SPBoot: Estimation of species relative abundance or detection...
In iNextPD: Interpolation and Extrapolation for Phylogenetic Diversity
Description
Usage
Arguments
Value
Examples
Description
SPBoot: Expand bootstraping species relative abundance or detection probability
Usage
1
SPBoot(x, datatype = "abundance")
Arguments
x
a vector/matrix/list of species abundances or a matrix of raw incidence table.
datatype
of input data: individual-based abundance data (datatype = "abundance"), sampling-unit-based incidence frequencies data (datatype = "incidence_freq") or species by sampling-units incidence matrix (datatype = "incidence_raw")..
Value
a list of vector with species relative abundance or detection probability distribution.
Examples
1
2
3
4
Example output
$North.site
Acanthiza_pusilla Rhipidura_albicollis
0.202970297 0.089108910
Pachycephala_pectoralis Zosterops_lateralis
0.079207914 0.079207914
Pardalotus_punctatus Gerygone_mouki
0.074257406 0.059405543
Cormobates_leucophaea Meliphaga_lewinii
0.054454394 0.054454394
Menura_novaehollandiae Rhipidura_rufifrons
0.044547402 0.039586152
Psophodes_olivaceus Cacomantis_flabelliformis
0.034609444 0.024505461
Eopsaltria_australis Calyptorhynchus_funereus
0.024505461 0.019252435
Colluricincla_harmonica Alisterus_scapularis
0.019252435 0.013711189
Strepera_graculina Dacelo_novaeguineae
0.013711189 0.007808497
Platycercus_elegans Ptilonorhynchus_violaceus
0.007808497 0.007808497
Sericornis_frontalis
0.007808497 0.005901447
0.005901447 0.005901447
0.005901447 0.005901447
Cacatua_galerita Corvus_coronoides
0.002085140 0.002085140
Leucosarcia_melanoleuca Monarcha_melanopsis
0.002085140 0.002085140
Oriolus_sagittatus Petroica_rosea
0.002085140 0.002085140
Acanthiza_lineata Acanthiza_nana
0.000000000 0.000000000
Acanthorhynchus_tenuirostris Lichenostomus_chrysops
0.000000000 0.000000000
Malurus_cyaneus Malurus_lamberti
0.000000000 0.000000000
Manorina_melanophrys Neochmia_temporalis
0.000000000 0.000000000
Pachycephala_olivacea Pachycephala_rufiventris
0.000000000 0.000000000
Phylidonyris_niger Ptiloris_paradiseus
0.000000000 0.000000000
Sericornis_citreogularis Zoothera_lunulata
0.000000000 0.000000000
$South.site
Cormobates_leucophaea Acanthiza_pusilla
0.104234528 0.100977199
Rhipidura_albicollis Acanthiza_nana
0.065146580 0.058631921
Meliphaga_lewinii Pardalotus_punctatus
0.058631921 0.055374591
Zosterops_lateralis Pachycephala_pectoralis
0.055374591 0.048859923
Rhipidura_rufifrons Gerygone_mouki
0.045602574 0.032571812
Monarcha_melanopsis Manorina_melanophrys
0.032571812 0.029312227
Neochmia_temporalis Platycercus_elegans
0.029312227 0.022778664
Psophodes_olivaceus Colluricincla_harmonica
0.022778664 0.019490072
Malurus_cyaneus Malurus_lamberti
0.019490072 0.019490072
Sericornis_frontalis Cacomantis_flabelliformis
0.019490072 0.016162296
Eopsaltria_australis Menura_novaehollandiae
0.016162296 0.016162296
Lichenostomus_chrysops Strepera_graculina
0.012754851 0.012754851
Acanthiza_lineata Pachycephala_rufiventris
0.009205941 0.009205941
Ptiloris_paradiseus Acanthorhynchus_tenuirostris
0.009205941 0.005480418
Cacatua_galerita Pachycephala_olivacea
0.005480418 0.005480418
Phylidonyris_niger Ptilonorhynchus_violaceus
0.005480418 0.005480418
