stimodels | R Documentation |
Function stimodels
performs two-way ANOVA to test space-time
interaction (STI) without replicates using one among a set of possible models
described in Legendre et al. (2010).
Function quicksti
allows performing space-time ANOVA in a simplified
way. In many models, degrees of freedom are saved by coding space and/or
time parsimoniously using distance-based Moran Eigenvector Maps (dbMEM;
Borcard & Legendre 2002; Dray et al. 2006).
stimodels(
Y,
S,
Ti,
model = "5",
nperm = 999,
nS = -1,
nT = -1,
Sfixed = TRUE,
Tfixed = TRUE,
COD.S = NULL,
COD.T = NULL,
save.X = FALSE,
print.res = TRUE
)
quicksti(
Y,
S,
Ti,
nperm = 999,
alpha = 0.05,
COD.S = NULL,
COD.T = NULL,
save.X = FALSE,
print.res = TRUE
)
Y |
Site-by-species response data table. Assumes row blocks corresponding to times, i.e. within each block all sites are provided, always in the same order. |
S |
Number of spatial points (when they are aligned on a transect or a time series and equispaced) or a matrix of spatial coordinates (when the sites are on a two-dimensional surface or on a line but very irregularly spaced). |
Ti |
Number of time campaigns (when equispaced) or a matrix (a vector) of temporal coordinates (when the time campaigns are very irregularly spaced). |
model |
Linear space-time model to be used (can be either "2", "3a", "3b", "4", "5", "6a", "6b", or "7"). |
nperm |
Number of permutations in the significance tests. |
nS |
Number of space dbMEMs to use (by default, -1, all dbMEMs with positive autocorrelation are used). |
nT |
Number of time dbMEMs to use (by default, -1, all dbMEMs with positive autocorrelation are used). |
Sfixed |
Logical: is factor Space fixed, or not (if FALSE, it is considered a random factor). |
Tfixed |
Logical: is factor Time fixed, or not (if FALSE, it is considered a random factor). |
COD.S |
Spatial coding functions to be used instead of dbMEM. The
number of columns must be lower than |
COD.T |
Temporal coding functions to be used instead of dbMEM. The
number of columns must be lower than |
save.X |
If TRUE, the explanatory bloc-diagonal matrix constructed for model 6a or 6b is saved in the output list with the label X. |
print.res |
If TRUE, displays the results and additional information onscreen (recommended). If FALSE, only R2, F and P are printed onscreen. |
alpha |
In |
The 'stimodels' and 'quicksti' functions should only be used (1) when each site has been sampled during each survey, with no missing data, and (2) when there are no replicate observations of the space-time points. When there is replication, use a regular permutational Manova function such as adonis2.
When the sites form a one-dimensional spatial transect, or a meandering line such as the course of a river, with regular sampling intervals, and the time series has fairly equal time intervals, one can use the S and Ti arguments to indicate the number of sites in space and the number of surveys along time. The order of the sites in each temporal block of the input data file will be taken to correspond to the spatial positions of the sites along the transect (from 1 to S), and the order of the time blocks in the data file will be taken to indicate the temporal order of the surveys (from 1 to Ti). The function will then compute dbMEM eigenfunctions corresponding to the spatial and temporal positions of the data rows in the input data file as if they were on straight lines.
When the sites do not form a regular, one-dimensional spatial transect, one must provide a file of spatial coordinates of the sites to argument S. Similarly, when the time series has unequal time intervals, one must provide a file of temporal coordinates of the surveys to argument Ti.
Alternatively, one can use arguments COD.S or COD.T to provide a matrix of Helmert contrasts to be used in the analysis in place of dbMEM eigenfunctions. One can do that, for example, when there are only a few surveys along time and it would not be useful to represent these few surveys by dbMEM eigenfunctions. That matrix can have the class "matrix" or "numeric"; they both work in functions stimodels and quicksti. Arguments COD.S and COD.T can also be used to provide matrices containing other types of eigenfunctions, for example AEM eigenfunctions, to be used instead of dbMEM matrices computed by stimodels or quicksti. However, do not code both the space and time factors as Helmert contrasts; that would not leave residual degrees of freedom for the test of the interaction.
In stimodels
, tests for space-time interaction and space or time main
effects are conducted using one of the following models:
Model 2 - Space and Time are coded using Helmert contrasts for the main effects. The interaction cannot be tested.
Model 3a - Space is coded using dbMEM variables whereas Time is coded using Helmert contrasts.
Model 3b - Space is coded using Helmert contrasts whereas Time is coded using dbMEM variables.
Model 4 - Both Space and Time are coded using dbMEM variables; the interaction is coded as the Hadamard (or elementwise) product of the space-coding by the time-coding dbMEMs.
