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).
Usage
CompadreData(object)
# S4 method for class 'CompadreDB'
CompadreData(object)
# S4 method for class 'CompadreDB'
x$name
# S4 method for class 'CompadreDB'
x$name <- value
# S4 method for class 'CompadreDB,ANY,missing'
x[[i, j, ...]]
# S4 method for class 'CompadreDB,ANY,missing'
x[[i, j]] <- value
VersionData(object)
# S4 method for class 'CompadreDB'
VersionData(object)
Version(object)
# S4 method for class 'CompadreDB'
Version(object)
DateCreated(object)
# S4 method for class '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
dataA tibble-style data frame with a list-column of matrix population models (column
mat) and a variety of other metadata columns.versionA list with elements
Version(database version number),DateCreated(date of version release), andAgreement(a url link to the User Agreement)
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))