contrmat.RdFunction to construct a matrix that indicates which two groups have been contrasted against each other in each row of a dataset.
contrmat(data, grp1, grp2, last, shorten=FALSE, minlen=2, check=TRUE, append=TRUE)a data frame in wide format.
either the name (given as a character string) or the position (given as a single number) of the first group variable in the data frame.
either the name (given as a character string) or the position (given as a single number) of the second group variable in the data frame.
optional character string to specify which group will be placed in the last column of the matrix (must be one of the groups in the group variables). If not given, the most frequently occurring second group is placed last.
logical to specify whether the variable names corresponding to the group names should be shortened (the default is FALSE).
integer to specify the minimum length of the shortened variable names (the default is 2).
logical to specify whether the variables names should be checked to ensure that they are syntactically valid variable names and if not, they are adjusted (by make.names) so that they are (the default is TRUE).
logical to specify whether the contrast matrix should be appended to the data frame specified via the data argument (the default is TRUE). If append=FALSE, only the contrast matrix is returned.
The function can be used to construct a matrix that indicates which two groups have been contrasted against each other in each row of a data frame (with 1 for the first group, -1 for the second group, and 0 otherwise).
The grp1 and grp2 arguments are used to specify the group variables in the dataset (either as character strings or as numbers indicating the column positions of these variables in the dataset). Optional argument last is used to specify which group will be placed in the last column of the matrix.
If shorten=TRUE, the variable names corresponding to the group names are shortened (to at least minlen; the actual length might be longer to ensure uniqueness of the variable names).
The examples below illustrate the use of this function.
A matrix with as many variables as there are groups.
Viechtbauer, W. (2010). Conducting meta-analyses in R with the metafor package. Journal of Statistical Software, 36(3), 1–48. https://doi.org/10.18637/jss.v036.i03
to.wide for a function to create ‘wide’ format datasets.
dat.senn2013, dat.hasselblad1998, dat.lopez2019 for illustrative examples.
### restructure to wide format
dat <- dat.senn2013
dat <- dat[c(1,4,3,2,5,6)]
dat <- to.wide(dat, study="study", grp="treatment", ref="placebo", grpvars=4:6)
dat
#> study comment treatment.1 ni.1 mi.1 sdi.1 treatment.2 ni.2 mi.2 sdi.2 id
#> 1 Alex (1998) change metformin 291 0.13 1.428 sulfonylurea 300 0.50 1.450 1
#> 2 Baksi (2004) change rosiglitazone 218 -1.20 1.112 placebo 233 0.10 1.036 2
