Calculates the abundance difference for species between two samples. Differences are on abundance values provided, if relative data is used, then differences in relative abundance will be calculated. There are three ways differences can be calculated. 1) Between treatments within a block (note: block.var and treatment.var need to be specified). 2) Between treatments, pooling all replicates into a single species pool (note: pool = TRUE, treatment.var needs to be specified, and block.var = NULL). 3) All pairwise combinations between all replicates (note: block.var = NULL, pool = FALSE and specifying treatment.var is optional. If treatment.var is specified, the treatment that each replicate belongs to will also be listed in the output).
Usage
abundance_difference(
df,
time.var = NULL,
species.var,
abundance.var,
replicate.var,
treatment.var = NULL,
pool = FALSE,
block.var = NULL,
reference.treatment = NULL
)Arguments
- df
A data frame containing a species, abundance, and replicate columns and optional time, treatment, and block columns.
- time.var
The name of the optional time column.
- species.var
The name of the species column.
- abundance.var
The name of the abundance column.
- replicate.var
The name of the replicate column. Replicate identifiers must be unique within the dataset and cannot be nested within treatments or blocks.
- treatment.var
The name of the optional treatment column.
- pool
An argument to allow abundance values to be pooled within a treatment. The default value is "FALSE", a value of "TRUE" averages abundance of each species within a treatment at a given time point.
- block.var
The name of the optional block column.
- reference.treatment
The name of the optional treatment that all other treatments will be compared to (e.g. only controls will be compared to all other treatments). If not specified all pairwise treatment comparisons will be made.
Value
The `abundance_difference()` function returns a data frame with a subset of the following columns: - **species.var**: A column that has same name and type as the `species.var` column. - **difference**: A numeric column of the abundance differences between the two samples being compared (replicates or treatments). A numeric column of the change in abundance between consecutive timepoints. A positive value occurs when a species has greater abundance in `replicate.var2` than in `replicate.var` and/or in `treatment.var2` than in `treatment.var`. - **replicate.var**: A column that has same name and type as the `replicate.var` column, represents the first replicate being compared. Note, a replicate column will be returned only when `pool = FALSE` or `block.var = NULL`. - **replicate.var2**: A column that has the same type as the `replicate.var` column, and is named `replicate.var` with a 2 appended to it, represents the second replicate being compared. Note, a `replicate.var` column will be returned only when `pool = FALSE` and `block.var = NULL`. - **time.var**: A column that has the same name and type as the `time.var` column, if `time.var` is specified. - **treatment.var**: A column that has same name and type as the `treatment.var` column, represents the first treatment being compared. A `treatment.var` column will be returned when `pool = TRUE`, `block.var` is specified, or `treatment.var` is specified. - **treatment.var2**: A column that has the same type as the `treatment.var` column, and is named `treatment.var` with a 2 appended to it, represents the second treatment being compared. A `treatment.var` column will be returned when `pool = TRUE`, `block.var` is specified, or `treatment.var` is specified. - **block.var**: A column that has same name and type as the `block.var` column, if `block.var` is specified.
Examples
data(pplots)
# With block and no time
df <- subset(pplots, year == 2002 & block < 3)
abundance_difference(df = df,
species.var = "species",
abundance.var = "relative_cover",
treatment.var = "treatment",
block.var = "block",
replicate.var = "plot")
#> block plot plot2 treatment treatment2 species
#> 2 1 25 29 N1P0 N2P0 ambrosia psilostachya
#> 3 1 29 13 N2P0 N2P3 ambrosia psilostachya
#> 4 1 25 13 N1P0 N2P3 amorpha canescens
#> 5 1 25 29 N1P0 N2P0 amorpha canescens
#> 6 1 29 13 N2P0 N2P3 amorpha canescens
#> 7 1 25 13 N1P0 N2P3 andropogon gerardii
#> 8 1 25 29 N1P0 N2P0 andropogon gerardii
#> 9 1 29 13 N2P0 N2P3 andropogon gerardii
#> 10 1 25 13 N1P0 N2P3 andropogon scoparius
#> 11 1 25 29 N1P0 N2P0 andropogon scoparius
#> 12 1 29 13 N2P0 N2P3 andropogon scoparius
#> 14 1 25 29 N1P0 N2P0 asclepias verticillata
#> 15 1 29 13 N2P0 N2P3 asclepias verticillata
#> 16 1 25 13 N1P0 N2P3 aster ericoides
#> 17 1 25 29 N1P0 N2P0 aster ericoides
#> 18 1 29 13 N2P0 N2P3 aster ericoides
#> 19 1 25 13 N1P0 N2P3 aster sericeus
#> 21 1 29 13 N2P0 N2P3 aster sericeus
#> 22 1 25 13 N1P0 N2P3 bouteloua curtipendula
#> 23 1 25 29 N1P0 N2P0 bouteloua curtipendula
#> 24 1 29 13 N2P0 N2P3 bouteloua curtipendula
#> 25 1 25 13 N1P0 N2P3 carex heliophila
#> 26 1 25 29 N1P0 N2P0 carex heliophila
#> 27 1 29 13 N2P0 N2P3 carex heliophila
#> 28 1 25 13 N1P0 N2P3 carex meadii
#> 29 1 25 29 N1P0 N2P0 carex meadii
#> 30 1 29 13 N2P0 N2P3 carex meadii
#> 31 1 25 13 N1P0 N2P3 dalea candida
#> 32 1 25 29 N1P0 N2P0 dalea candida
#> 33 1 29 13 N2P0 N2P3 dalea candida
#> 35 1 25 29 N1P0 N2P0 dalea purpurea
#> 36 1 29 13 N2P0 N2P3 dalea purpurea
#> 37 1 25 13 N1P0 N2P3 dichanthelium oligosanthes
#> 38 1 25 29 N1P0 N2P0 dichanthelium oligosanthes
#> 39 1 29 13 N2P0 N2P3 dichanthelium oligosanthes
#> 40 1 25 13 N1P0 N2P3 eragrostis spectabilis
#> 41 1 25 29 N1P0 N2P0 eragrostis spectabilis
#> 42 1 29 13 N2P0 N2P3 eragrostis spectabilis
#> 43 1 25 13 N1P0 N2P3 euphorbia serpens
#> 45 1 29 13 N2P0 N2P3 euphorbia serpens
#> 46 1 25 13 N1P0 N2P3 koeleria pyramidata
#> 47 1 25 29 N1P0 N2P0 koeleria pyramidata
#> 48 1 29 13 N2P0 N2P3 koeleria pyramidata
#> 49 1 25 13 N1P0 N2P3 kuhnia eupatorioides
#> 50 1 25 29 N1P0 N2P0 kuhnia eupatorioides
#> 52 1 25 13 N1P0 N2P3 linum sulcatum
#> 53 1 25 29 N1P0 N2P0 linum sulcatum
#> 54 1 29 13 N2P0 N2P3 linum sulcatum
#> 56 1 25 29 N1P0 N2P0 muhlenbergia cuspidata
#> 57 1 29 13 N2P0 N2P3 muhlenbergia cuspidata
#> 58 1 25 13 N1P0 N2P3 physalis pumila
#> 59 1 25 29 N1P0 N2P0 physalis pumila
#> 61 1 25 13 N1P0 N2P3 poa pratensis
#> 62 1 25 29 N1P0 N2P0 poa pratensis
#> 63 1 29 13 N2P0 N2P3 poa pratensis
#> 64 1 25 13 N1P0 N2P3 schrankia nuttallii
#> 66 1 29 13 N2P0 N2P3 schrankia nuttallii
#> 67 1 25 13 N1P0 N2P3 senecio plattensis
#> 68 1 25 29 N1P0 N2P0 senecio plattensis
#> 70 1 25 13 N1P0 N2P3 sisyrinchium campestre
#> 72 1 29 13 N2P0 N2P3 sisyrinchium campestre
#> 73 1 25 13 N1P0 N2P3 solidago missouriensis
#> 74 1 25 29 N1P0 N2P0 solidago missouriensis
#> 75 1 29 13 N2P0 N2P3 solidago missouriensis
#> 76 1 25 13 N1P0 N2P3 sorghastrum nutans
#> 77 1 25 29 N1P0 N2P0 sorghastrum nutans
#> 78 1 29 13 N2P0 N2P3 sorghastrum nutans
#> 79 1 25 13 N1P0 N2P3 sporobolus asper
#> 81 1 29 13 N2P0 N2P3 sporobolus asper
#> 82 1 25 13 N1P0 N2P3 triodanis perfoliata
#> 84 1 29 13 N2P0 N2P3 triodanis perfoliata
#> 85 2 27 21 N1P0 N2P3 ambrosia psilostachya
#> 86 2 27 32 N1P0 N2P0 ambrosia psilostachya
#> 87 2 32 21 N2P0 N2P3 ambrosia psilostachya
#> 88 2 27 21 N1P0 N2P3 amorpha canescens
#> 89 2 27 32 N1P0 N2P0 amorpha canescens
#> 90 2 32 21 N2P0 N2P3 amorpha canescens
#> 91 2 27 21 N1P0 N2P3 andropogon gerardii
#> 92 2 27 32 N1P0 N2P0 andropogon gerardii
#> 93 2 32 21 N2P0 N2P3 andropogon gerardii
#> 94 2 27 21 N1P0 N2P3 andropogon scoparius
#> 95 2 27 32 N1P0 N2P0 andropogon scoparius
#> 96 2 32 21 N2P0 N2P3 andropogon scoparius
#> 97 2 27 21 N1P0 N2P3 antennaria neglecta
#> 98 2 27 32 N1P0 N2P0 antennaria neglecta
#> 99 2 32 21 N2P0 N2P3 antennaria neglecta
#> 100 2 27 21 N1P0 N2P3 asclepias verticillata
#> 101 2 27 32 N1P0 N2P0 asclepias verticillata
#> 103 2 27 21 N1P0 N2P3 aster ericoides
#> 104 2 27 32 N1P0 N2P0 aster ericoides
#> 105 2 32 21 N2P0 N2P3 aster ericoides
#> 106 2 27 21 N1P0 N2P3 bouteloua curtipendula
#> 107 2 27 32 N1P0 N2P0 bouteloua curtipendula
#> 108 2 32 21 N2P0 N2P3 bouteloua curtipendula
#> 109 2 27 21 N1P0 N2P3 carex brevior
#> 111 2 32 21 N2P0 N2P3 carex brevior
#> 112 2 27 21 N1P0 N2P3 carex heliophila
#> 113 2 27 32 N1P0 N2P0 carex heliophila
#> 114 2 32 21 N2P0 N2P3 carex heliophila
#> 115 2 27 21 N1P0 N2P3 carex meadii
#> 116 2 27 32 N1P0 N2P0 carex meadii
#> 117 2 32 21 N2P0 N2P3 carex meadii
#> 118 2 27 21 N1P0 N2P3 dalea candida
#> 120 2 32 21 N2P0 N2P3 dalea candida
#> 122 2 27 32 N1P0 N2P0 dichanthelium acuminatum
#> 123 2 32 21 N2P0 N2P3 dichanthelium acuminatum
#> 124 2 27 21 N1P0 N2P3 dichanthelium oligosanthes
#> 125 2 27 32 N1P0 N2P0 dichanthelium oligosanthes
#> 126 2 32 21 N2P0 N2P3 dichanthelium oligosanthes
#> 127 2 27 21 N1P0 N2P3 eragrostis spectabilis
#> 128 2 27 32 N1P0 N2P0 eragrostis spectabilis
#> 129 2 32 21 N2P0 N2P3 eragrostis spectabilis
#> 130 2 27 21 N1P0 N2P3 koeleria pyramidata
#> 131 2 27 32 N1P0 N2P0 koeleria pyramidata
#> 134 2 27 32 N1P0 N2P0 kuhnia eupatorioides
#> 135 2 32 21 N2P0 N2P3 kuhnia eupatorioides
#> 136 2 27 21 N1P0 N2P3 linum sulcatum
#> 137 2 27 32 N1P0 N2P0 linum sulcatum
#> 138 2 32 21 N2P0 N2P3 linum sulcatum
#> 139 2 27 21 N1P0 N2P3 physalis pumila
#> 140 2 27 32 N1P0 N2P0 physalis pumila
#> 141 2 32 21 N2P0 N2P3 physalis pumila
#> 142 2 27 21 N1P0 N2P3 poa pratensis
#> 143 2 27 32 N1P0 N2P0 poa pratensis
#> 144 2 32 21 N2P0 N2P3 poa pratensis
#> 145 2 27 21 N1P0 N2P3 ruellia humilis