Model 5 - Space and Time are coded using Helmert contrasts for the main factor effects; the interaction is coded as the Hadamard product of the space-coding by the time-coding dbMEM variables.
Model 6a - Nested model. Testing for the existence of spatial structure (common or separate) using dbMEM (or other) variables coding for Space.
Model 6b - Nested model. Testing for the existence of temporal structure (common or separate) using dbMEM (or other) variables coding for Time.
Model 7 - Space and Time are coded using dbMEM variables for the main factor effects, but they are coded using Helmert contrasts for the interaction term (not recommended).
With Models 2, 6a and 6b, the interaction test is not available.
When using quicksti
, space-time interaction is first tested using
Model 5. Depending on the outcome of this test, the main factors are tested
using different strategies. If the interaction is not significant then the
test of main factors is also done following Model 5. If the interaction is
significant, then a nested model (6a) is used to know whether separate
spatial structures exist and another (6b) to know whether separate temporal
structures exist. In quicksti
function space and time are always
considered fixed factors (F ratios are constructed using residual MS in the
denominator).
For the interaction the permutations are unrestricted, whereas for the main
factors the permutations are restricted within time blocks (for the test of
factor Space) or space blocks (for the test of factor Time). By default, the
function computes dbMEM for space and time coding, but other space and/or
time descriptors can be provided by the user, through COD.S
and
COD.T
.
A list containing the following results:
testS
An object with the result of the space effect test, including
the mean squares for the F numerator (MS.num
), the mean squares for
the F denominator (MS.den
), the proportion of explained variance
(R2
), the adjusted proportion of explained variance (R2.adj
),
the F statistics (F
) and its p-value computed from a permutation test
(Prob
).
testT
An object with the result of the time effect test, like testS
.
teststi
An object with the result of the space-time interaction test,
like testS
.
X.matrix
The bloc-diagonal explanatory matrix used in test of model 6a or 6b
Pierre Legendre pierre.legendre@umontreal.ca, Miquel De Caceres and Daniel Borcard
Borcard, D. & P. Legendre. 2002. All-scale spatial analysis of ecological data by means of principal coordinates of neighbour matrices. Ecological Modelling 153: 51-68. https://doi.org/10.1016/S0304-3800(01)00501-4.
Dray, S., P. Legendre & P. R. Peres-Neto. 2006. Spatial modelling: a comprehensive framework for principal coordinate analysis of neighbour matrices (PCNM). Ecological Modelling 196: 483-493. https://doi.org/10.1016/j.ecolmodel.2006.02.015.
Legendre, P. & D. Borcard. 2018. Box-Cox-chord transformations for community composition data prior to beta diversity analysis. Ecography 41: 1820–1824. https://doi.org/10.1111/ecog.03498.
Legendre, P., M. De Caceres & D. Borcard. 2010. Community surveys through space and time: testing the space-time interaction in the absence of replication. Ecology 91: 262-272. https://doi.org/10.1890/09-0199.1.
trichoptera
# The "trichoptera" data set contains the abundances of 56 Trichoptera species captured
# during 100 consecutive days in 22 emergence traps along a stream. The 22 traps
# (sites) form a regular transect, with geographic positions 1 to 22. The original
# daily data collected at each site were pooled into 10 survey periods for the study
# of Legendre et al. (2010) in order to reduce the very high proportion of zeros in the
# original data matrix. Order of the observations in the data set: the 22 traps (sites)
# are nested within the survey weeks, as required by the 'stimodels' and 'quicksti'
# functions.
data(trichoptera)
# log-transform the species data, excluding the Site and Date colums
trich.log <- log1p(trichoptera[,-c(1,2)])
# A log-chord transformation (Legendre & Borcard 2018) would also be appropriate for
# these data: trich.tr <- decostand(log1p(trichoptera[,-c(1,2)]), method="norm")
# Example 1. Compute the space-time interaction test using model 5. By specifying the
# number of sites (traps), the sofware assumes that they form a regular transect with
# equispaced sites. Important note to users – In real analyses, use more than 99
# permutations.
out.1 <- stimodels(trich.log, S=22, Ti=10, model="5", nperm=99)
