Use RE_cor to generate the random effects correlation matrix, under the
assumption of common heterogeneity variance (i.e. all within-study
correlations are 0.5). Use which_RE to return a vector of IDs for the RE
deltas (0 means no RE delta on this arm).
Arguments
- study
A vector of study IDs (integer, character, or factor)
- trt
A factor vector of treatment codes (or coercible as such), with first level indicating the reference treatment
- contrast
A logical vector, of the same length as
studyandtrt, indicating whether the corresponding data are in contrast rather than arm format.- type
Character string, whether to generate RE structure under the "reference treatment" parameterisation, or the "baseline shift" parameterisation.
Value
For RE_cor(), a correlation matrix of dimension equal to the number
of random effects deltas (excluding those that are set equal to zero).
For which_RE(), an integer vector of IDs indexing the rows and columns of
the correlation matrix returned by RE_cor().
Examples
RE_cor(smoking$studyn, smoking$trtn, contrast = rep(FALSE, nrow(smoking)))
#> Coerced `trt` to factor.
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
#> [1,] 1.0 0.5 0.0 0.0 0.0 0 0 0 0 0 0 0 0
#> [2,] 0.5 1.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0
#> [3,] 0.0 0.0 1.0 0.5 0.5 0 0 0 0 0 0 0 0
#> [4,] 0.0 0.0 0.5 1.0 0.5 0 0 0 0 0 0 0 0
#> [5,] 0.0 0.0 0.5 0.5 1.0 0 0 0 0 0 0 0 0
#> [6,] 0.0 0.0 0.0 0.0 0.0 1 0 0 0 0 0 0 0
#> [7,] 0.0 0.0 0.0 0.0 0.0 0 1 0 0 0 0 0 0
#> [8,] 0.0 0.0 0.0 0.0 0.0 0 0 1 0 0 0 0 0
#> [9,] 0.0 0.0 0.0 0.0 0.0 0 0 0 1 0 0 0 0
#> [10,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 1 0 0 0
#> [11,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 1 0 0
#> [12,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 1 0
#> [13,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 1
#> [14,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0
#> [15,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0
#> [16,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0
#> [17,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0
#> [18,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0
#> [19,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0
#> [20,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0
#> [21,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0
#> [22,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0
#> [23,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0
#> [24,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0
#> [25,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0
#> [26,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0
#> [27,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0
#> [28,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0
#> [29,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0
#> [30,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0
#> [31,] 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0
#> [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
#> [1,] 0 0 0 0 0 0 0 0 0 0 0.0 0.0
#> [2,] 0 0 0 0 0 0 0 0 0 0 0.0 0.0
#> [3,] 0 0 0 0 0 0 0 0 0 0 0.0 0.0
#> [4,] 0 0 0 0 0 0 0 0 0 0 0.0 0.0
#> [5,] 0 0 0 0 0 0 0 0 0 0 0.0 0.0
#> [6,] 0 0 0 0 0 0 0 0 0 0 0.0 0.0
#> [7,] 0 0 0 0 0 0 0 0 0 0 0.0 0.0
#> [8,] 0 0 0 0 0 0 0 0 0 0 0.0 0.0
#> [9,] 0 0 0 0 0 0 0 0 0 0 0.0 0.0
#> [10,] 0 0 0 0 0 0 0 0 0 0 0.0 0.0
#> [11,] 0 0 0 0 0 0 0 0 0 0 0.0 0.0
#> [12,] 0 0 0 0 0 0 0 0 0 0 0.0 0.0
#> [13,] 0 0 0 0 0 0 0 0 0 0 0.0 0.0
#> [14,] 1 0 0 0 0 0 0 0 0 0 0.0 0.0
#> [15,] 0 1 0 0 0 0 0 0 0 0 0.0 0.0
#> [16,] 0 0 1 0 0 0 0 0 0 0 0.0 0.0
#> [17,] 0 0 0 1 0 0 0 0 0 0 0.0 0.0
#> [18,] 0 0 0 0 1 0 0 0 0 0 0.0 0.0
#> [19,] 0 0 0 0 0 1 0 0 0 0 0.0 0.0
#> [20,] 0 0 0 0 0 0 1 0 0 0 0.0 0.0
#> [21,] 0 0 0 0 0 0 0 1 0 0 0.0 0.0
#> [22,] 0 0 0 0 0 0 0 0 1 0 0.0 0.0
#> [23,] 0 0 0 0 0 0 0 0 0 1 0.0 0.0
#> [24,] 0 0 0 0 0 0 0 0 0 0 1.0 0.5
#> [25,] 0 0 0 0 0 0 0 0 0 0 0.5 1.0
#> [26,] 0 0 0 0 0 0 0 0 0 0 0.0 0.0
#> [27,] 0 0 0 0 0 0 0 0 0 0 0.0 0.0
#> [28,] 0 0 0 0 0 0 0 0 0 0 0.0 0.0
#> [29,] 0 0 0 0 0 0 0 0 0 0 0.0 0.0
#> [30,] 0 0 0 0 0 0 0 0 0 0 0.0 0.0
#> [31,] 0 0 0 0 0 0 0 0 0 0 0.0 0.0
#> [,26] [,27] [,28] [,29] [,30] [,31]
#> [1,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [2,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [3,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [4,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [5,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [6,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [7,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [8,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [9,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [10,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [11,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [12,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [13,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [14,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [15,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [16,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [17,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [18,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [19,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [20,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [21,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [22,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [23,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [24,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [25,] 0.0 0.0 0.0 0.0 0.0 0.0
#> [26,] 1.0 0.5 0.0 0.0 0.0 0.0
#> [27,] 0.5 1.0 0.0 0.0 0.0 0.0
#> [28,] 0.0 0.0 1.0 0.5 0.0 0.0
#> [29,] 0.0 0.0 0.5 1.0 0.0 0.0
#> [30,] 0.0 0.0 0.0 0.0 1.0 0.5
#> [31,] 0.0 0.0 0.0 0.0 0.5 1.0
RE_cor(smoking$studyn, smoking$trtn, contrast = rep(FALSE, nrow(smoking)), type = "blshift")
#> Coerced `trt` to factor.