#> 146 2 27 32 N1P0 N2P0 ruellia humilis
#> 147 2 32 21 N2P0 N2P3 ruellia humilis
#> 149 2 27 32 N1P0 N2P0 senecio plattensis
#> 150 2 32 21 N2P0 N2P3 senecio plattensis
#> 151 2 27 21 N1P0 N2P3 solidago canadensis
#> 153 2 32 21 N2P0 N2P3 solidago canadensis
#> 154 2 27 21 N1P0 N2P3 solidago missouriensis
#> 155 2 27 32 N1P0 N2P0 solidago missouriensis
#> 156 2 32 21 N2P0 N2P3 solidago missouriensis
#> 157 2 27 21 N1P0 N2P3 sorghastrum nutans
#> 158 2 27 32 N1P0 N2P0 sorghastrum nutans
#> 159 2 32 21 N2P0 N2P3 sorghastrum nutans
#> 160 2 27 21 N1P0 N2P3 sporobolus asper
#> 161 2 27 32 N1P0 N2P0 sporobolus asper
#> 162 2 32 21 N2P0 N2P3 sporobolus asper
#> difference
#> 2 0.009784736
#> 3 -0.009784736
#> 4 0.052532728
#> 5 0.011575488
#> 6 0.040957240
#> 7 -0.060255980
#> 8 0.015684662
#> 9 -0.075940642
#> 10 -0.029633737
#> 11 -0.021659375
#> 12 -0.007974362
#> 14 0.001956947
#> 15 -0.001956947
#> 16 -0.007357934
#> 17 0.017408936
#> 18 -0.024766870
#> 19 0.024291498
#> 21 0.024291498
#> 22 0.007108658
#> 23 0.010079732
#> 24 -0.002971074
#> 25 0.005677471
#> 26 0.034560269
#> 27 -0.028882798
#> 28 -0.021725677
#> 29 -0.024019345
#> 30 0.002293668
#> 31 -0.006369427
#> 32 -0.002455533
#> 33 -0.003913894
#> 35 0.001956947
#> 36 -0.001956947
#> 37 0.007405210
#> 38 0.006664423
#> 39 0.000740787
#> 40 0.005875172
#> 41 -0.004246285
#> 42 0.010121457
#> 43 0.002024291
#> 45 0.002024291
#> 46 -0.004345136
#> 47 -0.002455533
#> 48 -0.001889603
#> 49 -0.006369427
#> 50 -0.006369427
#> 52 -0.004246285
#> 53 -0.000332391
#> 54 -0.003913894
#> 56 0.005870841
#> 57 -0.005870841
#> 58 -0.004246285
#> 59 -0.004246285
#> 61 -0.056585609
#> 62 -0.016432539
#> 63 -0.040153070
#> 64 0.076923077
#> 66 0.076923077
#> 67 -0.002123142
#> 68 -0.002123142
#> 70 0.002024291
#> 72 0.002024291
#> 73 -0.003507053
#> 74 -0.022062398
#> 75 0.018555345
#> 76 0.010757540
#> 77 -0.009140730
#> 78 0.019898270
#> 79 0.010121457
#> 81 0.010121457
#> 82 0.002024291
#> 84 0.002024291
#> 85 -0.004474273
#> 86 -0.000671992
#> 87 -0.003802281
#> 88 0.046562410
#> 89 0.018339415
#> 90 0.028222995
#> 91 -0.310116353
#> 92 -0.147327770
#> 93 -0.162788583
#> 94 0.281782858
#> 95 -0.014970951
#> 96 0.296753809
#> 97 0.004784689
#> 98 0.002534854
#> 99 0.002249835
#> 100 -0.006711409
#> 101 -0.006711409
#> 103 -0.005469745
#> 104 0.045099991
#> 105 -0.050569736
#> 106 0.033471415
#> 107 0.083871352
#> 108 -0.050399937
#> 109 0.004784689
#> 111 0.004784689
#> 112 0.026760005
#> 113 0.017590867
#> 114 0.009169138
#> 115 0.008573906
#> 116 0.000144606
#> 117 0.008429300
#> 118 0.001594896
#> 120 0.001594896
#> 122 0.006337136
#> 123 -0.006337136
#> 124 -0.028793766
#> 125 -0.016859332
#> 126 -0.011934434
#> 127 0.019138756
#> 128 0.003802281
#> 129 0.015336475
#> 130 -0.004474273
#> 131 -0.004474273
#> 134 0.006337136
#> 135 -0.006337136
#> 136 0.000952657
#> 137 0.001565145
#> 138 -0.000612488
#> 139 -0.005116513
#> 140 -0.006711409
#> 141 0.001594896
#> 142 0.003810625
#> 143 0.004993152
#> 144 -0.001182527
#> 145 -0.000642240
#> 146 0.005367427
#> 147 -0.006009667
#> 149 0.001267427
#> 150 -0.001267427
#> 151 0.001594896
#> 153 0.001594896
#> 154 -0.035794183
#> 155 -0.023119912
#> 156 -0.012674271
#> 157 -0.025507638
#> 158 0.003691700
#> 159 -0.029199338
#> 160 -0.006711409
#> 161 0.019904561
#> 162 -0.026615970
# With blocks and time
df <- subset(pplots, year < 2004 & block < 3)
abundance_difference(df = df,
species.var = "species",
abundance.var = "relative_cover",
treatment.var = "treatment",
block.var = "block",
replicate.var = "plot",
time.var = "year")
#> year block plot plot2 treatment treatment2 species
#> 2 2002 1 25 29 N1P0 N2P0 ambrosia psilostachya
#> 3 2002 1 29 13 N2P0 N2P3 ambrosia psilostachya
#> 4 2002 1 25 13 N1P0 N2P3 amorpha canescens
#> 5 2002 1 25 29 N1P0 N2P0 amorpha canescens
#> 6 2002 1 29 13 N2P0 N2P3 amorpha canescens
#> 7 2002 1 25 13 N1P0 N2P3 andropogon gerardii
#> 8 2002 1 25 29 N1P0 N2P0 andropogon gerardii
#> 9 2002 1 29 13 N2P0 N2P3 andropogon gerardii
#> 10 2002 1 25 13 N1P0 N2P3 andropogon scoparius
#> 11 2002 1 25 29 N1P0 N2P0 andropogon scoparius
#> 12 2002 1 29 13 N2P0 N2P3 andropogon scoparius
#> 14 2002 1 25 29 N1P0 N2P0 asclepias verticillata
#> 15 2002 1 29 13 N2P0 N2P3 asclepias verticillata
#> 16 2002 1 25 13 N1P0 N2P3 aster ericoides
#> 17 2002 1 25 29 N1P0 N2P0 aster ericoides
#> 18 2002 1 29 13 N2P0 N2P3 aster ericoides
#> 19 2002 1 25 13 N1P0 N2P3 aster sericeus
#> 21 2002 1 29 13 N2P0 N2P3 aster sericeus
#> 22 2002 1 25 13 N1P0 N2P3 bouteloua curtipendula
#> 23 2002 1 25 29 N1P0 N2P0 bouteloua curtipendula
#> 24 2002 1 29 13 N2P0 N2P3 bouteloua curtipendula
#> 25 2002 1 25 13 N1P0 N2P3 carex heliophila
#> 26 2002 1 25 29 N1P0 N2P0 carex heliophila
#> 27 2002 1 29 13 N2P0 N2P3 carex heliophila
#> 28 2002 1 25 13 N1P0 N2P3 carex meadii
#> 29 2002 1 25 29 N1P0 N2P0 carex meadii
#> 30 2002 1 29 13 N2P0 N2P3 carex meadii
#> 31 2002 1 25 13 N1P0 N2P3 dalea candida
#> 32 2002 1 25 29 N1P0 N2P0 dalea candida
#> 33 2002 1 29 13 N2P0 N2P3 dalea candida
#> 35 2002 1 25 29 N1P0 N2P0 dalea purpurea
#> 36 2002 1 29 13 N2P0 N2P3 dalea purpurea
#> 37 2002 1 25 13 N1P0 N2P3 dichanthelium oligosanthes
#> 38 2002 1 25 29 N1P0 N2P0 dichanthelium oligosanthes
#> 39 2002 1 29 13 N2P0 N2P3 dichanthelium oligosanthes
#> 40 2002 1 25 13 N1P0 N2P3 eragrostis spectabilis
#> 41 2002 1 25 29 N1P0 N2P0 eragrostis spectabilis
#> 42 2002 1 29 13 N2P0 N2P3 eragrostis spectabilis
#> 43 2002 1 25 13 N1P0 N2P3 euphorbia serpens
#> 45 2002 1 29 13 N2P0 N2P3 euphorbia serpens
#> 46 2002 1 25 13 N1P0 N2P3 koeleria pyramidata
#> 47 2002 1 25 29 N1P0 N2P0 koeleria pyramidata
#> 48 2002 1 29 13 N2P0 N2P3 koeleria pyramidata
#> 49 2002 1 25 13 N1P0 N2P3 kuhnia eupatorioides
#> 50 2002 1 25 29 N1P0 N2P0 kuhnia eupatorioides
#> 52 2002 1 25 13 N1P0 N2P3 linum sulcatum
#> 53 2002 1 25 29 N1P0 N2P0 linum sulcatum
#> 54 2002 1 29 13 N2P0 N2P3 linum sulcatum
#> 56 2002 1 25 29 N1P0 N2P0 muhlenbergia cuspidata
#> 57 2002 1 29 13 N2P0 N2P3 muhlenbergia cuspidata
#> 58 2002 1 25 13 N1P0 N2P3 physalis pumila
#> 59 2002 1 25 29 N1P0 N2P0 physalis pumila
#> 61 2002 1 25 13 N1P0 N2P3 poa pratensis
#> 62 2002 1 25 29 N1P0 N2P0 poa pratensis
#> 63 2002 1 29 13 N2P0 N2P3 poa pratensis
#> 64 2002 1 25 13 N1P0 N2P3 schrankia nuttallii
#> 66 2002 1 29 13 N2P0 N2P3 schrankia nuttallii
#> 67 2002 1 25 13 N1P0 N2P3 senecio plattensis
#> 68 2002 1 25 29 N1P0 N2P0 senecio plattensis
#> 70 2002 1 25 13 N1P0 N2P3 sisyrinchium campestre
#> 72 2002 1 29 13 N2P0 N2P3 sisyrinchium campestre
#> 73 2002 1 25 13 N1P0 N2P3 solidago missouriensis
#> 74 2002 1 25 29 N1P0 N2P0 solidago missouriensis
#> 75 2002 1 29 13 N2P0 N2P3 solidago missouriensis
#> 76 2002 1 25 13 N1P0 N2P3 sorghastrum nutans
#> 77 2002 1 25 29 N1P0 N2P0 sorghastrum nutans
#> 78 2002 1 29 13 N2P0 N2P3 sorghastrum nutans
#> 79 2002 1 25 13 N1P0 N2P3 sporobolus asper
#> 81 2002 1 29 13 N2P0 N2P3 sporobolus asper
#> 82 2002 1 25 13 N1P0 N2P3 triodanis perfoliata
#> 84 2002 1 29 13 N2P0 N2P3 triodanis perfoliata
#> 85 2002 2 27 21 N1P0 N2P3 ambrosia psilostachya
#> 86 2002 2 27 32 N1P0 N2P0 ambrosia psilostachya
#> 87 2002 2 32 21 N2P0 N2P3 ambrosia psilostachya
#> 88 2002 2 27 21 N1P0 N2P3 amorpha canescens
#> 89 2002 2 27 32 N1P0 N2P0 amorpha canescens
#> 90 2002 2 32 21 N2P0 N2P3 amorpha canescens
#> 91 2002 2 27 21 N1P0 N2P3 andropogon gerardii
#> 92 2002 2 27 32 N1P0 N2P0 andropogon gerardii
#> 93 2002 2 32 21 N2P0 N2P3 andropogon gerardii
#> 94 2002 2 27 21 N1P0 N2P3 andropogon scoparius
#> 95 2002 2 27 32 N1P0 N2P0 andropogon scoparius
#> 96 2002 2 32 21 N2P0 N2P3 andropogon scoparius
#> 97 2002 2 27 21 N1P0 N2P3 antennaria neglecta
#> 98 2002 2 27 32 N1P0 N2P0 antennaria neglecta
#> 99 2002 2 32 21 N2P0 N2P3 antennaria neglecta
#> 100 2002 2 27 21 N1P0 N2P3 asclepias verticillata
#> 101 2002 2 27 32 N1P0 N2P0 asclepias verticillata
#> 103 2002 2 27 21 N1P0 N2P3 aster ericoides
#> 104 2002 2 27 32 N1P0 N2P0 aster ericoides
#> 105 2002 2 32 21 N2P0 N2P3 aster ericoides
#> 106 2002 2 27 21 N1P0 N2P3 bouteloua curtipendula
#> 107 2002 2 27 32 N1P0 N2P0 bouteloua curtipendula
#> 108 2002 2 32 21 N2P0 N2P3 bouteloua curtipendula
#> 109 2002 2 27 21 N1P0 N2P3 carex brevior
#> 111 2002 2 32 21 N2P0 N2P3 carex brevior
#> 112 2002 2 27 21 N1P0 N2P3 carex heliophila
#> 113 2002 2 27 32 N1P0 N2P0 carex heliophila
#> 114 2002 2 32 21 N2P0 N2P3 carex heliophila
#> 115 2002 2 27 21 N1P0 N2P3 carex meadii
#> 116 2002 2 27 32 N1P0 N2P0 carex meadii
#> 117 2002 2 32 21 N2P0 N2P3 carex meadii
#> 118 2002 2 27 21 N1P0 N2P3 dalea candida
#> 120 2002 2 32 21 N2P0 N2P3 dalea candida
#> 122 2002 2 27 32 N1P0 N2P0 dichanthelium acuminatum
#> 123 2002 2 32 21 N2P0 N2P3 dichanthelium acuminatum
#> 124 2002 2 27 21 N1P0 N2P3 dichanthelium oligosanthes
#> 125 2002 2 27 32 N1P0 N2P0 dichanthelium oligosanthes
#> 126 2002 2 32 21 N2P0 N2P3 dichanthelium oligosanthes
#> 127 2002 2 27 21 N1P0 N2P3 eragrostis spectabilis
#> 128 2002 2 27 32 N1P0 N2P0 eragrostis spectabilis
#> 129 2002 2 32 21 N2P0 N2P3 eragrostis spectabilis
#> 130 2002 2 27 21 N1P0 N2P3 koeleria pyramidata
#> 131 2002 2 27 32 N1P0 N2P0 koeleria pyramidata
#> 134 2002 2 27 32 N1P0 N2P0 kuhnia eupatorioides
#> 135 2002 2 32 21 N2P0 N2P3 kuhnia eupatorioides
#> 136 2002 2 27 21 N1P0 N2P3 linum sulcatum
#> 137 2002 2 27 32 N1P0 N2P0 linum sulcatum
#> 138 2002 2 32 21 N2P0 N2P3 linum sulcatum
#> 139 2002 2 27 21 N1P0 N2P3 physalis pumila
#> 140 2002 2 27 32 N1P0 N2P0 physalis pumila
