我发现，可以通过corSymm提供的一般相关结构，将正定相关矩阵传递给nlme函数gls。

# convert your variance covariance matrix into a correlation matrix
CM <- cov2cor(vcv_matrix)

# if your correlation matrix contains zeros, as mine did, you need to convert it to a positive-definite matrix that substitutes very small numbers for those zeros
CM <- nearPD(CM)$mat

# convert into a corStruct object using general correlation structure provided by corSymm
C <- corSymm(CM[lower.tri(CM)], fixed = T)

# correlation structure can now be included in a gls model
gls(y ~ x, correlation = C, method = "ML")