This page describes the CompadreDB class, including methods for accessing the slots (see functions CompadreData and VersionData), accessing ($) and replacing ($<-) columns within the data slot, accessing elements from the version slot (see functions VersionData and DateCreated), and converting legacy database objects to the CompadreDB class (see as_cdb).

CompadreData(object)

# S4 method for CompadreDB
CompadreData(object)

# S4 method for CompadreDB
$(x, name)

# S4 method for CompadreDB
$(x, name) <- value

# S4 method for CompadreDB,ANY,missing
[[(x, i, j, ...)

# S4 method for CompadreDB,ANY,missing
[[(x, i, j) <- value

VersionData(object)

# S4 method for CompadreDB
VersionData(object)

Version(object)

# S4 method for CompadreDB
Version(object)

DateCreated(object)

# S4 method for CompadreDB
DateCreated(object)

Arguments

object

A CompadreDB object

x

A CompadreDB object

name

The name of a column within x

value

Vector of values to assign to the column

i, j

elements to extract or replace (see [[.data.frame)

...

ignored

Slots

data

A tibble-style data frame with a list-column of matrix population models (column mat) and a variety of other metadata columns.

version

A list with elements Version (database version number), DateCreated (date of version release), and Agreement (a url link to the User Agreement)

See also

Examples

# extract entire 'data' slot dat <- CompadreData(Compadre) # access the date of database creation DateCreated(Compadre)
#> [1] "Nov_22_2017"
# extract column SpeciesAccepted Compadre$SpeciesAccepted
#> [1] "Setaria incrassata" #> [2] "Lechea cernua" #> [3] "Actinostemon concolor" #> [4] "Gaura neomexicana coloradensis" #> [5] "Eriogonum longifolium gnaphalifolium" #> [6] "Platanthera hookeri" #> [7] "Succisa pratensis" #> [8] "Pyrrocoma radiata" #> [9] "Astragalus tremolsianus" #> [10] "Plantago coronopus" #> [11] "Silene glaucifolia pseudoviscosa" #> [12] "Astragalus peckii" #> [13] "Jacquiniella leucomelana" #> [14] "Syngonanthus nitens" #> [15] "Astragalus scaphoides" #> [16] "Phyllanthus indofischeri" #> [17] "Heliconia metallica" #> [18] "Pediocactus bradyi" #> [19] "Clarkia xantiana" #> [20] "Trollius europaeus" #> [21] "Miconia prasina" #> [22] "Eriophorum angustifolium triste" #> [23] "Molinia caerulea" #> [24] "Saxifraga tridactylites" #> [25] "Pachycereus pecten-aboriginum" #> [26] "Brassica insularis" #> [27] "Limonium geronense" #> [28] "Myosotis ramosissima" #> [29] "Tradescantia brevifolia" #> [30] "Stenaria nigricans" #> [31] "Alyxia stellata" #> [32] "Trillium ovatum" #> [33] "Commelina benghalensis" #> [34] "Cleistesiopsis bifaria" #> [35] "Calochortus lyallii" #> [36] "Hypochaeris radicata" #> [37] "Eryngium cuneifolium" #> [38] "Plantago coronopus" #> [39] "Armeria caespitosa" #> [40] "Primula vulgaris" #> [41] "Primula veris" #> [42] "Lomatium bradshawii" #> [43] "Iriartea deltoidea" #> [44] "Sarcocapnos pulcherrima" #> [45] "Agropyron cristatum" #> [46] "Astragalus tyghensis" #> [47] "Gilia tenuiflora hoffmannii" #> [48] "Verbascum fontqueri" #> [49] "Pyrrocoma radiata" #> [50] "Phyllanthus