(rep("blue", 5), rep("red", 5)))

enter image description here

Jetzt ist es nur eine Frage der richtigen Zuordnung der grafischen Argumente zu polygon().

Quelle

2012-08-19 17:41:32

Woohoo! Danke @tim! – Margaret

Farbcodierung 95% Vertrauensellipsen für Zentroide

Antwort

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