#> 3 Costa (1997) change acarbose 36 -1.10 0.360 placebo 29 -0.30 0.700 3
#> 4 Davidson (2007) change rosiglitazone 117 -1.20 1.097 placebo 116 0.14 1.093 4
#> 5 De Fronzo (1995) change metformin 213 -1.70 1.459 placebo 209 0.20 1.446 5
#> 6 Derosa (2004) raw pioglitazone 45 6.80 0.800 rosiglitazone 42 6.70 0.900 6
#> 7 Garber (2008) change vildagliptin 132 -0.63 1.034 placebo 144 0.07 1.080 7
#> 8 Gonzalez-Ortiz (2004) change metformin 34 -1.30 1.861 placebo 37 -0.90 1.803 8
#> 9 Hanefeld (2004) raw metformin 320 7.45 1.073 pioglitazone 319 7.61 1.072 9
#> 10 Hermansen (2007) change sitagliptin 106 -0.30 0.940 placebo 106 0.27 0.940 10
#> 11 Johnston (1994) change miglitol 68 -0.41 1.072 placebo 63 0.33 1.032 11
#> 12 Johnston (1998a) change miglitol 91 -0.43 0.954 placebo 43 0.98 1.311 12
#> 13 Johnston (1998b) change miglitol 49 -0.12 1.400 placebo 34 0.56 1.166 13
#> 14 Kerenyi (2004) change rosiglitazone 160 -0.91 0.990 placebo 154 -0.14 0.920 14
#> 15 Kim (2007) change metformin 56 -1.10 1.139 rosiglitazone 57 -1.10 1.341 15
#> 16 Kipnes (2001) change pioglitazone 182 -1.20 1.369 placebo 181 0.10 1.024 16
#> 17 Lewin (2007) change metformin 431 -0.74 1.106 placebo 144 0.08 1.004 17
#> 18 Moulin (2006) change benfluorex 161 -0.82 1.028 placebo 156 0.19 1.374 18
#> 19 Oyama (2008) change acarbose 41 -0.70 0.800 sulfonylurea 43 -0.30 0.600 19
#> 20 Rosenstock (2008) change rosiglitazone 59 -1.17 1.229 placebo 57 -0.08 1.208 20
#> 21 Stucci (1996) raw benfluorex 28 8.03 1.290 placebo 30 8.26 1.350 21
#> 22 Vongthavaravat (2002) change rosiglitazone 164 -1.10 1.559 sulfonylurea 170 0.10 0.992 22
#> 23 Willms (1999) change acarbose 31 -2.30 1.782 placebo 29 -1.30 1.831 23
#> 24 Willms (1999) change metformin 29 -2.50 0.862 placebo 29 -1.30 1.831 24
#> 25 Wolffenbuttel (1999) change rosiglitazone 183 -0.90 1.100 placebo 192 0.20 1.110 25
#> 26 Yang (2003) change metformin 96 -0.95 1.500 rosiglitazone 102 -1.09 1.650 26
#> 27 Zhu (2003) change rosiglitazone 210 -1.90 1.470 placebo 105 -0.40 1.300 27
#> comp design
#> 1 me-su me-su
#> 2 ro-pl ro-pl
#> 3 ac-pl ac-pl
#> 4 ro-pl ro-pl
#> 5 me-pl me-pl
#> 6 pi-ro pi-ro
#> 7 vi-pl vi-pl
#> 8 me-pl me-pl
#> 9 me-pi me-pi
#> 10 si-pl si-pl
#> 11 mi-pl mi-pl
#> 12 mi-pl mi-pl
#> 13 mi-pl mi-pl
#> 14 ro-pl ro-pl
#> 15 me-ro me-ro
#> 16 pi-pl pi-pl
#> 17 me-pl me-pl
#> 18 be-pl be-pl
#> 19 ac-su ac-su
#> 20 ro-pl ro-pl
#> 21 be-pl be-pl
#> 22 ro-su ro-su
#> 23 ac-pl ac-me-pl
#> 24 me-pl ac-me-pl
#> 25 ro-pl ro-pl
#> 26 me-ro me-ro
#> 27 ro-pl ro-pl
### add contrast matrix
dat <- contrmat(dat, grp1="treatment.1", grp2="treatment.2")
dat
#> study comment treatment.1 ni.1 mi.1 sdi.1 treatment.2 ni.2 mi.2 sdi.2 id
#> 1 Alex (1998) change metformin 291 0.13 1.428 sulfonylurea 300 0.50 1.450 1
#> 2 Baksi (2004) change rosiglitazone 218 -1.20 1.112 placebo 233 0.10 1.036 2