#> 141 2002 2 32 21 N2P0 N2P3 physalis pumila
#> 142 2002 2 27 21 N1P0 N2P3 poa pratensis
#> 143 2002 2 27 32 N1P0 N2P0 poa pratensis
#> 144 2002 2 32 21 N2P0 N2P3 poa pratensis
#> 145 2002 2 27 21 N1P0 N2P3 ruellia humilis
#> 146 2002 2 27 32 N1P0 N2P0 ruellia humilis
#> 147 2002 2 32 21 N2P0 N2P3 ruellia humilis
#> 149 2002 2 27 32 N1P0 N2P0 senecio plattensis
#> 150 2002 2 32 21 N2P0 N2P3 senecio plattensis
#> 151 2002 2 27 21 N1P0 N2P3 solidago canadensis
#> 153 2002 2 32 21 N2P0 N2P3 solidago canadensis
#> 154 2002 2 27 21 N1P0 N2P3 solidago missouriensis
#> 155 2002 2 27 32 N1P0 N2P0 solidago missouriensis
#> 156 2002 2 32 21 N2P0 N2P3 solidago missouriensis
#> 157 2002 2 27 21 N1P0 N2P3 sorghastrum nutans
#> 158 2002 2 27 32 N1P0 N2P0 sorghastrum nutans
#> 159 2002 2 32 21 N2P0 N2P3 sorghastrum nutans
#> 160 2002 2 27 21 N1P0 N2P3 sporobolus asper
#> 161 2002 2 27 32 N1P0 N2P0 sporobolus asper
#> 162 2002 2 32 21 N2P0 N2P3 sporobolus asper
#> 164 2003 1 25 29 N1P0 N2P0 ambrosia psilostachya
#> 165 2003 1 29 13 N2P0 N2P3 ambrosia psilostachya
#> 166 2003 1 25 13 N1P0 N2P3 amorpha canescens
#> 167 2003 1 25 29 N1P0 N2P0 amorpha canescens
#> 168 2003 1 29 13 N2P0 N2P3 amorpha canescens
#> 169 2003 1 25 13 N1P0 N2P3 andropogon gerardii
#> 170 2003 1 25 29 N1P0 N2P0 andropogon gerardii
#> 171 2003 1 29 13 N2P0 N2P3 andropogon gerardii
#> 172 2003 1 25 13 N1P0 N2P3 andropogon scoparius
#> 173 2003 1 25 29 N1P0 N2P0 andropogon scoparius
#> 174 2003 1 29 13 N2P0 N2P3 andropogon scoparius
#> 176 2003 1 25 29 N1P0 N2P0 asclepias verticillata
#> 177 2003 1 29 13 N2P0 N2P3 asclepias verticillata
#> 178 2003 1 25 13 N1P0 N2P3 aster ericoides
#> 179 2003 1 25 29 N1P0 N2P0 aster ericoides
#> 180 2003 1 29 13 N2P0 N2P3 aster ericoides
#> 181 2003 1 25 13 N1P0 N2P3 aster sericeus
#> 183 2003 1 29 13 N2P0 N2P3 aster sericeus
#> 184 2003 1 25 13 N1P0 N2P3 bouteloua curtipendula
#> 185 2003 1 25 29 N1P0 N2P0 bouteloua curtipendula
#> 186 2003 1 29 13 N2P0 N2P3 bouteloua curtipendula
#> 188 2003 1 25 29 N1P0 N2P0 bouteloua gracilis
#> 189 2003 1 29 13 N2P0 N2P3 bouteloua gracilis
#> 190 2003 1 25 13 N1P0 N2P3 carex heliophila
#> 191 2003 1 25 29 N1P0 N2P0 carex heliophila
#> 192 2003 1 29 13 N2P0 N2P3 carex heliophila
#> 193 2003 1 25 13 N1P0 N2P3 carex meadii
#> 194 2003 1 25 29 N1P0 N2P0 carex meadii
#> 195 2003 1 29 13 N2P0 N2P3 carex meadii
#> 196 2003 1 25 13 N1P0 N2P3 dalea candida
#> 197 2003 1 25 29 N1P0 N2P0 dalea candida
#> 198 2003 1 29 13 N2P0 N2P3 dalea candida
#> 199 2003 1 25 13 N1P0 N2P3 dalea purpurea
#> 200 2003 1 25 29 N1P0 N2P0 dalea purpurea
#> 201 2003 1 29 13 N2P0 N2P3 dalea purpurea
#> 202 2003 1 25 13 N1P0 N2P3 dichanthelium acuminatum
#> 204 2003 1 29 13 N2P0 N2P3 dichanthelium acuminatum
#> 205 2003 1 25 13 N1P0 N2P3 dichanthelium oligosanthes
#> 206 2003 1 25 29 N1P0 N2P0 dichanthelium oligosanthes
#> 207 2003 1 29 13 N2P0 N2P3 dichanthelium oligosanthes
#> 208 2003 1 25 13 N1P0 N2P3 eragrostis spectabilis
#> 209 2003 1 25 29 N1P0 N2P0 eragrostis spectabilis
#> 210 2003 1 29 13 N2P0 N2P3 eragrostis spectabilis
#> 212 2003 1 25 29 N1P0 N2P0 euphorbia serpens
#> 213 2003 1 29 13 N2P0 N2P3 euphorbia serpens
#> 215 2003 1 25 29 N1P0 N2P0 koeleria pyramidata
#> 216 2003 1 29 13 N2P0 N2P3 koeleria pyramidata
#> 217 2003 1 25 13 N1P0 N2P3 kuhnia eupatorioides
#> 218 2003 1 25 29 N1P0 N2P0 kuhnia eupatorioides
#> 220 2003 1 25 13 N1P0 N2P3 physalis pumila
#> 221 2003 1 25 29 N1P0 N2P0 physalis pumila
#> 223 2003 1 25 13 N1P0 N2P3 poa pratensis
#> 224 2003 1 25 29 N1P0 N2P0 poa pratensis
#> 225 2003 1 29 13 N2P0 N2P3 poa pratensis
#> 226 2003 1 25 13 N1P0 N2P3 schrankia nuttallii
#> 228 2003 1 29 13 N2P0 N2P3 schrankia nuttallii
#> 229 2003 1 25 13 N1P0 N2P3 solidago missouriensis
#> 230 2003 1 25 29 N1P0 N2P0 solidago missouriensis
#> 231 2003 1 29 13 N2P0 N2P3 solidago missouriensis
#> 232 2003 1 25 13 N1P0 N2P3 sorghastrum nutans
#> 233 2003 1 25 29 N1P0 N2P0 sorghastrum nutans
#> 234 2003 1 29 13 N2P0 N2P3 sorghastrum nutans
#> 235 2003 1 25 13 N1P0 N2P3 sporobolus asper
#> 237 2003 1 29 13 N2P0 N2P3 sporobolus asper
#> 238 2003 1 25 13 N1P0 N2P3 viola rafinesquii
#> 239 2003 1 25 29 N1P0 N2P0 viola rafinesquii
#> 242 2003 2 27 32 N1P0 N2P0 ambrosia psilostachya
#> 243 2003 2 32 21 N2P0 N2P3 ambrosia psilostachya
#> 244 2003 2 27 21 N1P0 N2P3 amorpha canescens
#> 245 2003 2 27 32 N1P0 N2P0 amorpha canescens
#> 246 2003 2 32 21 N2P0 N2P3 amorpha canescens
#> 247 2003 2 27 21 N1P0 N2P3 andropogon gerardii
#> 248 2003 2 27 32 N1P0 N2P0 andropogon gerardii
#> 249 2003 2 32 21 N2P0 N2P3 andropogon gerardii
#> 250 2003 2 27 21 N1P0 N2P3 andropogon scoparius
#> 251 2003 2 27 32 N1P0 N2P0 andropogon scoparius
#> 252 2003 2 32 21 N2P0 N2P3 andropogon scoparius
#> 253 2003 2 27 21 N1P0 N2P3 antennaria neglecta
#> 255 2003 2 32 21 N2P0 N2P3 antennaria neglecta
#> 256 2003 2 27 21 N1P0 N2P3 asclepias stenophylla
#> 257 2003 2 27 32 N1P0 N2P0 asclepias stenophylla
#> 259 2003 2 27 21 N1P0 N2P3 asclepias tuberosa
#> 260 2003 2 27 32 N1P0 N2P0 asclepias tuberosa
#> 261 2003 2 32 21 N2P0 N2P3 asclepias tuberosa
#> 262 2003 2 27 21 N1P0 N2P3 asclepias verticillata
#> 263 2003 2 27 32 N1P0 N2P0 asclepias verticillata
#> 265 2003 2 27 21 N1P0 N2P3 aster ericoides
#> 266 2003 2 27 32 N1P0 N2P0 aster ericoides
#> 267 2003 2 32 21 N2P0 N2P3 aster ericoides
#> 269 2003 2 27 32 N1P0 N2P0 aster oblongifolius
#> 270 2003 2 32 21 N2P0 N2P3 aster oblongifolius
#> 271 2003 2 27 21 N1P0 N2P3 bouteloua curtipendula
#> 272 2003 2 27 32 N1P0 N2P0 bouteloua curtipendula
#> 273 2003 2 32 21 N2P0 N2P3 bouteloua curtipendula
#> 274 2003 2 27 21 N1P0 N2P3 carex heliophila
#> 275 2003 2 27 32 N1P0 N2P0 carex heliophila
#> 276 2003 2 32 21 N2P0 N2P3 carex heliophila
#> 277 2003 2 27 21 N1P0 N2P3 carex meadii
#> 278 2003 2 27 32 N1P0 N2P0 carex meadii
#> 279 2003 2 32 21 N2P0 N2P3 carex meadii
#> 280 2003 2 27 21 N1P0 N2P3 dalea candida
#> 282 2003 2 32 21 N2P0 N2P3 dalea candida
#> 284 2003 2 27 32 N1P0 N2P0 delphinium virescens
#> 285 2003 2 32 21 N2P0 N2P3 delphinium virescens
#> 286 2003 2 27 21 N1P0 N2P3 dichanthelium oligosanthes
#> 287 2003 2 27 32 N1P0 N2P0 dichanthelium oligosanthes
#> 288 2003 2 32 21 N2P0 N2P3 dichanthelium oligosanthes
#> 289 2003 2 27 21 N1P0 N2P3 eragrostis spectabilis
#> 291 2003 2 32 21 N2P0 N2P3 eragrostis spectabilis
#> 293 2003 2 27 32 N1P0 N2P0 euphorbia serpens
#> 294 2003 2 32 21 N2P0 N2P3 euphorbia serpens
#> 295 2003 2 27 21 N1P0 N2P3 koeleria pyramidata
#> 296 2003 2 27 32 N1P0 N2P0 koeleria pyramidata
#> 299 2003 2 27 32 N1P0 N2P0 kuhnia eupatorioides
#> 300 2003 2 32 21 N2P0 N2P3 kuhnia eupatorioides
#> 301 2003 2 27 21 N1P0 N2P3 linum sulcatum
#> 302 2003 2 27 32 N1P0 N2P0 linum sulcatum
#> 305 2003 2 27 32 N1P0 N2P0 panicum capillare
#> 306 2003 2 32 21 N2P0 N2P3 panicum capillare
#> 307 2003 2 27 21 N1P0 N2P3 physalis pumila
#> 308 2003 2 27 32 N1P0 N2P0 physalis pumila
#> 309 2003 2 32 21 N2P0 N2P3 physalis pumila
#> 310 2003 2 27 21 N1P0 N2P3 poa pratensis
#> 311 2003 2 27 32 N1P0 N2P0 poa pratensis
#> 312 2003 2 32 21 N2P0 N2P3 poa pratensis
#> 313 2003 2 27 21 N1P0 N2P3 ruellia humilis
#> 314 2003 2 27 32 N1P0 N2P0 ruellia humilis
#> 315 2003 2 32 21 N2P0 N2P3 ruellia humilis
#> 317 2003 2 27 32 N1P0 N2P0 senecio plattensis
#> 318 2003 2 32 21 N2P0 N2P3 senecio plattensis
#> 319 2003 2 27 21 N1P0 N2P3 solidago canadensis
#> 321 2003 2 32 21 N2P0 N2P3 solidago canadensis
#> 322 2003 2 27 21 N1P0 N2P3 solidago missouriensis
#> 323 2003 2 27 32 N1P0 N2P0 solidago missouriensis
#> 324 2003 2 32 21 N2P0 N2P3 solidago missouriensis
#> 325 2003 2 27 21 N1P0 N2P3 sorghastrum nutans
#> 326 2003 2 27 32 N1P0 N2P0 sorghastrum nutans
#> 327 2003 2 32 21 N2P0 N2P3 sorghastrum nutans
#> 328 2003 2 27 21 N1P0 N2P3 sporobolus asper
#> 329 2003 2 27 32 N1P0 N2P0 sporobolus asper
#> 330 2003 2 32 21 N2P0 N2P3 sporobolus asper
#> 331 2003 2 27 21 N1P0 N2P3 viola pedatifida
#> 333 2003 2 32 21 N2P0 N2P3 viola pedatifida
#> difference
#> 2 0.009784736
#> 3 -0.009784736
#> 4 0.052532728
#> 5 0.011575488
#> 6 0.040957240
#> 7 -0.060255980
#> 8 0.015684662
#> 9 -0.075940642
#> 10 -0.029633737
#> 11 -0.021659375
#> 12 -0.007974362
#> 14 0.001956947
#> 15 -0.001956947
#> 16 -0.007357934
#> 17 0.017408936
#> 18 -0.024766870
#> 19 0.024291498
#> 21 0.024291498
#> 22 0.007108658
#> 23 0.010079732
#> 24 -0.002971074
#> 25 0.005677471
#> 26 0.034560269
#> 27 -0.028882798
#> 28 -0.021725677
#> 29 -0.024019345
#> 30 0.002293668
#> 31 -0.006369427
#> 32 -0.002455533
#> 33 -0.003913894
#> 35 0.001956947
#> 36 -0.001956947
#> 37 0.007405210
#> 38 0.006664423
#> 39 0.000740787
#> 40 0.005875172
#> 41 -0.004246285
#> 42 0.010121457
#> 43 0.002024291
#> 45 0.002024291
#> 46 -0.004345136
#> 47 -0.002455533
#> 48 -0.001889603
#> 49 -0.006369427
#> 50 -0.006369427
#> 52 -0.004246285
#> 53 -0.000332391
#> 54 -0.003913894
#> 56 0.005870841
#> 57 -0.005870841
#> 58 -0.004246285
#> 59 -0.004246285
#> 61 -0.056585609
#> 62 -0.016432539
#> 63 -0.040153070
#> 64 0.076923077
#> 66 0.076923077
#> 67 -0.002123142
#> 68 -0.002123142
#> 70 0.002024291
#> 72 0.002024291
#> 73 -0.003507053
#> 74 -0.022062398
#> 75 0.018555345
#> 76 0.010757540
#> 77 -0.009140730
#> 78 0.019898270
#> 79 0.010121457
#> 81 0.010121457
#> 82 0.002024291
#> 84 0.002024291
#> 85 -0.004474273
#> 86 -0.000671992
#> 87 -0.003802281
#> 88 0.046562410
#> 89 0.018339415
#> 90 0.028222995
#> 91 -0.310116353
#> 92 -0.147327770
#> 93 -0.162788583
#> 94 0.281782858
#> 95 -0.014970951
#> 96 0.296753809