Sericornis_citreogularis
0.005480418 0.005386634
0.005386634 0.005386634
Alisterus_scapularis Calyptorhynchus_funereus
0.001844732 0.001844732
Leucosarcia_melanoleuca Petroica_rosea
0.001844732 0.001844732
Zoothera_lunulata Corvus_coronoides
0.001844732 0.000000000
Dacelo_novaeguineae Oriolus_sagittatus
0.000000000 0.000000000
$North.site
Acanthiza_pusilla Rhipidura_albicollis
1.00000000 0.83333333
Cormobates_leucophaea Pachycephala_pectoralis
0.74999992 0.58330304
Pardalotus_punctatus Meliphaga_lewinii
0.58330304 0.49976850
Cacomantis_flabelliformis Eopsaltria_australis
0.41544001 0.41544001
Gerygone_mouki Menura_novaehollandiae
0.41544001 0.41544001
Zosterops_lateralis Psophodes_olivaceus
0.41544001 0.23498208
Rhipidura_rufifrons Strepera_graculina
0.23498208 0.23498208
Alisterus_scapularis Colluricincla_harmonica
0.13121732 0.13121732
Ptilonorhynchus_violaceus Sericornis_frontalis
0.13121732 0.13121732
0.06939252 0.06939252
0.06939252 0.06939252
0.06939252 0.06939252
0.06939252 0.06939252
0.06939252 0.06939252
Cacatua_galerita Calyptorhynchus_funereus
0.02770571 0.02770571
Corvus_coronoides Dacelo_novaeguineae
0.02770571 0.02770571
Leucosarcia_melanoleuca Monarcha_melanopsis
0.02770571 0.02770571
Oriolus_sagittatus Petroica_rosea
0.02770571 0.02770571
Platycercus_elegans Acanthiza_lineata
0.02770571 0.00000000
Acanthiza_nana Acanthorhynchus_tenuirostris
0.00000000 0.00000000
Lichenostomus_chrysops Malurus_cyaneus
0.00000000 0.00000000
Malurus_lamberti Manorina_melanophrys
0.00000000 0.00000000
Neochmia_temporalis Pachycephala_olivacea
0.00000000 0.00000000
Pachycephala_rufiventris Phylidonyris_niger
0.00000000 0.00000000
Ptiloris_paradiseus Sericornis_citreogularis
0.00000000 0.00000000
Zoothera_lunulata
0.00000000
$South.site
Cormobates_leucophaea Meliphaga_lewinii
1.00000000 0.64705880
Rhipidura_albicollis Acanthiza_pusilla
0.64705880 0.52940938
Pardalotus_punctatus Gerygone_mouki
0.47057251 0.41168218
Pachycephala_pectoralis Rhipidura_rufifrons
0.41168218 0.41168218
Psophodes_olivaceus Zosterops_lateralis
0.35258365 0.35258365
Acanthiza_nana Monarcha_melanopsis
0.29280986 0.29280986
Cacomantis_flabelliformis Colluricincla_harmonica
0.23121484 0.23121484
Menura_novaehollandiae Eopsaltria_australis
0.23121484 0.16568647
Sericornis_frontalis Strepera_graculina
0.16568647 0.16568647
Acanthorhynchus_tenuirostris Malurus_cyaneus
0.09441605 0.09441605
Malurus_lamberti Neochmia_temporalis
0.09441605 0.09441605
Pachycephala_olivacea Phylidonyris_niger
0.09441605 0.09441605
Platycercus_elegans Ptiloris_paradiseus
0.09441605 0.09441605
0.07239819 0.07239819
0.07239819 0.07239819
0.07239819 0.07239819
0.07239819 0.07239819
Acanthiza_lineata
0.07239819 0.02402777
Alisterus_scapularis Cacatua_galerita
0.02402777 0.02402777
Calyptorhynchus_funereus Leucosarcia_melanoleuca
0.02402777 0.02402777
Lichenostomus_chrysops Manorina_melanophrys
0.02402777 0.02402777
Pachycephala_rufiventris Petroica_rosea
0.02402777 0.02402777
Ptilonorhynchus_violaceus Sericornis_citreogularis
0.02402777 0.02402777
Zoothera_lunulata Corvus_coronoides
0.02402777 0.00000000
Dacelo_novaeguineae Oriolus_sagittatus
0.00000000 0.00000000
iNextPD documentation built on May 2, 2019, 3:31 a.m.