#> 3 Costa (1997) change acarbose 36 -1.10 0.360 placebo 29 -0.30 0.700 3
#> 4 Davidson (2007) change rosiglitazone 117 -1.20 1.097 placebo 116 0.14 1.093 4
#> 5 De Fronzo (1995) change metformin 213 -1.70 1.459 placebo 209 0.20 1.446 5
#> 6 Derosa (2004) raw pioglitazone 45 6.80 0.800 rosiglitazone 42 6.70 0.900 6
#> 7 Garber (2008) change vildagliptin 132 -0.63 1.034 placebo 144 0.07 1.080 7
#> 8 Gonzalez-Ortiz (2004) change metformin 34 -1.30 1.861 placebo 37 -0.90 1.803 8
#> 9 Hanefeld (2004) raw metformin 320 7.45 1.073 pioglitazone 319 7.61 1.072 9
#> 10 Hermansen (2007) change sitagliptin 106 -0.30 0.940 placebo 106 0.27 0.940 10
#> 11 Johnston (1994) change miglitol 68 -0.41 1.072 placebo 63 0.33 1.032 11
#> 12 Johnston (1998a) change miglitol 91 -0.43 0.954 placebo 43 0.98 1.311 12
#> 13 Johnston (1998b) change miglitol 49 -0.12 1.400 placebo 34 0.56 1.166 13
#> 14 Kerenyi (2004) change rosiglitazone 160 -0.91 0.990 placebo 154 -0.14 0.920 14
#> 15 Kim (2007) change metformin 56 -1.10 1.139 rosiglitazone 57 -1.10 1.341 15
#> 16 Kipnes (2001) change pioglitazone 182 -1.20 1.369 placebo 181 0.10 1.024 16
#> 17 Lewin (2007) change metformin 431 -0.74 1.106 placebo 144 0.08 1.004 17
#> 18 Moulin (2006) change benfluorex 161 -0.82 1.028 placebo 156 0.19 1.374 18
#> 19 Oyama (2008) change acarbose 41 -0.70 0.800 sulfonylurea 43 -0.30 0.600 19
#> 20 Rosenstock (2008) change rosiglitazone 59 -1.17 1.229 placebo 57 -0.08 1.208 20
#> 21 Stucci (1996) raw benfluorex 28 8.03 1.290 placebo 30 8.26 1.350 21
#> 22 Vongthavaravat (2002) change rosiglitazone 164 -1.10 1.559 sulfonylurea 170 0.10 0.992 22
#> 23 Willms (1999) change acarbose 31 -2.30 1.782 placebo 29 -1.30 1.831 23
#> 24 Willms (1999) change metformin 29 -2.50 0.862 placebo 29 -1.30 1.831 24
#> 25 Wolffenbuttel (1999) change rosiglitazone 183 -0.90 1.100 placebo 192 0.20 1.110 25
#> 26 Yang (2003) change metformin 96 -0.95 1.500 rosiglitazone 102 -1.09 1.650 26
#> 27 Zhu (2003) change rosiglitazone 210 -1.90 1.470 placebo 105 -0.40 1.300 27
#> comp design acarbose benfluorex metformin miglitol pioglitazone rosiglitazone sitagliptin
#> 1 me-su me-su 0 0 1 0 0 0 0
#> 2 ro-pl ro-pl 0 0 0 0 0 1 0
#> 3 ac-pl ac-pl 1 0 0 0 0 0 0
#> 4 ro-pl ro-pl 0 0 0 0 0 1 0
#> 5 me-pl me-pl 0 0 1 0 0 0 0
#> 6 pi-ro pi-ro 0 0 0 0 1 -1 0
#> 7 vi-pl vi-pl 0 0 0 0 0 0 0
#> 8 me-pl me-pl 0 0 1 0 0 0 0
#> 9 me-pi me-pi 0 0 1 0 -1 0 0
#> 10 si-pl si-pl 0 0 0 0 0 0 1
#> 11 mi-pl mi-pl 0 0 0 1 0 0 0
#> 12 mi-pl mi-pl 0 0 0 1 0 0 0
#> 13 mi-pl mi-pl 0 0 0 1 0 0 0
#> 14 ro-pl ro-pl 0 0 0 0 0 1 0
#> 15 me-ro me-ro 0 0 1 0 0 -1 0
#> 16 pi-pl pi-pl 0 0 0 0 1 0 0
#> 17 me-pl me-pl 0 0 1 0 0 0 0
#> 18 be-pl be-pl 0 1 0 0 0 0 0
#> 19 ac-su ac-su 1 0 0 0 0 0 0
#> 20 ro-pl ro-pl 0 0 0 0 0 1 0
#> 21 be-pl be-pl 0 1 0 0 0 0 0
#> 22 ro-su ro-su 0 0 0 0 0 1 0
#> 23 ac-pl ac-me-pl 1 0 0 0 0 0 0
#> 24 me-pl ac-me-pl 0 0 1 0 0 0 0