#> 97 0.004784689
#> 98 0.002534854
#> 99 0.002249835
#> 100 -0.006711409
#> 101 -0.006711409
#> 103 -0.005469745
#> 104 0.045099991
#> 105 -0.050569736
#> 106 0.033471415
#> 107 0.083871352
#> 108 -0.050399937
#> 109 0.004784689
#> 111 0.004784689
#> 112 0.026760005
#> 113 0.017590867
#> 114 0.009169138
#> 115 0.008573906
#> 116 0.000144606
#> 117 0.008429300
#> 118 0.001594896
#> 120 0.001594896
#> 122 0.006337136
#> 123 -0.006337136
#> 124 -0.028793766
#> 125 -0.016859332
#> 126 -0.011934434
#> 127 0.019138756
#> 128 0.003802281
#> 129 0.015336475
#> 130 -0.004474273
#> 131 -0.004474273
#> 134 0.006337136
#> 135 -0.006337136
#> 136 0.000952657
#> 137 0.001565145
#> 138 -0.000612488
#> 139 -0.005116513
#> 140 -0.006711409
#> 141 0.001594896
#> 142 0.003810625
#> 143 0.004993152
#> 144 -0.001182527
#> 145 -0.000642240
#> 146 0.005367427
#> 147 -0.006009667
#> 149 0.001267427
#> 150 -0.001267427
#> 151 0.001594896
#> 153 0.001594896
#> 154 -0.035794183
#> 155 -0.023119912
#> 156 -0.012674271
#> 157 -0.025507638
#> 158 0.003691700
#> 159 -0.029199338
#> 160 -0.006711409
#> 161 0.019904561
#> 162 -0.026615970
#> 164 0.005468216
#> 165 -0.005468216
#> 166 0.100418410
#> 167 0.027341080
#> 168 0.073077330
#> 169 0.006551015
#> 170 0.020145290
#> 171 -0.013594275
#> 172 -0.033595076
#> 173 -0.079168309
#> 174 0.045573233
#> 176 0.001367054
#> 177 -0.001367054
#> 178 0.003752668
#> 179 0.068901276
#> 180 -0.065148608
#> 181 0.019525802
#> 183 0.019525802
#> 184 0.050085939
#> 185 0.050347147
#> 186 -0.000261208
#> 188 0.002734108
#> 189 -0.002734108
#> 190 -0.003563792
#> 191 0.012840856
#> 192 -0.016404648
#> 193 -0.010101883
#> 194 -0.012263049
#> 195 0.002161166
#> 196 -0.028510335
#> 197 -0.018940957
#> 198 -0.009569378
#> 199 -0.001425517
#> 200 0.005409753
#> 201 -0.006835270
#> 202 0.004184100
#> 204 0.004184100
#> 205 -0.000154083
#> 206 0.013378226
#> 207 -0.013532309
#> 208 0.027585837
#> 209 -0.014255167
#> 210 0.041841004
#> 212 0.006835270
#> 213 -0.006835270
#> 215 0.004101162
#> 216 -0.004101162
#> 217 -0.009978617
#> 218 -0.009978617
#> 220 -0.002851033
#> 221 -0.002851033
#> 223 0.006973501
#> 224 0.008202324
#> 225 -0.001228823
#> 226 0.069735007
#> 228 0.069735007
#> 229 -0.034212402
#> 230 -0.030111240
#> 231 -0.004101162
#> 232 -0.165783423
#> 233 -0.058077871
#> 234 -0.107705552
#> 235 0.002789400
#> 237 0.002789400
#> 238 -0.001425517
#> 239 -0.001425517
#> 242 0.002824859
#> 243 -0.002824859
#> 244 0.077244259
#> 245 0.028248588
#> 246 0.048995671
#> 247 -0.045922749
#> 248 0.174581361
#> 249 -0.220504110
#> 250 0.144695844
#> 251 -0.138647121
#> 252 0.283342965
#> 253 0.002087683
#> 255 0.002087683
#> 256 -0.001501502
#> 257 -0.001501502
#> 259 -0.001501502
#> 260 0.009797933
#> 261 -0.011299435
#> 262 -0.007507508
#> 263 -0.007507508
#> 265 -0.011754970
#> 266 0.027179722
#> 267 -0.038934692
#> 269 0.015065913
#> 270 -0.015065913
#> 271 -0.033763409
#> 272 -0.033720161
#> 273 -0.000043248
#> 274 -0.007507508
#> 275 0.031098895
#> 276 -0.038606403
#> 277 0.002180155
#> 278 0.052947015
#> 279 -0.050766860
#> 280 0.002087683
#> 282 0.002087683
#> 284 0.003766478
#> 285 -0.003766478
#> 286 -0.001861987
#> 287 -0.014506031
#> 288 0.012644044
#> 289 0.020876827
#> 291 0.020876827
#> 293 0.001883239
#> 294 -0.001883239
#> 295 -0.001501502
#> 296 -0.001501502
#> 299 0.009416196
#> 300 -0.009416196
#> 301 -0.003003003
#> 302 -0.003003003
#> 305 0.005649718
#> 306 -0.005649718
#> 307 -0.000915320
#> 308 -0.003003003
#> 309 0.002087683
#> 310 0.014613779
#> 311 0.005649718
#> 312 0.008964061
#> 313 -0.001501502
#> 314 0.007914694
#> 315 -0.009416196
#> 317 0.001883239
#> 318 -0.001883239
#> 319 0.002087683
#> 321 0.002087683
#> 322 -0.036786787
#> 323 -0.022662493
#> 324 -0.014124294
#> 325 -0.115020031
#> 326 -0.168804398
#> 327 0.053784367
#> 328 0.002087683
#> 329 0.016949153
#> 330 -0.014861470
#> 331 0.002087683
#> 333 0.002087683
# With blocks, time and reference treatment
df <- subset(pplots, year < 2004 & block < 3)
abundance_difference(df = df,
species.var = "species",
abundance.var = "relative_cover",
treatment.var = "treatment",
block.var = "block",
replicate.var = "plot",
time.var = "year",
reference.treatment = "N1P0")
#> year block plot plot2 treatment treatment2 species
#> 2 2002 1 25 29 N1P0 N2P0 ambrosia psilostachya
#> 3 2002 1 25 13 N1P0 N2P3 amorpha canescens
#> 4 2002 1 25 29 N1P0 N2P0 amorpha canescens
#> 5 2002 1 25 13 N1P0 N2P3 andropogon gerardii
#> 6 2002 1 25 29 N1P0 N2P0 andropogon gerardii
#> 7 2002 1 25 13 N1P0 N2P3 andropogon scoparius
#> 8 2002 1 25 29 N1P0 N2P0 andropogon scoparius
#> 10 2002 1 25 29 N1P0 N2P0 asclepias verticillata
#> 11 2002 1 25 13 N1P0 N2P3 aster ericoides
#> 12 2002 1 25 29 N1P0 N2P0 aster ericoides
#> 13 2002 1 25 13 N1P0 N2P3 aster sericeus
#> 15 2002 1 25 13 N1P0 N2P3 bouteloua curtipendula
#> 16 2002 1 25 29 N1P0 N2P0 bouteloua curtipendula
#> 17 2002 1 25 13 N1P0 N2P3 carex heliophila
#> 18 2002 1 25 29 N1P0 N2P0 carex heliophila
#> 19 2002 1 25 13 N1P0 N2P3 carex meadii
#> 20 2002 1 25 29 N1P0 N2P0 carex meadii
#> 21 2002 1 25 13 N1P0 N2P3 dalea candida
#> 22 2002 1 25 29 N1P0 N2P0 dalea candida
#> 24 2002 1 25 29 N1P0 N2P0 dalea purpurea
#> 25 2002 1 25 13 N1P0 N2P3 dichanthelium oligosanthes
#> 26 2002 1 25 29 N1P0 N2P0 dichanthelium oligosanthes
#> 27 2002 1 25 13 N1P0 N2P3 eragrostis spectabilis
#> 28 2002 1 25 29 N1P0 N2P0 eragrostis spectabilis
#> 29 2002 1 25 13 N1P0 N2P3 euphorbia serpens
#> 31 2002 1 25 13 N1P0 N2P3 koeleria pyramidata
#> 32 2002 1 25 29 N1P0 N2P0 koeleria pyramidata
#> 33 2002 1 25 13 N1P0 N2P3 kuhnia eupatorioides
#> 34 2002 1 25 29 N1P0 N2P0 kuhnia eupatorioides
#> 35 2002 1 25 13 N1P0 N2P3 linum sulcatum
#> 36 2002 1 25 29 N1P0 N2P0 linum sulcatum
#> 38 2002 1 25 29 N1P0 N2P0 muhlenbergia cuspidata
#> 39 2002 1 25 13 N1P0 N2P3 physalis pumila
#> 40 2002 1 25 29 N1P0 N2P0 physalis pumila
#> 41 2002 1 25 13 N1P0 N2P3 poa pratensis
#> 42 2002 1 25 29 N1P0 N2P0 poa pratensis
#> 43 2002 1 25 13 N1P0 N2P3 schrankia nuttallii
#> 45 2002 1 25 13 N1P0 N2P3 senecio plattensis
#> 46 2002 1 25 29 N1P0 N2P0 senecio plattensis
#> 47 2002 1 25 13 N1P0 N2P3 sisyrinchium campestre
#> 49 2002 1 25 13 N1P0 N2P3 solidago missouriensis
#> 50 2002 1 25 29 N1P0 N2P0 solidago missouriensis
#> 51 2002 1 25 13 N1P0 N2P3 sorghastrum nutans
#> 52 2002 1 25 29 N1P0 N2P0 sorghastrum nutans
#> 53 2002 1 25 13 N1P0 N2P3 sporobolus asper
#> 55 2002 1 25 13 N1P0 N2P3 triodanis perfoliata
#> 57 2002 2 27 21 N1P0 N2P3 ambrosia psilostachya
#> 58 2002 2 27 32 N1P0 N2P0 ambrosia psilostachya
#> 59 2002 2 27 21 N1P0 N2P3 amorpha canescens
#> 60 2002 2 27 32 N1P0 N2P0 amorpha canescens
#> 61 2002 2 27 21 N1P0 N2P3 andropogon gerardii
#> 62 2002 2 27 32 N1P0 N2P0 andropogon gerardii
#> 63 2002 2 27 21 N1P0 N2P3 andropogon scoparius
#> 64 2002 2 27 32 N1P0 N2P0 andropogon scoparius
#> 65 2002 2 27 21 N1P0 N2P3 antennaria neglecta
#> 66 2002 2 27 32 N1P0 N2P0 antennaria neglecta
#> 67 2002 2 27 21 N1P0 N2P3 asclepias verticillata
#> 68 2002 2 27 32 N1P0 N2P0 asclepias verticillata
#> 69 2002 2 27 21 N1P0 N2P3 aster ericoides
#> 70 2002 2 27 32 N1P0 N2P0 aster ericoides
#> 71 2002 2 27 21 N1P0 N2P3 bouteloua curtipendula
#> 72 2002 2 27 32 N1P0 N2P0 bouteloua curtipendula
#> 73 2002 2 27 21 N1P0 N2P3 carex brevior
#> 75 2002 2 27 21 N1P0 N2P3 carex heliophila
#> 76 2002 2 27 32 N1P0 N2P0 carex heliophila
#> 77 2002 2 27 21 N1P0 N2P3 carex meadii
#> 78 2002 2 27 32 N1P0 N2P0 carex meadii
#> 79 2002 2 27 21 N1P0 N2P3 dalea candida
#> 82 2002 2 27 32 N1P0 N2P0 dichanthelium acuminatum
#> 83 2002 2 27 21 N1P0 N2P3 dichanthelium oligosanthes
#> 84 2002 2 27 32 N1P0 N2P0 dichanthelium oligosanthes
#> 85 2002 2 27 21 N1P0 N2P3 eragrostis spectabilis
#> 86 2002 2 27 32 N1P0 N2P0 eragrostis spectabilis
#> 87 2002 2 27 21 N1P0 N2P3 koeleria pyramidata
#> 88 2002 2 27 32 N1P0 N2P0 koeleria pyramidata
#> 90 2002 2 27 32 N1P0 N2P0 kuhnia eupatorioides
#> 91 2002 2 27 21 N1P0 N2P3 linum sulcatum
#> 92 2002 2 27 32 N1P0 N2P0 linum sulcatum
#> 93 2002 2 27 21 N1P0 N2P3 physalis pumila
#> 94 2002 2 27 32 N1P0 N2P0 physalis pumila
#> 95 2002 2 27 21 N1P0 N2P3 poa pratensis
#> 96 2002 2 27 32 N1P0 N2P0 poa pratensis
#> 97 2002 2 27 21 N1P0 N2P3 ruellia humilis
#> 98 2002 2 27 32 N1P0 N2P0 ruellia humilis
#> 100 2002 2 27 32 N1P0 N2P0 senecio plattensis
#> 101 2002 2 27 21 N1P0 N2P3 solidago canadensis
#> 103 2002 2 27 21 N1P0 N2P3 solidago missouriensis
#> 104 2002 2 27 32 N1P0 N2P0 solidago missouriensis
#> 105 2002 2 27 21 N1P0 N2P3 sorghastrum nutans
#> 106 2002 2 27 32 N1P0 N2P0 sorghastrum nutans
#> 107 2002 2 27 21 N1P0 N2P3 sporobolus asper
#> 108 2002 2 27 32 N1P0 N2P0 sporobolus asper
#> 110 2003 1 25 29 N1P0 N2P0 ambrosia psilostachya
#> 111 2003 1 25 13 N1P0 N2P3 amorpha canescens
#> 112 2003 1 25 29 N1P0 N2P0 amorpha canescens
#> 113 2003 1 25 13 N1P0 N2P3 andropogon gerardii
#> 114 2003 1 25 29 N1P0 N2P0 andropogon gerardii
#> 115 2003 1 25 13 N1P0 N2P3 andropogon scoparius
#> 116 2003 1 25 29 N1P0 N2P0 andropogon scoparius
#> 118 2003 1 25 29 N1P0 N2P0 asclepias verticillata
#> 119 2003 1 25 13 N1P0 N2P3 aster ericoides
#> 120 2003 1 25 29 N1P0 N2P0 aster ericoides
#> 121 2003 1 25 13 N1P0 N2P3 aster sericeus
#> 123 2003 1 25 13 N1P0 N2P3 bouteloua curtipendula
#> 124 2003 1 25 29 N1P0 N2P0 bouteloua curtipendula
#> 126 2003 1 25 29 N1P0 N2P0 bouteloua gracilis
#> 127 2003 1 25 13 N1P0 N2P3 carex heliophila
#> 128 2003 1 25 29 N1P0 N2P0 carex heliophila
#> 129 2003 1 25 13 N1P0 N2P3 carex meadii