indofischeri" #> [51] "Carduus nutans" #> [52] "Impatiens capensis" #> [53] "Cirsium scariosum" #> [54] "Solidago mollis" #> [55] "Hypericum cumulicola" #> [56] "Viola biflora" #> [57] "Lepidium davisii" #> [58] "Cleistesiopsis bifaria" #> [59] "Armeria caespitosa" #> [60] "Lepanthes rupestris" #> [61] "Aechmea nudicaulis" #> [62] "Androsace elongata" #> [63] "Borassus aethiopum" #> [64] "Themeda triandra" #> [65] "Abies magnifica" #> [66] "Echinacea angustifolia" #> [67] "Asplenium adulterinum" #> [68] "Vella pseudocytisus" #> [69] "Viola biflora" #> [70] "Cheirolophus metlesicsii" #> [71] "Castanea dentata" #> [72] "Anthericum ramosum" #> [73] "Plantago media" #> [74] "Lepidium davisii" #> [75] "Lupinus lepidus" #> [76] "Cirsium pitcheri" #> [77] "Melampyrum pratense" #> [78] "Cleistesiopsis bifaria" #> [79] "Lepanthes rupestris" #> [80] "Pterocereus gaumeri" #> [81] "Sambucus sieboldiana" #> [82] "Pyrrocoma radiata" #> [83] "Daphne rodriguezii" #> [84] "Fucus vesiculosus" #> [85] "Carduus nutans" #> [86] "Tragopogon orientalis" #> [87] "Asarum canadense" #> [88] "Helianthus divaricatus" #> [89] "Himatanthus drasticus" #> [90] "Armeria maritima" #> [91] "Astragalus alopecurus" #> [92] "Phyllanthus emblica" #> [93] "Dorycnium spectabile" #> [94] "Lotus corniculatus" #> [95] "Astragalus scaphoides" #> [96] "Asplenium adulterinum" #> [97] "Miscanthus giganteus" #> [98] "Androsace elongata" #> [99] "Asarum canadense" #> [100] "Magnolia salicifolia" #> [101] "Lepidium davisii" #> [102] "Echinacea angustifolia" #> [103] "Hordeum spontaneum" #> [104] "Phyllanthus indofischeri" #> [105] "Paronychia jamesii" #> [106] "Aster amellus" #> [107] "Tragopogon pratensis" #> [108] "Ambrosia dumosa" #> [109] "Succisa pratensis" #> [110] "Lupinus lepidus" #> [111] "Physaria ovalifolia" #> [112] "Sphaeralcea coccinea" #> [113] "Lotus corniculatus" #> [114] "Mammillaria crucigera" #> [115] "Calochortus lyallii" #> [116] "Cirsium dissectum" #> [117] "Heliconia acuminata" #> [118] "Saxifraga tridactylites" #> [119] "Vella pseudocytisus" #> [120] "Daphne rodriguezii" #> [121] "Astragalus peckii" #> [122] "Pyrrocoma radiata" #> [123] "Trillium ovatum" #> [124] "Hordeum spontaneum" #> [125] "Acer palmatum" #> [126] "Lupinus tidestromii" #> [127] "Cleistesiopsis bifaria" #> [128] "Manilkara zapota" #> [129] "Collinsia verna" #> [130] "Primula vulgaris" #> [131] "Gracilaria gracilis" #> [132] "Commelina benghalensis" #> [133] "Stenaria nigricans" #> [134] "Echinacea angustifolia" #> [135] "Chamaedorea radicalis" #> [136] "Carex aquatilis minor" #> [137] "Cucurbita pepo" #> [138] "Rhododendron ponticum" #> [139] "Festuca gracillima" #> [140] "Platanthera hookeri" #> [141] "Molinia caerulea" #> [142] "Aster amellus" #> [143] "Helenium virginicum" #> [144] "Lactuca serriola" #> [145] "Chamaedorea radicalis" #> [146] "Antirrhinum subbaeticum" #> [147] "Geranium sylvaticum" #> [148] "Aster amellus" #> [149] "Bromus tectorum" #> [150] "Echinacea angustifolia"
# create new list-column with stage-specific survival Compadre$stage_survival <- lapply(Compadre$mat, function(x) colSums(x@matU))