#> 25 ro-pl ro-pl 0 0 0 0 0 1 0
#> 26 me-ro me-ro 0 0 1 0 0 -1 0
#> 27 ro-pl ro-pl 0 0 0 0 0 1 0
#> sulfonylurea vildagliptin placebo
#> 1 -1 0 0
#> 2 0 0 -1
#> 3 0 0 -1
#> 4 0 0 -1
#> 5 0 0 -1
#> 6 0 0 0
#> 7 0 1 -1
#> 8 0 0 -1
#> 9 0 0 0
#> 10 0 0 -1
#> 11 0 0 -1
#> 12 0 0 -1
#> 13 0 0 -1
#> 14 0 0 -1
#> 15 0 0 0
#> 16 0 0 -1
#> 17 0 0 -1
#> 18 0 0 -1
#> 19 -1 0 0
#> 20 0 0 -1
#> 21 0 0 -1
#> 22 -1 0 0
#> 23 0 0 -1
#> 24 0 0 -1
#> 25 0 0 -1
#> 26 0 0 0
#> 27 0 0 -1
### data in long format
dat <- dat.hasselblad1998
dat
#> id study authors year trt xi ni
#> 1 1 1 Reid et al. 1974 no_contact 75 731
#> 2 2 1 Reid et al. 1974 ind_counseling 363 714
#> 3 3 2 Cottraux et al. 1983 no_contact 9 140
#> 4 4 2 Cottraux et al. 1983 ind_counseling 23 140
#> 5 5 2 Cottraux et al. 1983 grp_counseling 10 138
#> 6 6 3 Slama et al. 1990 no_contact 2 106
#> 7 7 3 Slama et al. 1990 ind_counseling 9 205
#> 8 8 4 Jamrozik et al. 1984 no_contact 58 549
#> 9 9 4 Jamrozik et al. 1984 ind_counseling 237 1561
#> 10 10 5 Rabkin et al. 1984 no_contact 0 33
#> 11 11 5 Rabkin et al. 1984 ind_counseling 9 48
#> 12 12 6 Decker and Evans 1989 self_help 20 49
#> 13 13 6 Decker and Evans 1989 ind_counseling 16 43
#> 14 14 7 Richmond et al. 1986 no_contact 3 100
#> 15 15 7 Richmond et al. 1986 ind_counseling 31 98
#> 16 16 8 Leung 1991 no_contact 1 31
#> 17 17 8 Leung 1991 ind_counseling 26 95
#> 18 18 9 Mothersill et al. 1988 self_help 11 78
#> 19 19 9 Mothersill et al. 1988 ind_counseling 12 85
#> 20 20 9 Mothersill et al. 1988 grp_counseling 29 170
#> 21 21 10 Langford et al. 1983 no_contact 6 39
#> 22 22 10 Langford et al. 1983 ind_counseling 17 77
#> 23 23 11 Gritz et al. 1992 no_contact 79 702
#> 24 24 11 Gritz et al. 1992 self_help 77 694
#> 25 25 12 Campbell et al. 1986 no_contact 18 671
#> 26 26 12 Campbell et al. 1986 self_help 21 535
#> 27 27 13 Sanders et al. 1989 no_contact 64 642
#> 28 28 13 Sanders et al. 1989 ind_counseling 107 761
#> 29 29 14 Hilleman et al. 1993 ind_counseling 12 76
#> 30 30 14 Hilleman et al. 1993 grp_counseling 20 74
#> 31 31 15 Gillams et al. 1984 ind_counseling 9 55
#> 32 32 15 Gillams et al. 1984 grp_counseling 3 26
#> 33 33 16 Mogielnicki et al. 1986 self_help 7 66
#> 34 34 16 Mogielnicki et al. 1986 grp_counseling 32 127
#> 35 35 17 Page et al. 1986 no_contact 5 62
#> 36 36 17 Page et al. 1986 ind_counseling 8 90
#> 37 37 18 Vetter and Ford 1990 no_contact 20 234
#> 38 38 18 Vetter and Ford 1990 ind_counseling 34 237
#> 39 39 19 Williams and Hall 1988 no_contact 0 20
#> 40 40 19 Williams and Hall 1988 grp_counseling 9 20
#> 41 41 20 Pallonen et al. 1994 no_contact 8 116
#> 42 42 20 Pallonen et al. 1994 self_help 19 149
#> 43 43 21 Russell et al. 1983 no_contact 95 1107
#> 44 44 21 Russell et al. 1983 ind_counseling 143 1031
#> 45 45 22 Stewart and Rosser 1982 no_contact 15 187
#> 46 46 22 Stewart and Rosser 1982 ind_counseling 36 504