#> 130 2003 1 25 29 N1P0 N2P0 carex meadii
#> 131 2003 1 25 13 N1P0 N2P3 dalea candida
#> 132 2003 1 25 29 N1P0 N2P0 dalea candida
#> 133 2003 1 25 13 N1P0 N2P3 dalea purpurea
#> 134 2003 1 25 29 N1P0 N2P0 dalea purpurea
#> 135 2003 1 25 13 N1P0 N2P3 dichanthelium acuminatum
#> 137 2003 1 25 13 N1P0 N2P3 dichanthelium oligosanthes
#> 138 2003 1 25 29 N1P0 N2P0 dichanthelium oligosanthes
#> 139 2003 1 25 13 N1P0 N2P3 eragrostis spectabilis
#> 140 2003 1 25 29 N1P0 N2P0 eragrostis spectabilis
#> 142 2003 1 25 29 N1P0 N2P0 euphorbia serpens
#> 144 2003 1 25 29 N1P0 N2P0 koeleria pyramidata
#> 145 2003 1 25 13 N1P0 N2P3 kuhnia eupatorioides
#> 146 2003 1 25 29 N1P0 N2P0 kuhnia eupatorioides
#> 147 2003 1 25 13 N1P0 N2P3 physalis pumila
#> 148 2003 1 25 29 N1P0 N2P0 physalis pumila
#> 149 2003 1 25 13 N1P0 N2P3 poa pratensis
#> 150 2003 1 25 29 N1P0 N2P0 poa pratensis
#> 151 2003 1 25 13 N1P0 N2P3 schrankia nuttallii
#> 153 2003 1 25 13 N1P0 N2P3 solidago missouriensis
#> 154 2003 1 25 29 N1P0 N2P0 solidago missouriensis
#> 155 2003 1 25 13 N1P0 N2P3 sorghastrum nutans
#> 156 2003 1 25 29 N1P0 N2P0 sorghastrum nutans
#> 157 2003 1 25 13 N1P0 N2P3 sporobolus asper
#> 159 2003 1 25 13 N1P0 N2P3 viola rafinesquii
#> 160 2003 1 25 29 N1P0 N2P0 viola rafinesquii
#> 162 2003 2 27 32 N1P0 N2P0 ambrosia psilostachya
#> 163 2003 2 27 21 N1P0 N2P3 amorpha canescens
#> 164 2003 2 27 32 N1P0 N2P0 amorpha canescens
#> 165 2003 2 27 21 N1P0 N2P3 andropogon gerardii
#> 166 2003 2 27 32 N1P0 N2P0 andropogon gerardii
#> 167 2003 2 27 21 N1P0 N2P3 andropogon scoparius
#> 168 2003 2 27 32 N1P0 N2P0 andropogon scoparius
#> 169 2003 2 27 21 N1P0 N2P3 antennaria neglecta
#> 171 2003 2 27 21 N1P0 N2P3 asclepias stenophylla
#> 172 2003 2 27 32 N1P0 N2P0 asclepias stenophylla
#> 173 2003 2 27 21 N1P0 N2P3 asclepias tuberosa
#> 174 2003 2 27 32 N1P0 N2P0 asclepias tuberosa
#> 175 2003 2 27 21 N1P0 N2P3 asclepias verticillata
#> 176 2003 2 27 32 N1P0 N2P0 asclepias verticillata
#> 177 2003 2 27 21 N1P0 N2P3 aster ericoides
#> 178 2003 2 27 32 N1P0 N2P0 aster ericoides
#> 180 2003 2 27 32 N1P0 N2P0 aster oblongifolius
#> 181 2003 2 27 21 N1P0 N2P3 bouteloua curtipendula
#> 182 2003 2 27 32 N1P0 N2P0 bouteloua curtipendula
#> 183 2003 2 27 21 N1P0 N2P3 carex heliophila
#> 184 2003 2 27 32 N1P0 N2P0 carex heliophila
#> 185 2003 2 27 21 N1P0 N2P3 carex meadii
#> 186 2003 2 27 32 N1P0 N2P0 carex meadii
#> 187 2003 2 27 21 N1P0 N2P3 dalea candida
#> 190 2003 2 27 32 N1P0 N2P0 delphinium virescens
#> 191 2003 2 27 21 N1P0 N2P3 dichanthelium oligosanthes
#> 192 2003 2 27 32 N1P0 N2P0 dichanthelium oligosanthes
#> 193 2003 2 27 21 N1P0 N2P3 eragrostis spectabilis
#> 196 2003 2 27 32 N1P0 N2P0 euphorbia serpens
#> 197 2003 2 27 21 N1P0 N2P3 koeleria pyramidata
#> 198 2003 2 27 32 N1P0 N2P0 koeleria pyramidata
#> 200 2003 2 27 32 N1P0 N2P0 kuhnia eupatorioides
#> 201 2003 2 27 21 N1P0 N2P3 linum sulcatum
#> 202 2003 2 27 32 N1P0 N2P0 linum sulcatum
#> 204 2003 2 27 32 N1P0 N2P0 panicum capillare
#> 205 2003 2 27 21 N1P0 N2P3 physalis pumila
#> 206 2003 2 27 32 N1P0 N2P0 physalis pumila
#> 207 2003 2 27 21 N1P0 N2P3 poa pratensis
#> 208 2003 2 27 32 N1P0 N2P0 poa pratensis
#> 209 2003 2 27 21 N1P0 N2P3 ruellia humilis
#> 210 2003 2 27 32 N1P0 N2P0 ruellia humilis
#> 212 2003 2 27 32 N1P0 N2P0 senecio plattensis
#> 213 2003 2 27 21 N1P0 N2P3 solidago canadensis
#> 215 2003 2 27 21 N1P0 N2P3 solidago missouriensis
#> 216 2003 2 27 32 N1P0 N2P0 solidago missouriensis
#> 217 2003 2 27 21 N1P0 N2P3 sorghastrum nutans
#> 218 2003 2 27 32 N1P0 N2P0 sorghastrum nutans
#> 219 2003 2 27 21 N1P0 N2P3 sporobolus asper
#> 220 2003 2 27 32 N1P0 N2P0 sporobolus asper
#> 221 2003 2 27 21 N1P0 N2P3 viola pedatifida
#> difference
#> 2 0.009784736
#> 3 0.052532728
#> 4 0.011575488
#> 5 -0.060255980
#> 6 0.015684662
#> 7 -0.029633737
#> 8 -0.021659375
#> 10 0.001956947
#> 11 -0.007357934
#> 12 0.017408936
#> 13 0.024291498
#> 15 0.007108658
#> 16 0.010079732
#> 17 0.005677471
#> 18 0.034560269
#> 19 -0.021725677
#> 20 -0.024019345
#> 21 -0.006369427
#> 22 -0.002455533
#> 24 0.001956947
#> 25 0.007405210
#> 26 0.006664423
#> 27 0.005875172
#> 28 -0.004246285
#> 29 0.002024291
#> 31 -0.004345136
#> 32 -0.002455533
#> 33 -0.006369427
#> 34 -0.006369427
#> 35 -0.004246285
#> 36 -0.000332391
#> 38 0.005870841
#> 39 -0.004246285
#> 40 -0.004246285
#> 41 -0.056585609
#> 42 -0.016432539
#> 43 0.076923077
#> 45 -0.002123142
#> 46 -0.002123142
#> 47 0.002024291
#> 49 -0.003507053
#> 50 -0.022062398
#> 51 0.010757540
#> 52 -0.009140730
#> 53 0.010121457
#> 55 0.002024291
#> 57 -0.004474273
#> 58 -0.000671992
#> 59 0.046562410
#> 60 0.018339415
#> 61 -0.310116353
#> 62 -0.147327770
#> 63 0.281782858
#> 64 -0.014970951
#> 65 0.004784689
#> 66 0.002534854
#> 67 -0.006711409
#> 68 -0.006711409
#> 69 -0.005469745
#> 70 0.045099991
#> 71 0.033471415
#> 72 0.083871352
#> 73 0.004784689
#> 75 0.026760005
#> 76 0.017590867
#> 77 0.008573906
#> 78 0.000144606
#> 79 0.001594896
#> 82 0.006337136
#> 83 -0.028793766
#> 84 -0.016859332
#> 85 0.019138756
#> 86 0.003802281
#> 87 -0.004474273
#> 88 -0.004474273
#> 90 0.006337136
#> 91 0.000952657
#> 92 0.001565145
#> 93 -0.005116513
#> 94 -0.006711409
#> 95 0.003810625
#> 96 0.004993152
#> 97 -0.000642240
#> 98 0.005367427
#> 100 0.001267427
#> 101 0.001594896
#> 103 -0.035794183
#> 104 -0.023119912
#> 105 -0.025507638
#> 106 0.003691700
#> 107 -0.006711409
#> 108 0.019904561
#> 110 0.005468216
#> 111 0.100418410
#> 112 0.027341080
#> 113 0.006551015
#> 114 0.020145290
#> 115 -0.033595076
#> 116 -0.079168309
#> 118 0.001367054
#> 119 0.003752668
#> 120 0.068901276
#> 121 0.019525802
#> 123 0.050085939
#> 124 0.050347147
#> 126 0.002734108
#> 127 -0.003563792
#> 128 0.012840856
#> 129 -0.010101883
#> 130 -0.012263049
#> 131 -0.028510335
#> 132 -0.018940957
#> 133 -0.001425517
#> 134 0.005409753
#> 135 0.004184100
#> 137 -0.000154083
#> 138 0.013378226
#> 139 0.027585837
#> 140 -0.014255167
#> 142 0.006835270
#> 144 0.004101162
#> 145 -0.009978617
#> 146 -0.009978617
#> 147 -0.002851033
#> 148 -0.002851033
#> 149 0.006973501
#> 150 0.008202324
#> 151 0.069735007
#> 153 -0.034212402
#> 154 -0.030111240
#> 155 -0.165783423
#> 156 -0.058077871
#> 157 0.002789400
#> 159 -0.001425517
#> 160 -0.001425517
#> 162 0.002824859
#> 163 0.077244259
#> 164 0.028248588
#> 165 -0.045922749
#> 166 0.174581361
#> 167 0.144695844
#> 168 -0.138647121
#> 169 0.002087683
#> 171 -0.001501502
#> 172 -0.001501502
#> 173 -0.001501502
#> 174 0.009797933
#> 175 -0.007507508
#> 176 -0.007507508
#> 177 -0.011754970
#> 178 0.027179722
#> 180 0.015065913
#> 181 -0.033763409
#> 182 -0.033720161
#> 183 -0.007507508
#> 184 0.031098895
#> 185 0.002180155
#> 186 0.052947015
#> 187 0.002087683
#> 190 0.003766478
#> 191 -0.001861987
#> 192 -0.014506031
#> 193 0.020876827
#> 196 0.001883239
#> 197 -0.001501502
#> 198 -0.001501502
#> 200 0.009416196
#> 201 -0.003003003
#> 202 -0.003003003
#> 204 0.005649718
#> 205 -0.000915320
#> 206 -0.003003003
#> 207 0.014613779
#> 208 0.005649718
#> 209 -0.001501502
#> 210 0.007914694
#> 212 0.001883239
#> 213 0.002087683
#> 215 -0.036786787
#> 216 -0.022662493
#> 217 -0.115020031
#> 218 -0.168804398
#> 219 0.002087683
#> 220 0.016949153
#> 221 0.002087683
# Pooling by treatment with time
df <- subset(pplots, year < 2004)
abundance_difference(df = df,
species.var = "species",
abundance.var = "relative_cover",
treatment.var = "treatment",
pool = TRUE,
replicate.var = "plot",
time.var = "year")
#> year treatment treatment2 species difference
#> 2 2002 N1P0 N2P0 achillea millefolium 1.010101e-03
#> 3 2002 N2P0 N2P3 achillea millefolium -1.010101e-03
#> 4 2002 N2P0 N2P3 ambrosia psilostachya 2.384359e-03
#> 5 2002 N1P0 N2P3 ambrosia psilostachya 2.669693e-03
#> 6 2002 N1P0 N2P0 ambrosia psilostachya 2.853340e-04
#> 7 2002 N2P0 N2P3 amorpha canescens -3.379951e-02
#> 8 2002 N1P0 N2P3 amorpha canescens -9.733626e-03
#> 9 2002 N1P0 N2P0 amorpha canescens 2.406589e-02
#> 10 2002 N2P0 N2P3 andropogon gerardii -7.188126e-02
#> 11 2002 N1P0 N2P3 andropogon gerardii -6.204108e-02
#> 12 2002 N1P0 N2P0 andropogon gerardii 9.840181e-03
#> 13 2002 N1P0 N2P0 andropogon scoparius -4.854132e-02
#> 14 2002 N1P0 N2P3 andropogon scoparius 5.282351e-02
#> 15 2002 N2P0 N2P3 andropogon scoparius 1.013648e-01
#> 16 2002 N2P0 N2P3 antennaria neglecta -1.172517e-05
#> 17 2002 N1P0 N2P3 antennaria neglecta -5.848583e-04
#> 18 2002 N1P0 N2P0 antennaria neglecta -5.731332e-04
#> 19 2002 N2P0 N2P3 asclepias stenophylla -3.211303e-04
#> 20 2002 N1P0 N2P3 asclepias stenophylla -5.527917e-04
#> 21 2002 N1P0 N2P0 asclepias stenophylla -2.316613e-04
#> 22 2002 N2P0 N2P3 asclepias verticillata -5.977432e-04
#> 23 2002 N1P0 N2P3 asclepias verticillata -2.101134e-03
#> 24 2002 N1P0 N2P0 asclepias verticillata -1.503391e-03
#> 25 2002 N2P0 N2P3 asclepias viridis -1.605652e-03
#> 26 2002 N1P0 N2P0 asclepias viridis 1.605652e-03
#> 28 2002 N2P0 N2P3 aster ericoides -2.408576e-02
#> 29 2002 N1P0 N2P3 aster ericoides -2.388115e-02
#> 30 2002 N1P0 N2P0 aster ericoides 2.046082e-04
#> 31 2002 N2P0 N2P3 aster oblongifolius 3.395586e-03
#> 32 2002 N1P0 N2P0 aster oblongifolius -3.040354e-03
#> 33 2002 N1P0 N2P3 aster oblongifolius 3.552318e-04
#> 34 2002 N2P0 N2P3 aster sericeus 4.048583e-03
#> 36 2002 N1P0 N2P3 aster sericeus 4.048583e-03
#> 38 2002 N1P0 N2P0 baptisia australis -1.152605e-03
#> 39 2002 N1P0 N2P3 baptisia australis -1.152605e-03
#> 40 2002 N1P0 N2P3 baptisia bracteata 2.256609e-03