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Description Usage Arguments Value Examples
Description
SPBoot: Expand bootstraping species relative abundance or detection probability
Usage
1 | SPBoot(x, datatype = "abundance")
|
Arguments
x |
a vector/matrix/list of species abundances or a matrix of raw incidence table. |
datatype |
of input data: individual-based abundance data (datatype = "abundance"), sampling-unit-based incidence frequencies data (datatype = "incidence_freq") or species by sampling-units incidence matrix (datatype = "incidence_raw").. |
Value
a list of vector with species relative abundance or detection probability distribution.
Examples
1 2 3 4 |
Example output
$North.site
Acanthiza_pusilla Rhipidura_albicollis
0.202970297 0.089108910
Pachycephala_pectoralis Zosterops_lateralis
0.079207914 0.079207914
Pardalotus_punctatus Gerygone_mouki
0.074257406 0.059405543
Cormobates_leucophaea Meliphaga_lewinii
0.054454394 0.054454394
Menura_novaehollandiae Rhipidura_rufifrons
0.044547402 0.039586152
Psophodes_olivaceus Cacomantis_flabelliformis
0.034609444 0.024505461
Eopsaltria_australis Calyptorhynchus_funereus
0.024505461 0.019252435
Colluricincla_harmonica Alisterus_scapularis
0.019252435 0.013711189
Strepera_graculina Dacelo_novaeguineae
0.013711189 0.007808497
Platycercus_elegans Ptilonorhynchus_violaceus
0.007808497 0.007808497
Sericornis_frontalis
0.007808497 0.005901447
0.005901447 0.005901447
0.005901447 0.005901447
Cacatua_galerita Corvus_coronoides
0.002085140 0.002085140
Leucosarcia_melanoleuca Monarcha_melanopsis
0.002085140 0.002085140
Oriolus_sagittatus Petroica_rosea
0.002085140 0.002085140
Acanthiza_lineata Acanthiza_nana
0.000000000 0.000000000
Acanthorhynchus_tenuirostris Lichenostomus_chrysops
0.000000000 0.000000000
Malurus_cyaneus Malurus_lamberti
0.000000000 0.000000000
Manorina_melanophrys Neochmia_temporalis
0.000000000 0.000000000
Pachycephala_olivacea Pachycephala_rufiventris
0.000000000 0.000000000
Phylidonyris_niger Ptiloris_paradiseus
0.000000000 0.000000000
Sericornis_citreogularis Zoothera_lunulata
0.000000000 0.000000000
$South.site
Cormobates_leucophaea Acanthiza_pusilla
0.104234528 0.100977199
Rhipidura_albicollis Acanthiza_nana
0.065146580 0.058631921
Meliphaga_lewinii Pardalotus_punctatus
0.058631921 0.055374591
Zosterops_lateralis Pachycephala_pectoralis
0.055374591 0.048859923
Rhipidura_rufifrons Gerygone_mouki
0.045602574 0.032571812
Monarcha_melanopsis Manorina_melanophrys
0.032571812 0.029312227
Neochmia_temporalis Platycercus_elegans
0.029312227 0.022778664
Psophodes_olivaceus Colluricincla_harmonica
0.022778664 0.019490072
Malurus_cyaneus Malurus_lamberti
0.019490072 0.019490072
Sericornis_frontalis Cacomantis_flabelliformis
0.019490072 0.016162296
Eopsaltria_australis Menura_novaehollandiae
0.016162296 0.016162296
Lichenostomus_chrysops Strepera_graculina
0.012754851 0.012754851
Acanthiza_lineata Pachycephala_rufiventris
0.009205941 0.009205941
Ptiloris_paradiseus Acanthorhynchus_tenuirostris
0.009205941 0.005480418
Cacatua_galerita Pachycephala_olivacea
0.005480418 0.005480418
Phylidonyris_niger Ptilonorhynchus_violaceus
0.005480418 0.005480418
Sericornis_citreogularis
