Calculates the abundance change for species in a replicate between two time points. Changes are on abundance values provided, if relative data is used, then changes in relative abundance will be calculated.
Usage
abundance_change(
df,
time.var,
species.var,
abundance.var,
replicate.var = NULL,
reference.time = NULL
)Arguments
- df
A data frame containing time, species, and abundance columns and an optional columns of replicates.
- time.var
The name of the time column.
- species.var
The name of the species column.
- abundance.var
The name of the abundance column.
- replicate.var
The name of the optional replicate column. If specified, replicate must be unique within the dataset and cannot be nested within treatments or blocks.
- reference.time
The name of the optional time point that all other time points should be compared to (e.g. the first year of data). If not specified, each comparison is between consecutive time points (the first and second year, second and third year, etc.)
Value
The `abundance_change()` function returns a data frame with a subset of the following columns: - **replicate.var**: A column with the specified `replicate.var`, if it is specified. - **time.var**: A column with the specified `time.var` and a second column, with '2' appended to the name. Time is subtracted from time2. - **species.var**: A column with the specified `species.var`. - **change**: A numeric column of the change in abundance between time points. A positive value occurs when a species increases in abundance over time, and a negative value when a species decreases in abundance over time.#' @references Avolio et al. Submitted
Examples
data(pplots)
# Without replicates
df <- subset(pplots, plot == 25)
abundance_change(df = df,
species.var = "species",
abundance.var = "relative_cover",
time.var = "year")
#> year year2 species change
#> 2 2002 2003 amorpha canescens -0.002123142
#> 23 2002 2003 andropogon gerardii -0.082504430
#> 28 2003 2004 andropogon gerardii 0.207558855
#> 29 2004 2005 andropogon gerardii -0.304927630
#> 34 2004 2005 andropogon scoparius 0.078196997
#> 44 2002 2003 andropogon scoparius 0.062022085
#> 45 2003 2004 andropogon scoparius -0.126299880
#> 50 2003 2004 antennaria neglecta 0.002114165
#> 55 2004 2005 antennaria neglecta -0.000948664
#> 66 2002 2003 aster ericoides -0.007643615
#> 71 2003 2004 aster ericoides 0.018097734
#> 76 2004 2005 aster ericoides -0.010082940
#> 87 2002 2003 bouteloua curtipendula -0.015529356
#> 92 2003 2004 bouteloua curtipendula 0.006982922
#> 93 2004 2005 bouteloua curtipendula 0.017618041
#> 98 2004 2005 carex heliophila 0.025044723
#> 108 2002 2003 carex heliophila -0.004928777
#> 109 2003 2004 carex heliophila 0.013349527
#> 114 2003 2004 carex meadii 0.001232635
#> 119 2004 2005 carex meadii 0.064671763
#> 125 2002 2003 carex meadii -0.016166450
#> 135 2003 2004 conyza canadensis 0.002114165
#> 140 2004 2005 conyza canadensis -0.002114165
#> 157 2004 2005 cyperus lupulinus 0.002331002
#> 162 2004 2005 dalea candida 0.001816013
#> 172 2002 2003 dalea candida 0.022140908
#> 173 2003 2004 dalea candida -0.022167840
#> 178 2003 2004 dalea purpurea 0.004916978
#> 183 2004 2005 dalea purpurea -0.006342495
#> 189 2002 2003 dalea purpurea 0.001425517
