What object class in adonis R is required as input?-CodePudding

This question might sound obvious - but does adonis in R require to have a distance matrix as input data or does it transform it within the function? I have two metric variables (isotope data, all negative but I could use its absolute values instead)? I cannot see this within the adonis code if I view it.

This are my 2 VAR

structure(list(`CSIA_fish_EFA_eyes[1:5, 8]` = structure(c(3L, 
3L, 3L, 3L, 3L), .Label = c("epilithon", "inverts", "salmonid.eyes"
), class = "factor"), ALA.d13C = c(48, 43, 49, 47, 52), LIN.d13C = c(38, 
36, 42, 40, 44)), class = "data.frame", row.names = c(84L, 88L, 
92L, 96L, 104L))

I do not have a community matrix but I want to check if two groups differ in both of these parameters.

CodePudding user response：

It takes a formula, data.frame, and provides some other options. You will have to pick your preferred method.

I just changed some of the names in your data.frame. From a substantive perspective, if you are interested in using the absolute value, you can consider Manhattan distance.


df <- structure(list(eyes = structure(c(3L, 
                                              3L, 3L, 3L, 3L), .Label = c("epilithon", "inverts", "salmonid.eyes"
                                              ), class = "factor"), Ad13C = c(48, 43, 49, 47, 52), Ld13C = c(38, 
                                              36, 42, 40, 44)), class = "data.frame", row.names = c(84L, 88L,                                                                                                                                                                                 92L, 96L, 104L))

m1 <- vegan::adonis(data = df, Ad13C ~ Ld13C, method = "bray" ) # see ?vegan::vegdist

m1


# Call:
#   vegan::adonis(formula = Ad13C ~ Ld13C, data = df) 
# 
# Permutation: free
# Number of permutations: 119
# 
# Terms added sequentially (first to last)
# 
# Df SumsOfSqs   MeanSqs F.Model      R2 Pr(>F)  
# Ld13C      1 0.0039911 0.0039911   15.15 0.83472   0.05 *
#   Residuals  3 0.0007903 0.0002634         0.16528         
# Total      4 0.0047814                   1.00000         
# ---
#   Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
m2 <- vegan::adonis(data = df, Ad13C ~ Ld13C, method = "manhattan" )
m2
# Call:
#   vegan::adonis(formula = Ad13C ~ Ld13C, data = df, method = "manhattan") 
# 
# Permutation: free
# Number of permutations: 119
# 
# Terms added sequentially (first to last)
# 
# Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)  
# Ld13C      1      36.1  36.100  16.164 0.84346   0.05 *
#   Residuals  3       6.7   2.233         0.15654         
# Total      4      42.8                 1.00000         
# ---
#   Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Or, with a matrix as a response

df$oth <- rnorm(length(df$Ad13C), 10*df$Ld13C, 10) 

m3 <- vegan::adonis(data = df, df[,c("Ad13C","oth")] ~ Ld13C, method = "bray" ) # see ?vegan::vegdist

m3