0.005480418 0.005386634
0.005386634 0.005386634
Alisterus_scapularis Calyptorhynchus_funereus
0.001844732 0.001844732
Leucosarcia_melanoleuca Petroica_rosea
0.001844732 0.001844732
Zoothera_lunulata Corvus_coronoides
0.001844732 0.000000000
Dacelo_novaeguineae Oriolus_sagittatus
0.000000000 0.000000000
$North.site
Acanthiza_pusilla Rhipidura_albicollis
1.00000000 0.83333333
Cormobates_leucophaea Pachycephala_pectoralis
0.74999992 0.58330304
Pardalotus_punctatus Meliphaga_lewinii
0.58330304 0.49976850
Cacomantis_flabelliformis Eopsaltria_australis
0.41544001 0.41544001
Gerygone_mouki Menura_novaehollandiae
0.41544001 0.41544001
Zosterops_lateralis Psophodes_olivaceus
0.41544001 0.23498208
Rhipidura_rufifrons Strepera_graculina
0.23498208 0.23498208
Alisterus_scapularis Colluricincla_harmonica
0.13121732 0.13121732
Ptilonorhynchus_violaceus Sericornis_frontalis
0.13121732 0.13121732
0.06939252 0.06939252
0.06939252 0.06939252
0.06939252 0.06939252
0.06939252 0.06939252
0.06939252 0.06939252
Cacatua_galerita Calyptorhynchus_funereus
0.02770571 0.02770571
Corvus_coronoides Dacelo_novaeguineae
0.02770571 0.02770571
Leucosarcia_melanoleuca Monarcha_melanopsis
0.02770571 0.02770571
Oriolus_sagittatus Petroica_rosea
0.02770571 0.02770571
Platycercus_elegans Acanthiza_lineata
0.02770571 0.00000000
Acanthiza_nana Acanthorhynchus_tenuirostris
0.00000000 0.00000000
Lichenostomus_chrysops Malurus_cyaneus
0.00000000 0.00000000
Malurus_lamberti Manorina_melanophrys
0.00000000 0.00000000
Neochmia_temporalis Pachycephala_olivacea
0.00000000 0.00000000
Pachycephala_rufiventris Phylidonyris_niger
0.00000000 0.00000000
Ptiloris_paradiseus Sericornis_citreogularis
0.00000000 0.00000000
Zoothera_lunulata
0.00000000
$South.site
Cormobates_leucophaea Meliphaga_lewinii
1.00000000 0.64705880
Rhipidura_albicollis Acanthiza_pusilla
0.64705880 0.52940938
Pardalotus_punctatus Gerygone_mouki
0.47057251 0.41168218
Pachycephala_pectoralis Rhipidura_rufifrons
0.41168218 0.41168218
Psophodes_olivaceus Zosterops_lateralis
0.35258365 0.35258365
Acanthiza_nana Monarcha_melanopsis
0.29280986 0.29280986
Cacomantis_flabelliformis Colluricincla_harmonica
0.23121484 0.23121484
Menura_novaehollandiae Eopsaltria_australis
0.23121484 0.16568647
Sericornis_frontalis Strepera_graculina
0.16568647 0.16568647
Acanthorhynchus_tenuirostris Malurus_cyaneus
0.09441605 0.09441605
Malurus_lamberti Neochmia_temporalis
0.09441605 0.09441605
Pachycephala_olivacea Phylidonyris_niger
0.09441605 0.09441605
Platycercus_elegans Ptiloris_paradiseus
0.09441605 0.09441605
0.07239819 0.07239819
0.07239819 0.07239819
0.07239819 0.07239819
0.07239819 0.07239819
Acanthiza_lineata
0.07239819 0.02402777
Alisterus_scapularis Cacatua_galerita
0.02402777 0.02402777
Calyptorhynchus_funereus Leucosarcia_melanoleuca
0.02402777 0.02402777
Lichenostomus_chrysops Manorina_melanophrys
0.02402777 0.02402777
Pachycephala_rufiventris Petroica_rosea
0.02402777 0.02402777
Ptilonorhynchus_violaceus Sericornis_citreogularis
0.02402777 0.02402777
Zoothera_lunulata Corvus_coronoides
0.02402777 0.00000000
Dacelo_novaeguineae Oriolus_sagittatus
0.00000000 0.00000000
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