#> 194 2002 2003 dichanthelium oligosanthes -0.007734412
#> 199 2003 2004 dichanthelium oligosanthes -0.002899254
#> 204 2004 2005 dichanthelium oligosanthes 0.000433675
#> 210 2002 2003 eragrostis spectabilis 0.010008882
#> 215 2003 2004 eragrostis spectabilis -0.007912672
#> 220 2004 2005 eragrostis spectabilis 0.025126036
#> 231 2002 2003 koeleria pyramidata -0.006369427
#> 242 2004 2005 kuhnia eupatorioides -0.002412317
#> 252 2002 2003 kuhnia eupatorioides 0.003609190
#> 253 2003 2004 kuhnia eupatorioides 0.000592208
#> 258 2003 2004 linum sulcatum 0.012684989
#> 263 2004 2005 linum sulcatum -0.012684989
#> 269 2002 2003 linum sulcatum -0.004246285
#> 274 2002 2003 physalis pumila -0.001395252
#> 279 2003 2004 physalis pumila -0.000736868
#> 284 2004 2005 physalis pumila -0.000948664
#> 300 2003 2004 plantago rhodosperma 0.002114165
#> 301 2004 2005 plantago rhodosperma -0.002114165
#> 316 2002 2003 poa pratensis -0.084925690
#> 322 2003 2004 ruellia humilis 0.002114165
#> 327 2004 2005 ruellia humilis -0.002114165
#> 338 2002 2003 senecio plattensis -0.002123142
#> 364 2003 2004 sisyrinchium campestre 0.002114165
#> 365 2004 2005 sisyrinchium campestre 0.000216837
#> 370 2004 2005 solidago missouriensis 0.040467285
#> 380 2002 2003 solidago missouriensis 0.002365268
#> 381 2003 2004 solidago missouriensis 0.008070896
#> 386 2003 2004 sorghastrum nutans -0.122615537
#> 391 2004 2005 sorghastrum nutans 0.088767822
#> 397 2002 2003 sorghastrum nutans 0.132692607
#> 402 2002 2003 viola rafinesquii 0.001425517
#> 407 2003 2004 viola rafinesquii -0.001425517
# With replicates
df <- subset(pplots, year < 2004 & plot %in% c(6, 25, 32))
abundance_change(df = df,
species.var = "species",
abundance.var = "relative_cover",
replicate.var = "plot",
time.var = "year")
#> year year2 plot species change
#> 1 2002 2003 6 ambrosia psilostachya 0.001881712
#> 2 2002 2003 6 andropogon gerardii -0.038493392
#> 3 2002 2003 6 andropogon scoparius -0.062873948
#> 4 2002 2003 6 asclepias stenophylla 0.002890173
#> 5 2002 2003 6 asclepias verticillata -0.002453548
#> 6 2002 2003 6 aster ericoides 0.001777485
#> 7 2002 2003 6 bouteloua curtipendula 0.058775310
#> 8 2002 2003 6 carex heliophila -0.035087719
#> 9 2002 2003 6 carex meadii 0.000873249
#> 10 2002 2003 6 dalea candida 0.014315655
#> 11 2002 2003 6 dalea purpurea 0.001445087
#> 12 2002 2003 6 dichanthelium oligosanthes 0.011960699
#> 13 2002 2003 6 draba reptans -0.001949318
#> 14 2002 2003 6 koeleria pyramidata -0.002084530
#> 15 2002 2003 6 kuhnia eupatorioides 0.026380579
#> 16 2002 2003 6 linum sulcatum -0.009746589
#> 17 2002 2003 6 poa pratensis 0.001746498
#> 18 2002 2003 6 ratibida columnifera -0.003898635
#> 19 2002 2003 6 ruellia humilis -0.002453548
#> 20 2002 2003 6 senecio plattensis -0.002453548
#> 21 2002 2003 6 sisyrinchium campestre -0.001949318
#> 22 2002 2003 6 solidago missouriensis -0.003898635
#> 23 2002 2003 6 sorghastrum nutans 0.053363982
#> 24 2002 2003 6 sporobolus asper -0.006118379
#> 25 2002 2003 6 triodanis perfoliata -0.001949318
#> 26 2002 2003 25 amorpha canescens -0.002123142
#> 27 2002 2003 25 andropogon gerardii -0.082504430
#> 28 2002 2003 25 andropogon scoparius 0.062022085
#> 29 2002 2003 25 aster ericoides -0.007643615