#> 42 2002 N2P0 N2P3 baptisia bracteata 2.256609e-03
#> 43 2002 N2P0 N2P3 bouteloua curtipendula -3.729620e-03
#> 44 2002 N1P0 N2P0 bouteloua curtipendula 1.289029e-02
#> 45 2002 N1P0 N2P3 bouteloua curtipendula 9.160668e-03
#> 46 2002 N2P0 N2P3 bouteloua gracilis 5.659310e-04
#> 48 2002 N1P0 N2P3 bouteloua gracilis 5.659310e-04
#> 49 2002 N2P0 N2P3 carex brevior 7.974482e-04
#> 51 2002 N1P0 N2P3 carex brevior 7.974482e-04
#> 52 2002 N1P0 N2P3 carex heliophila 3.789989e-03
#> 53 2002 N1P0 N2P0 carex heliophila 5.908710e-04
#> 54 2002 N2P0 N2P3 carex heliophila 3.199118e-03
#> 55 2002 N2P0 N2P3 carex meadii -1.881362e-03
#> 56 2002 N1P0 N2P0 carex meadii -1.118458e-02
#> 57 2002 N1P0 N2P3 carex meadii -1.306594e-02
#> 58 2002 N1P0 N2P0 dalea candida -2.943957e-03
#> 59 2002 N1P0 N2P3 dalea candida -2.226235e-03
#> 60 2002 N2P0 N2P3 dalea candida 7.177222e-04
#> 61 2002 N1P0 N2P0 dalea purpurea 3.261578e-04
#> 62 2002 N1P0 N2P3 dalea purpurea 1.921230e-03
#> 63 2002 N2P0 N2P3 dalea purpurea 1.595072e-03
#> 64 2002 N2P0 N2P3 dichanthelium acuminatum -1.056189e-03
#> 65 2002 N1P0 N2P0 dichanthelium acuminatum 1.056189e-03
#> 67 2002 N2P0 N2P3 dichanthelium oligosanthes -5.564620e-03
#> 68 2002 N1P0 N2P0 dichanthelium oligosanthes -3.852048e-04
#> 69 2002 N1P0 N2P3 dichanthelium oligosanthes -5.949825e-03
#> 70 2002 N1P0 N2P3 draba reptans -3.248863e-04
#> 71 2002 N1P0 N2P0 draba reptans -3.248863e-04
#> 73 2002 N1P0 N2P0 eragrostis spectabilis -2.798988e-03
#> 74 2002 N1P0 N2P3 eragrostis spectabilis 5.688483e-03
#> 75 2002 N2P0 N2P3 eragrostis spectabilis 8.487471e-03
#> 76 2002 N2P0 N2P3 euphorbia serpens 5.775355e-04
#> 78 2002 N1P0 N2P3 euphorbia serpens 5.775355e-04
#> 79 2002 N1P0 N2P3 euphorbia spathulata 2.401537e-04
#> 81 2002 N2P0 N2P3 euphorbia spathulata 2.401537e-04
#> 82 2002 N1P0 N2P3 koeleria pyramidata -1.552866e-03
#> 83 2002 N1P0 N2P0 koeleria pyramidata -3.660833e-03
#> 84 2002 N2P0 N2P3 koeleria pyramidata 2.107967e-03
#> 85 2002 N1P0 N2P0 kuhnia eupatorioides -2.140531e-03
#> 86 2002 N1P0 N2P3 kuhnia eupatorioides -4.528819e-03
#> 87 2002 N2P0 N2P3 kuhnia eupatorioides -2.388289e-03
#> 88 2002 N1P0 N2P0 liatris punctata 3.198977e-04
#> 90 2002 N2P0 N2P3 liatris punctata -3.198977e-04
#> 91 2002 N1P0 N2P3 linum sulcatum -2.552010e-03
#> 92 2002 N1P0 N2P0 linum sulcatum -1.135327e-03
#> 93 2002 N2P0 N2P3 linum sulcatum -1.416683e-03
#> 94 2002 N2P0 N2P3 muhlenbergia cuspidata -9.784735e-04
#> 95 2002 N1P0 N2P0 muhlenbergia cuspidata 9.784735e-04
#> 97 2002 N1P0 N2P3 oxalis stricta -1.974723e-04
#> 98 2002 N1P0 N2P0 oxalis stricta -1.974723e-04
#> 100 2002 N1P0 N2P3 physalis pumila -2.236095e-03
#> 101 2002 N1P0 N2P0 physalis pumila -3.702679e-03
#> 102 2002 N2P0 N2P3 physalis pumila 1.466584e-03
#> 103 2002 N1P0 N2P3 poa pratensis 9.608113e-03
#> 104 2002 N1P0 N2P0 poa pratensis 2.188519e-02
#> 105 2002 N2P0 N2P3 poa pratensis -1.227708e-02
#> 107 2002 N1P0 N2P0 ratibida columnifera -6.497725e-04
#> 108 2002 N1P0 N2P3 ratibida columnifera -6.497725e-04
#> 109 2002 N1P0 N2P3 ruellia humilis 2.384479e-03
#> 110 2002 N1P0 N2P0 ruellia humilis 1.106038e-03
#> 111 2002 N2P0 N2P3 ruellia humilis 1.278441e-03
#> 112 2002 N1P0 N2P3 salvia azurea 9.276235e-03
#> 113 2002 N1P0 N2P0 salvia azurea -3.949447e-04
#> 114 2002 N2P0 N2P3 salvia azurea 9.671180e-03
#> 115 2002 N1P0 N2P3 schrankia nuttallii 1.282051e-02
#> 117 2002 N2P0 N2P3 schrankia nuttallii 1.282051e-02
#> 118 2002 N2P0 N2P3 senecio plattensis -2.112378e-04
#> 119 2002 N1P0 N2P3 senecio plattensis -1.003629e-03
#> 120 2002 N1P0 N2P0 senecio plattensis -7.923917e-04
#> 121 2002 N1P0 N2P3 sisyrinchium campestre -4.613727e-04
#> 122 2002 N1P0 N2P0 sisyrinchium campestre -2.855080e-04
#> 123 2002 N2P0 N2P3 sisyrinchium campestre -1.758647e-04
#> 124 2002 N2P0 N2P3 solidago canadensis 2.658160e-04
#> 125 2002 N1P0 N2P3 solidago canadensis 2.658160e-04
#> 127 2002 N2P0 N2P3 solidago missouriensis 1.867275e-03
#> 128 2002 N1P0 N2P3 solidago missouriensis -2.515332e-03
#> 129 2002 N1P0 N2P0 solidago missouriensis -4.382607e-03
#> 130 2002 N2P0 N2P3 sorghastrum nutans 1.632421e-02
#> 131 2002 N1P0 N2P3 sorghastrum nutans 1.336085e-02
#> 132 2002 N1P0 N2P0 sorghastrum nutans -2.963363e-03
#> 133 2002 N1P0 N2P0 spermolepis inermis 3.367003e-04
#> 135 2002 N2P0 N2P3 spermolepis inermis -3.367003e-04
#> 136 2002 N2P0 N2P3 sporobolus asper 5.735291e-03
#> 137 2002 N1P0 N2P3 sporobolus asper 6.101063e-03
#> 138 2002 N1P0 N2P0 sporobolus asper 3.657718e-04
#> 139 2002 N2P0 N2P3 sporobolus heterolepis -1.862556e-02
#> 140 2002 N1P0 N2P3 sporobolus heterolepis -2.962085e-03
#> 141 2002 N1P0 N2P0 sporobolus heterolepis 1.566348e-02
#> 142 2002 N2P0 N2P3 triodanis perfoliata 1.443467e-03
#> 143 2002 N1P0 N2P3 triodanis perfoliata 1.561460e-03
#> 144 2002 N1P0 N2P0 triodanis perfoliata 1.179933e-04
#> 145 2002 N2P0 N2P3 viola rafinesquii -3.367003e-04
#> 146 2002 N1P0 N2P0 viola rafinesquii 3.367003e-04
#> 148 2003 N1P0 N2P0 achillea millefolium 2.391200e-04
#> 150 2003 N2P0 N2P3 achillea millefolium -2.391200e-04
#> 152 2003 N1P0 N2P3 ambrosia artemisiifolia 2.472800e-04
#> 153 2003 N2P0 N2P3 ambrosia artemisiifolia 2.472800e-04
#> 154 2003 N1P0 N2P0 ambrosia psilostachya -4.219591e-03
#> 155 2003 N1P0 N2P3 ambrosia psilostachya 1.864372e-02
#> 156 2003 N2P0 N2P3 ambrosia psilostachya 2.286331e-02
#> 157 2003 N1P0 N2P0 amorpha canescens 9.876721e-03
#> 158 2003 N1P0 N2P3 amorpha canescens -1.145582e-02
#> 159 2003 N2P0 N2P3 amorpha canescens -2.133254e-02
#> 160 2003 N1P0 N2P0 andropogon gerardii 3.942949e-02
#> 161 2003 N1P0 N2P3 andropogon gerardii 3.326461e-02
#> 162 2003 N2P0 N2P3 andropogon gerardii -6.164879e-03
#> 163 2003 N1P0 N2P0 andropogon scoparius -5.999543e-02
#> 164 2003 N1P0 N2P3 andropogon scoparius 4.910991e-02
#> 165 2003 N2P0 N2P3 andropogon scoparius 1.091053e-01
#> 166 2003 N1P0 N2P3 antennaria neglecta -2.420602e-03
#> 167 2003 N1P0 N2P0 antennaria neglecta -2.411661e-03
#> 168 2003 N2P0 N2P3 antennaria neglecta -8.940833e-06
#> 169 2003 N1P0 N2P3 asclepias stenophylla -1.154560e-03
#> 170 2003 N1P0 N2P0 asclepias stenophylla -9.906955e-04
#> 171 2003 N2P0 N2P3 asclepias stenophylla -1.638643e-04
#> 172 2003 N2P0 N2P3 asclepias tuberosa -1.883239e-03
#> 173 2003 N1P0 N2P0 asclepias tuberosa 1.632989e-03
#> 174 2003 N1P0 N2P3 asclepias tuberosa -2.502503e-04
#> 175 2003 N1P0 N2P0 asclepias verticillata -2.053912e-03
#> 176 2003 N1P0 N2P3 asclepias verticillata -2.346545e-03
#> 177 2003 N2P0 N2P3 asclepias verticillata -2.926322e-04
#> 179 2003 N1P0 N2P0 asclepias viridis 4.257130e-04
#> 180 2003 N2P0 N2P3 asclepias viridis -4.257130e-04
#> 181 2003 N1P0 N2P3 aster ericoides -9.455183e-03
#> 182 2003 N1P0 N2P0 aster ericoides 5.791998e-03
#> 183 2003 N2P0 N2P3 aster ericoides -1.524718e-02
#> 184 2003 N2P0 N2P3 aster oblongifolius -1.382317e-03
#> 185 2003 N1P0 N2P0 aster oblongifolius 1.153660e-04
#> 186 2003 N1P0 N2P3 aster oblongifolius -1.266951e-03
#> 187 2003 N1P0 N2P3 aster sericeus 3.254300e-03
#> 189 2003 N2P0 N2P3 aster sericeus 3.254300e-03
#> 191 2003 N1P0 N2P3 baptisia australis -8.992805e-04
#> 192 2003 N1P0 N2P0 baptisia australis -8.992805e-04
#> 193 2003 N2P0 N2P3 bouteloua curtipendula -1.376923e-02
#> 194 2003 N1P0 N2P0 bouteloua curtipendula 1.442992e-03
#> 195 2003 N1P0 N2P3 bouteloua curtipendula -1.232624e-02
#> 196 2003 N1P0 N2P0 bouteloua gracilis 4.556847e-04
#> 198 2003 N2P0 N2P3 bouteloua gracilis -4.556847e-04
#> 199 2003 N1P0 N2P3 carex heliophila -1.142505e-02
#> 200 2003 N1P0 N2P0 carex heliophila -8.652405e-03
#> 201 2003 N2P0 N2P3 carex heliophila -2.772648e-03
#> 202 2003 N2P0 N2P3 carex meadii -7.648920e-03
#> 203 2003 N1P0 N2P3 carex meadii -1.852583e-02
#> 204 2003 N1P0 N2P0 carex meadii -1.087691e-02
#> 205 2003 N2P0 N2P3 cyperus lupulinus 5.236973e-04
#> 207 2003 N1P0 N2P3 cyperus lupulinus 5.236973e-04
#> 208 2003 N1P0 N2P3 dalea candida -8.932125e-03
#> 209 2003 N1P0 N2P0 dalea candida -1.085009e-02
#> 210 2003 N2P0 N2P3 dalea candida 1.917963e-03
#> 211 2003 N2P0 N2P3 dalea purpurea -1.139212e-03
#> 212 2003 N1P0 N2P0 dalea purpurea 6.125733e-05
#> 213 2003 N1P0 N2P3 dalea purpurea -1.077954e-03
#> 214 2003 N1P0 N2P3 delphinium virescens 2.472800e-04
#> 215 2003 N1P0 N2P0 delphinium virescens 1.345106e-03
#> 216 2003 N2P0 N2P3 delphinium virescens -1.097826e-03
#> 217 2003 N2P0 N2P3 dichanthelium acuminatum 6.973500e-04
#> 219 2003 N1P0 N2P3 dichanthelium acuminatum 6.973500e-04
#> 220 2003 N1P0 N2P3 dichanthelium oligosanthes 4.244633e-05
#> 221 2003 N1P0 N2P0 dichanthelium oligosanthes 1.962984e-03
#> 222 2003 N2P0 N2P3 dichanthelium oligosanthes -1.920537e-03
#> 223 2003 N2P0 N2P3 eragrostis spectabilis 1.054411e-02
#> 224 2003 N1P0 N2P0 eragrostis spectabilis -3.659027e-04
#> 225 2003 N1P0 N2P3 eragrostis spectabilis 1.017821e-02
#> 226 2003 N1P0 N2P3 erigeron strigosus -2.997602e-04
#> 227 2003 N1P0 N2P0 erigeron strigosus -2.997602e-04
#> 229 2003 N2P0 N2P3 euphorbia serpens -6.897548e-04
#> 230 2003 N1P0 N2P3 euphorbia serpens 8.433630e-04
#> 231 2003 N1P0 N2P0 euphorbia serpens 1.533118e-03
#> 232 2003 N2P0 N2P3 koeleria pyramidata -1.587480e-03
#> 233 2003 N1P0 N2P0 koeleria pyramidata -1.573776e-03
#> 234 2003 N1P0 N2P3 koeleria pyramidata -3.161256e-03
#> 235 2003 N1P0 N2P0 kuhnia eupatorioides -6.799394e-03
#> 236 2003 N1P0 N2P3 kuhnia eupatorioides -7.059517e-03
#> 237 2003 N2P0 N2P3 kuhnia eupatorioides -2.601227e-04
#> 238 2003 N1P0 N2P3 linum sulcatum -2.386518e-04
#> 239 2003 N1P0 N2P0 linum sulcatum -5.005005e-04