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
#> [1,] 1.0 0.5 0.0 0.0 0 0 0 0 0 0 0 0 0
#> [2,] 0.5 1.0 0.0 0.0 0 0 0 0 0 0 0 0 0
#> [3,] 0.0 0.0 1.0 0.5 0 0 0 0 0 0 0 0 0
#> [4,] 0.0 0.0 0.5 1.0 0 0 0 0 0 0 0 0 0
#> [5,] 0.0 0.0 0.0 0.0 1 0 0 0 0 0 0 0 0
#> [6,] 0.0 0.0 0.0 0.0 0 1 0 0 0 0 0 0 0
#> [7,] 0.0 0.0 0.0 0.0 0 0 1 0 0 0 0 0 0
#> [8,] 0.0 0.0 0.0 0.0 0 0 0 1 0 0 0 0 0
#> [9,] 0.0 0.0 0.0 0.0 0 0 0 0 1 0 0 0 0
#> [10,] 0.0 0.0 0.0 0.0 0 0 0 0 0 1 0 0 0
#> [11,] 0.0 0.0 0.0 0.0 0 0 0 0 0 0 1 0 0
#> [12,] 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 1 0
#> [13,] 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0 1
#> [14,] 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0 0
#> [15,] 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0 0
#> [16,] 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0 0
#> [17,] 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0 0
#> [18,] 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0 0
#> [19,] 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0 0
#> [20,] 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0 0
#> [21,] 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0 0
#> [22,] 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0 0
#> [23,] 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0 0
#> [24,] 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0 0
#> [25,] 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0 0
#> [26,] 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 0 0
#> [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
#> [1,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [5,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [6,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [7,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [8,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [9,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [10,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [11,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [12,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [13,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [14,] 1 0 0 0 0 0 0 0 0 0 0 0
#> [15,] 0 1 0 0 0 0 0 0 0 0 0 0
#> [16,] 0 0 1 0 0 0 0 0 0 0 0 0
#> [17,] 0 0 0 1 0 0 0 0 0 0 0 0
#> [18,] 0 0 0 0 1 0 0 0 0 0 0 0
#> [19,] 0 0 0 0 0 1 0 0 0 0 0 0
#> [20,] 0 0 0 0 0 0 1 0 0 0 0 0
#> [21,] 0 0 0 0 0 0 0 1 0 0 0 0
#> [22,] 0 0 0 0 0 0 0 0 1 0 0 0
#> [23,] 0 0 0 0 0 0 0 0 0 1 0 0
#> [24,] 0 0 0 0 0 0 0 0 0 0 1 0
#> [25,] 0 0 0 0 0 0 0 0 0 0 0 1
#> [26,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [,26]
#> [1,] 0
#> [2,] 0
#> [3,] 0
#> [4,] 0
#> [5,] 0
#> [6,] 0
#> [7,] 0
#> [8,] 0
#> [9,] 0
#> [10,] 0
#> [11,] 0
#> [12,] 0
#> [13,] 0
#> [14,] 0
#> [15,] 0
#> [16,] 0
#> [17,] 0
#> [18,] 0
#> [19,] 0
#> [20,] 0
#> [21,] 0
#> [22,] 0
#> [23,] 0
#> [24,] 0
#> [25,] 0
#> [26,] 1
which_RE(smoking$studyn, smoking$trtn, contrast = rep(FALSE, nrow(smoking)))
#> Coerced `trt` to factor.
#> [1] 0 1 2 3 4 5 0 6 0 7 0 8 0 9 0 10 0 11 0 12 0 13 0 14 0
#> [26] 15 0 16 0 17 0 18 0 19 0 20 0 21 0 22 0 23 24 25 26 27 28 29 30 31
which_RE(smoking$studyn, smoking$trtn, contrast = rep(FALSE, nrow(smoking)), type = "blshift")
#> Coerced `trt` to factor.
#> [1] 0 1 2 0 3 4 0 5 0 6 0 7 0 8 0 9 0 10 0 11 0 12 0 13 0
#> [26] 14 0 15 0 16 0 17 0 18 0 19 0 20 0 21 0 22 0 23 0 24 0 25 0 26