#> 30 2002 2003 25 bouteloua curtipendula -0.015529356
#> 31 2002 2003 25 carex heliophila -0.004928777
#> 32 2002 2003 25 carex meadii -0.016166450
#> 33 2002 2003 25 dalea candida 0.022140908
#> 34 2002 2003 25 dalea purpurea 0.001425517
#> 35 2002 2003 25 dichanthelium oligosanthes -0.007734412
#> 36 2002 2003 25 eragrostis spectabilis 0.010008882
#> 37 2002 2003 25 koeleria pyramidata -0.006369427
#> 38 2002 2003 25 kuhnia eupatorioides 0.003609190
#> 39 2002 2003 25 linum sulcatum -0.004246285
#> 40 2002 2003 25 physalis pumila -0.001395252
#> 41 2002 2003 25 poa pratensis -0.084925690
#> 42 2002 2003 25 senecio plattensis -0.002123142
#> 43 2002 2003 25 solidago missouriensis 0.002365268
#> 44 2002 2003 25 sorghastrum nutans 0.132692607
#> 45 2002 2003 25 viola rafinesquii 0.001425517
#> 46 2002 2003 32 ambrosia psilostachya -0.000977422
#> 47 2002 2003 32 amorpha canescens 0.005434900
#> 48 2002 2003 32 andropogon gerardii 0.343172004
#> 49 2002 2003 32 andropogon scoparius -0.181922336
#> 50 2002 2003 32 antennaria neglecta -0.002534854
#> 51 2002 2003 32 asclepias tuberosa 0.011299435
#> 52 2002 2003 32 aster ericoides -0.024510752
#> 53 2002 2003 32 aster oblongifolius 0.015065913
#> 54 2002 2003 32 bouteloua curtipendula -0.076224642
#> 55 2002 2003 32 carex heliophila 0.003118444
#> 56 2002 2003 32 carex meadii 0.040926439
#> 57 2002 2003 32 delphinium virescens 0.003766478
#> 58 2002 2003 32 dichanthelium acuminatum -0.006337136
#> 59 2002 2003 32 dichanthelium oligosanthes 0.011664626
#> 60 2002 2003 32 eragrostis spectabilis -0.003802281
#> 61 2002 2003 32 euphorbia serpens 0.001883239
#> 62 2002 2003 32 kuhnia eupatorioides 0.003079060
#> 63 2002 2003 32 linum sulcatum -0.003802281
#> 64 2002 2003 32 panicum capillare 0.005649718
#> 65 2002 2003 32 poa pratensis -0.008291980
#> 66 2002 2003 32 ruellia humilis 0.001811633
#> 67 2002 2003 32 senecio plattensis 0.000615812
#> 68 2002 2003 32 solidago missouriensis 0.001450023
#> 69 2002 2003 32 sorghastrum nutans -0.130867221
#> 70 2002 2003 32 sporobolus asper -0.009666817
# With reference year
df <- subset(pplots, year < 2005 & plot %in% c(6, 25, 32))
abundance_change(df = df,
species.var = "species",
abundance.var = "relative_cover",
replicate.var = "plot",
time.var = "year",
reference.time = 2002)
#> year year2 plot species change
#> 1 2002 2003 6 ambrosia psilostachya 0.001881712
#> 2 2002 2004 6 ambrosia psilostachya 0.002812774
#> 3 2002 2003 6 andropogon gerardii -0.038493392
#> 4 2002 2004 6 andropogon gerardii -0.161054202
#> 5 2002 2003 6 andropogon scoparius -0.062873948
#> 6 2002 2004 6 andropogon scoparius 0.131873308
#> 7 2002 2004 6 asclepias stenophylla 0.001677852
#> 8 2002 2003 6 asclepias stenophylla 0.002890173
#> 9 2002 2004 6 asclepias verticillata -0.002220783
#> 10 2002 2003 6 asclepias verticillata -0.002453548
#> 11 2002 2003 6 aster ericoides 0.001777485
#> 12 2002 2004 6 aster ericoides -0.019345998
#> 13 2002 2003 6 bouteloua curtipendula 0.058775310
#> 14 2002 2004 6 bouteloua curtipendula -0.040935673
#> 15 2002 2004 6 carex heliophila 0.011892147
#> 16 2002 2003 6 carex heliophila -0.035087719
#> 17 2002 2004 6 carex meadii 0.007303400
#> 18 2002 2003 6 carex meadii 0.000873249