#> 240 2003 N2P0 N2P3 linum sulcatum 2.618487e-04
#> 241 2003 N2P0 N2P3 oxalis stricta 5.091287e-04
#> 242 2003 N1P0 N2P3 oxalis stricta -4.458117e-05
#> 243 2003 N1P0 N2P0 oxalis stricta -5.537098e-04
#> 244 2003 N2P0 N2P3 panicum capillare -9.416197e-04
#> 245 2003 N1P0 N2P0 panicum capillare 9.416197e-04
#> 247 2003 N1P0 N2P3 physalis pumila 1.128015e-04
#> 248 2003 N1P0 N2P0 physalis pumila -1.806238e-03
#> 249 2003 N2P0 N2P3 physalis pumila 1.919039e-03
#> 250 2003 N2P0 N2P3 poa pratensis 1.530744e-03
#> 251 2003 N1P0 N2P0 poa pratensis 5.034822e-03
#> 252 2003 N1P0 N2P3 poa pratensis 6.565566e-03
#> 253 2003 N2P0 N2P3 ruellia humilis 5.368031e-03
#> 254 2003 N1P0 N2P0 ruellia humilis 4.242950e-05
#> 255 2003 N1P0 N2P3 ruellia humilis 5.410461e-03
#> 256 2003 N1P0 N2P0 salvia azurea -3.045404e-03
#> 257 2003 N1P0 N2P3 salvia azurea 2.291899e-02
#> 258 2003 N2P0 N2P3 salvia azurea 2.596439e-02
#> 259 2003 N1P0 N2P3 schrankia nuttallii 1.162250e-02
#> 261 2003 N2P0 N2P3 schrankia nuttallii 1.162250e-02
#> 262 2003 N2P0 N2P3 senecio plattensis -3.138732e-04
#> 263 2003 N1P0 N2P0 senecio plattensis 7.302533e-05
#> 264 2003 N1P0 N2P3 senecio plattensis -2.408478e-04
#> 265 2003 N2P0 N2P3 solidago canadensis 3.479472e-04
#> 267 2003 N1P0 N2P3 solidago canadensis 3.479472e-04
#> 268 2003 N1P0 N2P0 solidago missouriensis -8.625903e-03
#> 269 2003 N1P0 N2P3 solidago missouriensis -1.294062e-02
#> 270 2003 N2P0 N2P3 solidago missouriensis -4.314715e-03
#> 271 2003 N1P0 N2P0 sorghastrum nutans 2.949173e-02
#> 272 2003 N1P0 N2P3 sorghastrum nutans -5.664992e-02
#> 273 2003 N2P0 N2P3 sorghastrum nutans -8.614165e-02
#> 274 2003 N1P0 N2P0 sporobolus asper 2.736163e-03
#> 275 2003 N1P0 N2P3 sporobolus asper 1.109136e-03
#> 276 2003 N2P0 N2P3 sporobolus asper -1.627027e-03
#> 277 2003 N1P0 N2P0 sporobolus heterolepis 2.212582e-02
#> 278 2003 N1P0 N2P3 sporobolus heterolepis -3.078374e-03
#> 279 2003 N2P0 N2P3 sporobolus heterolepis -2.520419e-02
#> 281 2003 N1P0 N2P3 viola pedatifida 3.479472e-04
#> 282 2003 N2P0 N2P3 viola pedatifida 3.479472e-04
#> 283 2003 N1P0 N2P0 viola rafinesquii -2.375862e-04
#> 284 2003 N1P0 N2P3 viola rafinesquii -2.375862e-04
# All pairwise replicates with treatment
df <- subset(pplots, year < 2004 & plot %in% c(21, 25, 32))
abundance_difference(df = df,
species.var = "species",
abundance.var = "relative_cover",
replicate.var = "plot",
time.var = "year",
treatment.var = "treatment")
#> year plot plot2 treatment treatment2 species
#> 2 2002 21 32 N2P3 N2P0 ambrosia psilostachya
#> 3 2002 25 32 N1P0 N2P0 ambrosia psilostachya
#> 4 2002 21 25 N2P3 N1P0 amorpha canescens
#> 5 2002 21 32 N2P3 N2P0 amorpha canescens
#> 6 2002 25 32 N1P0 N2P0 amorpha canescens
#> 7 2002 21 25 N2P3 N1P0 andropogon gerardii
#> 8 2002 21 32 N2P3 N2P0 andropogon gerardii
#> 9 2002 25 32 N1P0 N2P0 andropogon gerardii
#> 10 2002 21 25 N2P3 N1P0 andropogon scoparius
#> 11 2002 21 32 N2P3 N2P0 andropogon scoparius
#> 12 2002 25 32 N1P0 N2P0 andropogon scoparius
#> 13 2002 21 25 N2P3 N1P0 antennaria neglecta
#> 14 2002 21 32 N2P3 N2P0 antennaria neglecta
#> 15 2002 25 32 N1P0 N2P0 antennaria neglecta
#> 16 2002 21 25 N2P3 N1P0 aster ericoides
#> 17 2002 21 32 N2P3 N2P0 aster ericoides
#> 18 2002 25 32 N1P0 N2P0 aster ericoides
#> 19 2002 21 25 N2P3 N1P0 bouteloua curtipendula
#> 20 2002 21 32 N2P3 N2P0 bouteloua curtipendula
#> 21 2002 25 32 N1P0 N2P0 bouteloua curtipendula
#> 22 2002 21 25 N2P3 N1P0 carex brevior
#> 23 2002 21 32 N2P3 N2P0 carex brevior
#> 25 2002 21 25 N2P3 N1P0 carex heliophila
#> 26 2002 21 32 N2P3 N2P0 carex heliophila
#> 27 2002 25 32 N1P0 N2P0 carex heliophila
#> 28 2002 21 25 N2P3 N1P0 carex meadii
#> 29 2002 21 32 N2P3 N2P0 carex meadii
#> 30 2002 25 32 N1P0 N2P0 carex meadii
#> 31 2002 21 25 N2P3 N1P0 dalea candida
#> 32 2002 21 32 N2P3 N2P0 dalea candida
#> 33 2002 25 32 N1P0 N2P0 dalea candida
#> 35 2002 21 32 N2P3 N2P0 dichanthelium acuminatum
#> 36 2002 25 32 N1P0 N2P0 dichanthelium acuminatum
#> 37 2002 21 25 N2P3 N1P0 dichanthelium oligosanthes
#> 38 2002 21 32 N2P3 N2P0 dichanthelium oligosanthes
#> 39 2002 25 32 N1P0 N2P0 dichanthelium oligosanthes
#> 40 2002 21 25 N2P3 N1P0 eragrostis spectabilis
#> 41 2002 21 32 N2P3 N2P0 eragrostis spectabilis
#> 42 2002 25 32 N1P0 N2P0 eragrostis spectabilis
#> 43 2002 21 25 N2P3 N1P0 koeleria pyramidata
#> 45 2002 25 32 N1P0 N2P0 koeleria pyramidata
#> 46 2002 21 25 N2P3 N1P0 kuhnia eupatorioides
#> 47 2002 21 32 N2P3 N2P0 kuhnia eupatorioides
#> 48 2002 25 32 N1P0 N2P0 kuhnia eupatorioides
#> 49 2002 21 25 N2P3 N1P0 linum sulcatum
#> 50 2002 21 32 N2P3 N2P0 linum sulcatum
#> 51 2002 25 32 N1P0 N2P0 linum sulcatum
#> 52 2002 21 25 N2P3 N1P0 physalis pumila
#> 53 2002 21 32 N2P3 N2P0 physalis pumila
#> 54 2002 25 32 N1P0 N2P0 physalis pumila
#> 55 2002 21 25 N2P3 N1P0 poa pratensis
#> 56 2002 21 32 N2P3 N2P0 poa pratensis
#> 57 2002 25 32 N1P0 N2P0 poa pratensis
#> 58 2002 21 25 N2P3 N1P0 ruellia humilis
#> 59 2002 21 32 N2P3 N2P0 ruellia humilis
#> 60 2002 25 32 N1P0 N2P0 ruellia humilis
#> 61 2002 21 25 N2P3 N1P0 senecio plattensis
#> 62 2002 21 32 N2P3 N2P0 senecio plattensis
#> 63 2002 25 32 N1P0 N2P0 senecio plattensis
#> 64 2002 21 25 N2P3 N1P0 solidago canadensis
#> 65 2002 21 32 N2P3 N2P0 solidago canadensis
#> 67 2002 21 25 N2P3 N1P0 solidago missouriensis
#> 68 2002 21 32 N2P3 N2P0 solidago missouriensis
#> 69 2002 25 32 N1P0 N2P0 solidago missouriensis
#> 70 2002 21 25 N2P3 N1P0 sorghastrum nutans
#> 71 2002 21 32 N2P3 N2P0 sorghastrum nutans
#> 72 2002 25 32 N1P0 N2P0 sorghastrum nutans
#> 74 2002 21 32 N2P3 N2P0 sporobolus asper
#> 75 2002 25 32 N1P0 N2P0 sporobolus asper
#> 77 2003 21 32 N2P3 N2P0 ambrosia psilostachya
#> 78 2003 25 32 N1P0 N2P0 ambrosia psilostachya
#> 79 2003 21 25 N2P3 N1P0 amorpha canescens
#> 80 2003 21 32 N2P3 N2P0 amorpha canescens
#> 81 2003 25 32 N1P0 N2P0 amorpha canescens
#> 82 2003 21 25 N2P3 N1P0 andropogon gerardii
#> 83 2003 21 32 N2P3 N2P0 andropogon gerardii
#> 84 2003 25 32 N1P0 N2P0 andropogon gerardii
#> 85 2003 21 25 N2P3 N1P0 andropogon scoparius
#> 86 2003 21 32 N2P3 N2P0 andropogon scoparius
#> 87 2003 25 32 N1P0 N2P0 andropogon scoparius
#> 88 2003 21 25 N2P3 N1P0 antennaria neglecta
#> 89 2003 21 32 N2P3 N2P0 antennaria neglecta
#> 92 2003 21 32 N2P3 N2P0 asclepias tuberosa
#> 93 2003 25 32 N1P0 N2P0 asclepias tuberosa
#> 94 2003 21 25 N2P3 N1P0 aster ericoides
#> 95 2003 21 32 N2P3 N2P0 aster ericoides
#> 96 2003 25 32 N1P0 N2P0 aster ericoides
#> 98 2003 21 32 N2P3 N2P0 aster oblongifolius
#> 99 2003 25 32 N1P0 N2P0 aster oblongifolius
#> 100 2003 21 25 N2P3 N1P0 bouteloua curtipendula
#> 101 2003 21 32 N2P3 N2P0 bouteloua curtipendula
#> 102 2003 25 32 N1P0 N2P0 bouteloua curtipendula
#> 103 2003 21 25 N2P3 N1P0 carex heliophila
#> 104 2003 21 32 N2P3 N2P0 carex heliophila
#> 105 2003 25 32 N1P0 N2P0 carex heliophila
#> 106 2003 21 25 N2P3 N1P0 carex meadii
#> 107 2003 21 32 N2P3 N2P0 carex meadii
#> 108 2003 25 32 N1P0 N2P0 carex meadii
#> 109 2003 21 25 N2P3 N1P0 dalea candida
#> 110 2003 21 32 N2P3 N2P0 dalea candida
#> 111 2003 25 32 N1P0 N2P0 dalea candida
#> 112 2003 21 25 N2P3 N1P0 dalea purpurea
#> 114 2003 25 32 N1P0 N2P0 dalea purpurea
#> 116 2003 21 32 N2P3 N2P0 delphinium virescens
#> 117 2003 25 32 N1P0 N2P0 delphinium virescens
#> 118 2003 21 25 N2P3 N1P0 dichanthelium oligosanthes
#> 119 2003 21 32 N2P3 N2P0 dichanthelium oligosanthes
#> 120 2003 25 32 N1P0 N2P0 dichanthelium oligosanthes
#> 121 2003 21 25 N2P3 N1P0 eragrostis spectabilis
#> 122 2003 21 32 N2P3 N2P0 eragrostis spectabilis
#> 123 2003 25 32 N1P0 N2P0 eragrostis spectabilis
#> 125 2003 21 32 N2P3 N2P0 euphorbia serpens
#> 126 2003 25 32 N1P0 N2P0 euphorbia serpens
#> 127 2003 21 25 N2P3 N1P0 kuhnia eupatorioides
#> 128 2003 21 32 N2P3 N2P0 kuhnia eupatorioides
#> 129 2003 25 32 N1P0 N2P0 kuhnia eupatorioides
#> 131 2003 21 32 N2P3 N2P0 panicum capillare
#> 132 2003 25 32 N1P0 N2P0 panicum capillare
#> 133 2003 21 25 N2P3 N1P0 physalis pumila
#> 134 2003 21 32 N2P3 N2P0 physalis pumila
#> 135 2003 25 32 N1P0 N2P0 physalis pumila
#> 136 2003 21 25 N2P3 N1P0 poa pratensis
#> 137 2003 21 32 N2P3 N2P0 poa pratensis
#> 138 2003 25 32 N1P0 N2P0 poa pratensis
#> 140 2003 21 32 N2P3 N2P0 ruellia humilis
#> 141 2003 25 32 N1P0 N2P0 ruellia humilis
#> 143 2003 21 32 N2P3 N2P0 senecio plattensis
#> 144 2003 25 32 N1P0 N2P0 senecio plattensis
#> 145 2003 21 25 N2P3 N1P0 solidago canadensis
#> 146 2003 21 32 N2P3 N2P0 solidago canadensis
#> 148 2003 21 25 N2P3 N1P0 solidago missouriensis
#> 149 2003 21 32 N2P3 N2P0 solidago missouriensis
#> 150 2003 25 32 N1P0 N2P0 solidago missouriensis
#> 151 2003 21 25 N2P3 N1P0 sorghastrum nutans
#> 152 2003 21 32 N2P3 N2P0 sorghastrum nutans
#> 153 2003 25 32 N1P0 N2P0 sorghastrum nutans
#> 154 2003 21 25 N2P3 N1P0 sporobolus asper
#> 155 2003 21 32 N2P3 N2P0 sporobolus asper
#> 156 2003 25 32 N1P0 N2P0 sporobolus asper
#> 157 2003 21 25 N2P3 N1P0 viola pedatifida
#> 158 2003 21 32 N2P3 N2P0 viola pedatifida
#> 160 2003 21 25 N2P3 N1P0 viola rafinesquii
#> 162 2003 25 32 N1P0 N2P0 viola rafinesquii
#> difference
#> 2 0.003802281
#> 3 0.003802281
#> 4 -0.048913541
#> 5 -0.028222995
#> 6 0.020690546
#> 7 0.365617286
#> 8 0.162788583
#> 9 -0.202828703
#> 10 -0.348540720
#> 11 -0.296753809
#> 12 0.051786911
#> 13 -0.004784689
#> 14 -0.002249835
#> 15 0.002534854
#> 16 0.008462093
#> 17 0.050569736
#> 18 0.042107643
#> 19 -0.023425674
#> 20 0.050399937
#> 21 0.073825611
#> 22 -0.004784689
#> 23 -0.004784689