# The interaction is significant. Because of that, test results for the main effects,
# space and time, obtained with model 5, cannot be interpreted. Tests of spatial
# variation can be done for individual times using simple RDA against dbMEM.S
# variables. Likewise, tests of temporal variation can be done for individual sites
# using simple RDA against dbMEM.T variables. A global test of the hypothesis that none
# of the times shows a significant spatial structure can be done with model 6a. For a
# global test of temporal structure at the various sites, use model 6b.
# Code not run during CRAN software tests
# Example 2. Run space-time analysis with global tests for main effects after testing
# the interaction, which is significant in this example
out.2 <- quicksti(trich.log, S=22, Ti=10, nperm=999)
# Since the interaction is significant, function 'quicksti' will carry out the
# tests of existence of a spatial (at least in one of the time periods) and temporal
# (at least at one of the sites) structures using models 6a and 6b, respectively.
# 3. Run space-time analysis for two time blocks only, i.e. time periods 6 and 7,
# then time periods 8 and 9.
# Example 3.1. Time periods 6 and 7. The interaction is not significant. In that case,
# function 'quicksti' carries out the tests of the main effects using model 5.
out.3 <- quicksti(trich.log[111:154,], S=22, Ti=2, nperm=999)
# Example 3.2. Time periods 8 and 9. The interaction is significant. In that case,
# 'quicksti' carries out the tests of the spatial effects using model 6a. Model 6b
# cannot proceed with the test of the temporal effect because Ti=2. An explanation is
# printed in the output list.
out.4 <- quicksti(trich.log[155:198,], S=22, Ti=2, nperm=999)
# 4. Illustrations of the use of 'COD.S' and 'COD.T' in STI analysis
# The following examples illustrate how to use other representations of the spatial or
# temporal relationships among observations, through arguments 'COD.S' and
# 'COD.T' of functions 'stimodels' and 'quicksti'. The trichoptera data
# are used again.
# Example 4.1. Explicitly compute dbMEMs for the spatial structure along the regular
# transect, using function 'dbmem' of adespatial, and provide it to 'stimodels'
# or 'quicksti' as argument 'COD.S'. The dbMEMs must first be computed on the
# transect, then repeated (Ti-1) times to provide Ti repeats in total.
dbMEM.S1 <- as.matrix(dbmem(1:22))
dbMEM.S10 <- dbMEM.S1
for(j in 2:10) dbMEM.S10 <- rbind(dbMEM.S10, dbMEM.S1)
out.5 <- stimodels(trich.log, S=22, Ti=10, model="5", COD.S=dbMEM.S10, nperm=999)
# Results should be identical to those in output file out.1 of Example 1, except for
# P-values which can vary slightly.
# Example 4.2. Assume now that the sampling sites have irregular positions, as
# described by the following matrix of geographic coordinates 'xy.trich'. Provide
# this matrix to argument S of 'stimodels'
xy.trich = matrix(c(1:5,11:15,21:25,31:35,41,42,rep(c(1,2),11)),22,2)
plot(xy.trich, asp=1) # Plot a quick map of the site positions
out.6 <- stimodels(trich.log, S=xy.trich, Ti=10, model="5", nperm=999)
# Example 4.3. Compute a matrix of dbMEMs for the sites. The coding matrix provided to
# argument 'COD.S' must contain repeated dbMEM.S codes because that matrix must have
# the same number of rows as matrix Y. Construct coding matrix dbMEM.S10 containing the
# dbMEM.S codes repeated 10 times.
dbMEM.S1 <- as.matrix(dbmem(xy.trich))
dbMEM.S10 = dbMEM.S1
for(i in 1:9) dbMEM.S10 <- rbind(dbMEM.S10, dbMEM.S1)
out.7 <- stimodels(trich.log, S=22, Ti=10, model="5", COD.S=dbMEM.S10, nperm=999)
# Compare the results with those obtained in the output file out6, example 4.2.
# Careful: If an analysis requires a dbMEM coding matrix for 'COD.T', the dbMEM.T
# codes must follow the required data arrangement: sites must be nested within times.
# The following function can be used to construct a dbMEM.T matrix.
MEM.T <- function(s, tt, coord.T=NULL)
# Documentation of function MEM.T –
# Generate a matrix of temporal eigenfunctions for input into stimodels,
# with sites nested within times.
# Arguments –
# s : number of space points (sites)
# tt : number of time points
# coord.T : optional matrix or vector giving the time point coordinates
{
n <- s*tt
if(is.null(coord.T)) coord.T <- as.matrix(1:tt)
MEM.TT <- as.matrix(dbmem(coord.T))
dbMEM.T <- matrix(0,n,ncol(MEM.TT)) # Empty matrix to house dbMEM.T
beg.x <- seq(1, n, by=s)
for(i in 1:tt) { # Fill tt blocks of rows with identical MEM.TT values
for(j in 1:s) dbMEM.T[(beg.x[i]+j-1),] <- MEM.TT[i,]
}
dbMEM.T
}
# Example of use of function MEM.T
dbMEM.T <- MEM.T(s=6, tt=5)
# Check the size of the dbMEM.T output matrix
dim(dbMEM.T)
# End of code not run during CRAN software tests
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