#> 20 2002 2004 6 conyza canadensis 0.005033557
#> 21 2002 2003 6 dalea candida 0.014315655
#> 22 2002 2004 6 dalea candida 0.005082617
#> 24 2002 2003 6 dalea purpurea 0.001445087
#> 25 2002 2004 6 dichanthelium oligosanthes 0.021736856
#> 26 2002 2003 6 dichanthelium oligosanthes 0.011960699
#> 27 2002 2003 6 draba reptans -0.001949318
#> 28 2002 2004 6 draba reptans -0.001949318
#> 30 2002 2004 6 erigeron strigosus 0.001677852
#> 31 2002 2003 6 koeleria pyramidata -0.002084530
#> 32 2002 2004 6 koeleria pyramidata 0.029978937
#> 33 2002 2004 6 kuhnia eupatorioides -0.009746589
#> 34 2002 2003 6 kuhnia eupatorioides 0.026380579
#> 35 2002 2004 6 linum sulcatum 0.010387639
#> 36 2002 2003 6 linum sulcatum -0.009746589
#> 37 2002 2003 6 poa pratensis 0.001746498
#> 38 2002 2004 6 poa pratensis -0.007205280
#> 39 2002 2003 6 ratibida columnifera -0.003898635
#> 40 2002 2004 6 ratibida columnifera -0.003898635
#> 41 2002 2004 6 ruellia humilis 0.002812774
#> 42 2002 2003 6 ruellia humilis -0.002453548
#> 43 2002 2004 6 senecio plattensis -0.003898635
#> 44 2002 2003 6 senecio plattensis -0.002453548
#> 46 2002 2004 6 silene antirrhina 0.010067114
#> 47 2002 2003 6 sisyrinchium campestre -0.001949318
#> 48 2002 2004 6 sisyrinchium campestre -0.001949318
#> 49 2002 2004 6 solidago missouriensis 0.012879888
#> 50 2002 2003 6 solidago missouriensis -0.003898635
#> 51 2002 2004 6 sorghastrum nutans 0.004686867
#> 52 2002 2003 6 sorghastrum nutans 0.053363982
#> 53 2002 2003 6 sporobolus asper -0.006118379
#> 54 2002 2004 6 sporobolus asper -0.020850504
#> 55 2002 2003 6 triodanis perfoliata -0.001949318
#> 56 2002 2004 6 triodanis perfoliata 0.009795648
#> 58 2002 2004 6 viola rafinesquii 0.003355705
#> 59 2002 2003 25 amorpha canescens -0.002123142
#> 60 2002 2004 25 amorpha canescens -0.002123142
#> 61 2002 2003 25 andropogon gerardii -0.082504430
#> 62 2002 2004 25 andropogon gerardii 0.125054425
#> 63 2002 2003 25 andropogon scoparius 0.062022085
#> 64 2002 2004 25 andropogon scoparius -0.064277795
#> 66 2002 2004 25 antennaria neglecta 0.002114165
#> 67 2002 2003 25 aster ericoides -0.007643615
#> 68 2002 2004 25 aster ericoides 0.010454119
#> 69 2002 2003 25 bouteloua curtipendula -0.015529356
#> 70 2002 2004 25 bouteloua curtipendula -0.008546434
#> 71 2002 2003 25 carex heliophila -0.004928777
#> 72 2002 2004 25 carex heliophila 0.008420750
#> 73 2002 2003 25 carex meadii -0.016166450
#> 74 2002 2004 25 carex meadii -0.014933815
#> 76 2002 2004 25 conyza canadensis 0.002114165
#> 77 2002 2003 25 dalea candida 0.022140908
#> 78 2002 2004 25 dalea candida -0.000026932
#> 79 2002 2003 25 dalea purpurea 0.001425517
#> 80 2002 2004 25 dalea purpurea 0.006342495
#> 81 2002 2003 25 dichanthelium oligosanthes -0.007734412
#> 82 2002 2004 25 dichanthelium oligosanthes -0.010633666
#> 83 2002 2004 25 eragrostis spectabilis 0.002096210
#> 84 2002 2003 25 eragrostis spectabilis 0.010008882
#> 85 2002 2003 25 koeleria pyramidata -0.006369427
#> 86 2002 2004 25 koeleria pyramidata -0.006369427
#> 87 2002 2003 25 kuhnia eupatorioides 0.003609190
#> 88 2002 2004 25 kuhnia eupatorioides 0.004201398
#> 89 2002 2003 25 linum sulcatum -0.004246285
#> 90 2002 2004 25 linum sulcatum 0.008438704