#> 25 -0.036164528
#> 26 -0.009169138
#> 27 0.026995390
#> 28 0.003139000
#> 29 -0.008429300
#> 30 -0.011568300
#> 31 0.004774531
#> 32 -0.001594896
#> 33 -0.006369427
#> 35 0.006337136
#> 36 0.006337136
#> 37 -0.001086967
#> 38 0.011934434
#> 39 0.013021401
#> 40 -0.014892471
#> 41 -0.015336475
#> 42 -0.000444004
#> 43 0.006369427
#> 45 -0.006369427
#> 46 0.006369427
#> 47 0.006337136
#> 48 -0.000032291
#> 49 0.001056492
#> 50 0.000612488
#> 51 -0.000444004
#> 52 0.002651389
#> 53 -0.001594896
#> 54 -0.004246285
#> 55 0.072166519
#> 56 0.001182527
#> 57 -0.070983992
#> 58 -0.001594896
#> 59 0.006009667
#> 60 0.007604563
#> 61 0.002123142
#> 62 0.001267427
#> 63 -0.000855715
#> 64 -0.001594896
#> 65 -0.001594896
#> 67 0.031847134
#> 68 0.012674271
#> 69 -0.019172863
#> 70 -0.018793364
#> 71 0.029199338
#> 72 0.047992702
#> 74 0.026615970
#> 75 0.026615970
#> 77 0.002824859
#> 78 0.002824859
#> 79 -0.077244259
#> 80 -0.048995671
#> 81 0.028248588
#> 82 -0.002343621
#> 83 0.220504110
#> 84 0.222847731
#> 85 -0.091185455
#> 86 -0.283342965
#> 87 -0.192157510
#> 88 -0.002087683
#> 89 -0.002087683
#> 92 0.011299435
#> 93 0.011299435
#> 94 0.013694186
#> 95 0.038934692
#> 96 0.025240506
#> 98 0.015065913
#> 99 0.015065913
#> 100 -0.013087077
#> 101 0.000043248
#> 102 0.013130325
#> 103 0.003563792
#> 104 0.038606403
#> 105 0.035042611
#> 106 0.005242271
#> 107 0.050766860
#> 108 0.045524589
#> 109 0.026422652
#> 110 -0.002087683
#> 111 -0.028510335
#> 112 0.001425517
#> 114 -0.001425517
#> 116 0.003766478
#> 117 0.003766478
#> 118 -0.045064483
#> 119 -0.012644044
#> 120 0.032420439
#> 121 -0.006621660
#> 122 -0.020876827
#> 123 -0.014255167
#> 125 0.001883239
#> 126 0.001883239
#> 127 0.009978617
#> 128 0.009416196
#> 129 -0.000562421
#> 131 0.005649718
#> 132 0.005649718
#> 133 0.000763350
#> 134 -0.002087683
#> 135 -0.002851033
#> 136 -0.014613779
#> 137 -0.008964061
#> 138 0.005649718
#> 140 0.009416196
#> 141 0.009416196
#> 143 0.001883239
#> 144 0.001883239
#> 145 -0.002087683
#> 146 -0.002087683
#> 148 0.034212402
#> 149 0.014124294
#> 150 -0.020088108
#> 151 0.161782759
#> 152 -0.053784367
#> 153 -0.215567126
#> 154 -0.002087683
#> 155 0.014861470
#> 156 0.016949153
#> 157 -0.002087683
#> 158 -0.002087683
#> 160 0.001425517
#> 162 -0.001425517
# All pairwise replicates without treatment
df <- subset(pplots, year < 2004 & plot %in% c(21, 25, 32))
abundance_difference(df = df,
species.var = "species",
abundance.var = "relative_cover",
replicate.var = "plot",
time.var = "year")
#> year plot plot2 species difference
#> 2 2002 21 32 ambrosia psilostachya 0.003802281
#> 3 2002 25 32 ambrosia psilostachya 0.003802281
#> 4 2002 21 25 amorpha canescens -0.048913541
#> 5 2002 21 32 amorpha canescens -0.028222995
#> 6 2002 25 32 amorpha canescens 0.020690546
#> 7 2002 21 25 andropogon gerardii 0.365617286
#> 8 2002 21 32 andropogon gerardii 0.162788583
#> 9 2002 25 32 andropogon gerardii -0.202828703
#> 10 2002 21 25 andropogon scoparius -0.348540720
#> 11 2002 21 32 andropogon scoparius -0.296753809
#> 12 2002 25 32 andropogon scoparius 0.051786911
#> 13 2002 21 25 antennaria neglecta -0.004784689
#> 14 2002 21 32 antennaria neglecta -0.002249835
#> 15 2002 25 32 antennaria neglecta 0.002534854
#> 16 2002 21 25 aster ericoides 0.008462093
#> 17 2002 21 32 aster ericoides 0.050569736
#> 18 2002 25 32 aster ericoides 0.042107643
#> 19 2002 21 25 bouteloua curtipendula -0.023425674
#> 20 2002 21 32 bouteloua curtipendula 0.050399937
#> 21 2002 25 32 bouteloua curtipendula 0.073825611
#> 22 2002 21 25 carex brevior -0.004784689
#> 23 2002 21 32 carex brevior -0.004784689
#> 25 2002 21 25 carex heliophila -0.036164528
#> 26 2002 21 32 carex heliophila -0.009169138
#> 27 2002 25 32 carex heliophila 0.026995390
#> 28 2002 21 25 carex meadii 0.003139000
#> 29 2002 21 32 carex meadii -0.008429300
#> 30 2002 25 32 carex meadii -0.011568300
#> 31 2002 21 25 dalea candida 0.004774531
#> 32 2002 21 32 dalea candida -0.001594896
#> 33 2002 25 32 dalea candida -0.006369427
#> 35 2002 21 32 dichanthelium acuminatum 0.006337136
#> 36 2002 25 32 dichanthelium acuminatum 0.006337136
#> 37 2002 21 25 dichanthelium oligosanthes -0.001086967
#> 38 2002 21 32 dichanthelium oligosanthes 0.011934434
#> 39 2002 25 32 dichanthelium oligosanthes 0.013021401
#> 40 2002 21 25 eragrostis spectabilis -0.014892471
#> 41 2002 21 32 eragrostis spectabilis -0.015336475
#> 42 2002 25 32 eragrostis spectabilis -0.000444004
#> 43 2002 21 25 koeleria pyramidata 0.006369427
#> 45 2002 25 32 koeleria pyramidata -0.006369427
#> 46 2002 21 25 kuhnia eupatorioides 0.006369427
#> 47 2002 21 32 kuhnia eupatorioides 0.006337136
#> 48 2002 25 32 kuhnia eupatorioides -0.000032291
#> 49 2002 21 25 linum sulcatum 0.001056492
#> 50 2002 21 32 linum sulcatum 0.000612488
#> 51 2002 25 32 linum sulcatum -0.000444004
#> 52 2002 21 25 physalis pumila 0.002651389
#> 53 2002 21 32 physalis pumila -0.001594896
#> 54 2002 25 32 physalis pumila -0.004246285
#> 55 2002 21 25 poa pratensis 0.072166519
#> 56 2002 21 32 poa pratensis 0.001182527
#> 57 2002 25 32 poa pratensis -0.070983992
#> 58 2002 21 25 ruellia humilis -0.001594896
#> 59 2002 21 32 ruellia humilis 0.006009667
#> 60 2002 25 32 ruellia humilis 0.007604563
#> 61 2002 21 25 senecio plattensis 0.002123142
#> 62 2002 21 32 senecio plattensis 0.001267427
#> 63 2002 25 32 senecio plattensis -0.000855715
#> 64 2002 21 25 solidago canadensis -0.001594896
#> 65 2002 21 32 solidago canadensis -0.001594896
#> 67 2002 21 25 solidago missouriensis 0.031847134
#> 68 2002 21 32 solidago missouriensis 0.012674271
#> 69 2002 25 32 solidago missouriensis -0.019172863
#> 70 2002 21 25 sorghastrum nutans -0.018793364
#> 71 2002 21 32 sorghastrum nutans 0.029199338
#> 72 2002 25 32 sorghastrum nutans 0.047992702
#> 74 2002 21 32 sporobolus asper 0.026615970
#> 75 2002 25 32 sporobolus asper 0.026615970
#> 77 2003 21 32 ambrosia psilostachya 0.002824859
#> 78 2003 25 32 ambrosia psilostachya 0.002824859
#> 79 2003 21 25 amorpha canescens -0.077244259
#> 80 2003 21 32 amorpha canescens -0.048995671
#> 81 2003 25 32 amorpha canescens 0.028248588
#> 82 2003 21 25 andropogon gerardii -0.002343621
#> 83 2003 21 32 andropogon gerardii 0.220504110
#> 84 2003 25 32 andropogon gerardii 0.222847731
#> 85 2003 21 25 andropogon scoparius -0.091185455
#> 86 2003 21 32 andropogon scoparius -0.283342965
#> 87 2003 25 32 andropogon scoparius -0.192157510
#> 88 2003 21 25 antennaria neglecta -0.002087683
#> 89 2003 21 32 antennaria neglecta -0.002087683
#> 92 2003 21 32 asclepias tuberosa 0.011299435
#> 93 2003 25 32 asclepias tuberosa 0.011299435
#> 94 2003 21 25 aster ericoides 0.013694186
#> 95 2003 21 32 aster ericoides 0.038934692
#> 96 2003 25 32 aster ericoides 0.025240506
#> 98 2003 21 32 aster oblongifolius 0.015065913
#> 99 2003 25 32 aster oblongifolius 0.015065913
#> 100 2003 21 25 bouteloua curtipendula -0.013087077
#> 101 2003 21 32 bouteloua curtipendula 0.000043248
#> 102 2003 25 32 bouteloua curtipendula 0.013130325
#> 103 2003 21 25 carex heliophila 0.003563792
#> 104 2003 21 32 carex heliophila 0.038606403
#> 105 2003 25 32 carex heliophila 0.035042611
#> 106 2003 21 25 carex meadii 0.005242271
#> 107 2003 21 32 carex meadii 0.050766860
#> 108 2003 25 32 carex meadii 0.045524589
#> 109 2003 21 25 dalea candida 0.026422652
#> 110 2003 21 32 dalea candida -0.002087683
#> 111 2003 25 32 dalea candida -0.028510335
#> 112 2003 21 25 dalea purpurea 0.001425517
#> 114 2003 25 32 dalea purpurea -0.001425517
#> 116 2003 21 32 delphinium virescens 0.003766478
#> 117 2003 25 32 delphinium virescens 0.003766478
#> 118 2003 21 25 dichanthelium oligosanthes -0.045064483
#> 119 2003 21 32 dichanthelium oligosanthes -0.012644044
#> 120 2003 25 32 dichanthelium oligosanthes 0.032420439
#> 121 2003 21 25 eragrostis spectabilis -0.006621660
#> 122 2003 21 32 eragrostis spectabilis -0.020876827
#> 123 2003 25 32 eragrostis spectabilis -0.014255167
#> 125 2003 21 32 euphorbia serpens 0.001883239
#> 126 2003 25 32 euphorbia serpens 0.001883239
#> 127 2003 21 25 kuhnia eupatorioides 0.009978617
#> 128 2003 21 32 kuhnia eupatorioides 0.009416196
#> 129 2003 25 32 kuhnia eupatorioides -0.000562421
#> 131 2003 21 32 panicum capillare 0.005649718
#> 132 2003 25 32 panicum capillare 0.005649718
#> 133 2003 21 25 physalis pumila 0.000763350
#> 134 2003 21 32 physalis pumila -0.002087683
#> 135 2003 25 32 physalis pumila -0.002851033
#> 136 2003 21 25 poa pratensis -0.014613779
#> 137 2003 21 32 poa pratensis -0.008964061
#> 138 2003 25 32 poa pratensis 0.005649718
#> 140 2003 21 32 ruellia humilis 0.009416196
#> 141 2003 25 32 ruellia humilis 0.009416196
#> 143 2003 21 32 senecio plattensis 0.001883239
#> 144 2003 25 32 senecio plattensis 0.001883239
#> 145 2003 21 25 solidago canadensis -0.002087683
#> 146 2003 21 32 solidago canadensis -0.002087683
#> 148 2003 21 25 solidago missouriensis 0.034212402
#> 149 2003 21 32 solidago missouriensis 0.014124294
#> 150 2003 25 32 solidago missouriensis -0.020088108
#> 151 2003 21 25 sorghastrum nutans 0.161782759
#> 152 2003 21 32 sorghastrum nutans -0.053784367
#> 153 2003 25 32 sorghastrum nutans -0.215567126
#> 154 2003 21 25 sporobolus asper -0.002087683
#> 155 2003 21 32 sporobolus asper 0.014861470
#> 156 2003 25 32 sporobolus asper 0.016949153
#> 157 2003 21 25 viola pedatifida -0.002087683
#> 158 2003 21 32 viola pedatifida -0.002087683
#> 160 2003 21 25 viola rafinesquii 0.001425517
#> 162 2003 25 32 viola rafinesquii -0.001425517