#> 91 2002 2003 25 physalis pumila -0.001395252
#> 92 2002 2004 25 physalis pumila -0.002132120
#> 94 2002 2004 25 plantago rhodosperma 0.002114165
#> 95 2002 2003 25 poa pratensis -0.084925690
#> 96 2002 2004 25 poa pratensis -0.084925690
#> 98 2002 2004 25 ruellia humilis 0.002114165
#> 99 2002 2003 25 senecio plattensis -0.002123142
#> 100 2002 2004 25 senecio plattensis -0.002123142
#> 102 2002 2004 25 sisyrinchium campestre 0.002114165
#> 103 2002 2003 25 solidago missouriensis 0.002365268
#> 104 2002 2004 25 solidago missouriensis 0.010436164
#> 105 2002 2003 25 sorghastrum nutans 0.132692607
#> 106 2002 2004 25 sorghastrum nutans 0.010077070
#> 107 2002 2003 25 viola rafinesquii 0.001425517
#> 109 2002 2003 32 ambrosia psilostachya -0.000977422
#> 110 2002 2004 32 ambrosia psilostachya -0.003802281
#> 111 2002 2003 32 amorpha canescens 0.005434900
#> 112 2002 2004 32 amorpha canescens -0.019792540
#> 113 2002 2004 32 andropogon gerardii 0.019892096
#> 114 2002 2003 32 andropogon gerardii 0.343172004
#> 115 2002 2004 32 andropogon scoparius -0.072216543
#> 116 2002 2003 32 andropogon scoparius -0.181922336
#> 117 2002 2004 32 antennaria neglecta -0.002534854
#> 118 2002 2003 32 antennaria neglecta -0.002534854
#> 119 2002 2003 32 asclepias tuberosa 0.011299435
#> 121 2002 2004 32 aster ericoides -0.004753809
#> 122 2002 2003 32 aster ericoides -0.024510752
#> 123 2002 2004 32 aster oblongifolius 0.012084592
#> 124 2002 2003 32 aster oblongifolius 0.015065913
#> 125 2002 2004 32 bouteloua curtipendula -0.078440720
#> 126 2002 2003 32 bouteloua curtipendula -0.076224642
#> 127 2002 2003 32 carex heliophila 0.003118444
#> 128 2002 2004 32 carex heliophila -0.015850497
#> 129 2002 2004 32 carex meadii 0.053739293
#> 130 2002 2003 32 carex meadii 0.040926439
#> 131 2002 2004 32 conyza canadensis 0.004531722
#> 134 2002 2003 32 delphinium virescens 0.003766478
#> 135 2002 2003 32 dichanthelium acuminatum -0.006337136
#> 136 2002 2004 32 dichanthelium acuminatum 0.005747456
#> 137 2002 2003 32 dichanthelium oligosanthes 0.011664626
#> 138 2002 2004 32 dichanthelium oligosanthes 0.034050138
#> 139 2002 2004 32 eragrostis spectabilis -0.003802281
#> 140 2002 2003 32 eragrostis spectabilis -0.003802281
#> 142 2002 2003 32 euphorbia serpens 0.001883239
#> 143 2002 2004 32 kuhnia eupatorioides 0.007258030
#> 144 2002 2003 32 kuhnia eupatorioides 0.003079060
#> 145 2002 2003 32 linum sulcatum -0.003802281
#> 146 2002 2004 32 linum sulcatum -0.003802281
#> 148 2002 2003 32 panicum capillare 0.005649718
#> 149 2002 2004 32 poa pratensis 0.005695764
#> 150 2002 2003 32 poa pratensis -0.008291980
#> 151 2002 2004 32 ruellia humilis -0.007604563
#> 152 2002 2003 32 ruellia humilis 0.001811633
#> 153 2002 2003 32 senecio plattensis 0.000615812
#> 154 2002 2004 32 senecio plattensis -0.001267427
#> 155 2002 2004 32 solidago missouriensis -0.000589679
#> 156 2002 2003 32 solidago missouriensis 0.001450023
#> 157 2002 2004 32 sorghastrum nutans 0.069373447
#> 158 2002 2003 32 sorghastrum nutans -0.130867221
#> 159 2002 2004 32 sporobolus asper -0.020573674
#> 160 2002 2003 32 sporobolus asper -0.009666817
#> 162 2002 2004 32 triodanis perfoliata 0.006042296
#> 164 2002 2004 32 viola rafinesquii 0.016616314