#> 47 47 23 Russell et al. 1979 no_contact 78 584
#> 48 48 23 Russell et al. 1979 ind_counseling 73 675
#> 49 49 24 Kendrick et al. 1995 no_contact 69 1177
#> 50 50 24 Kendrick et al. 1995 ind_counseling 54 888
### restructure to wide format
dat <- to.wide(dat, study="study", grp="trt", ref="no_contact", grpvars=6:7)
dat
#> id study authors year trt.1 xi.1 ni.1 trt.2 xi.2 ni.2 comp design
#> 1 1 1 Reid et al. 1974 ind_counseling 363 714 no_contact 75 731 in-no in-no
#> 2 2 2 Cottraux et al. 1983 grp_counseling 10 138 no_contact 9 140 gr-no gr-in-no
#> 3 3 2 Cottraux et al. 1983 ind_counseling 23 140 no_contact 9 140 in-no gr-in-no
#> 4 4 3 Slama et al. 1990 ind_counseling 9 205 no_contact 2 106 in-no in-no
#> 5 5 4 Jamrozik et al. 1984 ind_counseling 237 1561 no_contact 58 549 in-no in-no
#> 6 6 5 Rabkin et al. 1984 ind_counseling 9 48 no_contact 0 33 in-no in-no
#> 7 7 6 Decker and Evans 1989 ind_counseling 16 43 self_help 20 49 in-se in-se
#> 8 8 7 Richmond et al. 1986 ind_counseling 31 98 no_contact 3 100 in-no in-no
#> 9 9 8 Leung 1991 ind_counseling 26 95 no_contact 1 31 in-no in-no
#> 10 10 9 Mothersill et al. 1988 grp_counseling 29 170 self_help 11 78 gr-se gr-in-se
#> 11 11 9 Mothersill et al. 1988 ind_counseling 12 85 self_help 11 78 in-se gr-in-se
#> 12 12 10 Langford et al. 1983 ind_counseling 17 77 no_contact 6 39 in-no in-no
#> 13 13 11 Gritz et al. 1992 self_help 77 694 no_contact 79 702 se-no se-no
#> 14 14 12 Campbell et al. 1986 self_help 21 535 no_contact 18 671 se-no se-no
#> 15 15 13 Sanders et al. 1989 ind_counseling 107 761 no_contact 64 642 in-no in-no
#> 16 16 14 Hilleman et al. 1993 grp_counseling 20 74 ind_counseling 12 76 gr-in gr-in
#> 17 17 15 Gillams et al. 1984 grp_counseling 3 26 ind_counseling 9 55 gr-in gr-in
#> 18 18 16 Mogielnicki et al. 1986 grp_counseling 32 127 self_help 7 66 gr-se gr-se
#> 19 19 17 Page et al. 1986 ind_counseling 8 90 no_contact 5 62 in-no in-no
#> 20 20 18 Vetter and Ford 1990 ind_counseling 34 237 no_contact 20 234 in-no in-no
#> 21 21 19 Williams and Hall 1988 grp_counseling 9 20 no_contact 0 20 gr-no gr-no
#> 22 22 20 Pallonen et al. 1994 self_help 19 149 no_contact 8 116 se-no se-no
#> 23 23 21 Russell et al. 1983 ind_counseling 143 1031 no_contact 95 1107 in-no in-no
#> 24 24 22 Stewart and Rosser 1982 ind_counseling 36 504 no_contact 15 187 in-no in-no
#> 25 25 23 Russell et al. 1979 ind_counseling 73 675 no_contact 78 584 in-no in-no
#> 26 26 24 Kendrick et al. 1995 ind_counseling 54 888 no_contact 69 1177 in-no in-no
### add contrast matrix
dat <- contrmat(dat, grp1="trt.1", grp2="trt.2", shorten=TRUE, minlen=3)
dat
#> id study authors year trt.1 xi.1 ni.1 trt.2 xi.2 ni.2 comp design
#> 1 1 1 Reid et al. 1974 ind_counseling 363 714 no_contact 75 731 in-no in-no
#> 2 2 2 Cottraux et al. 1983 grp_counseling 10 138 no_contact 9 140 gr-no gr-in-no
#> 3 3 2 Cottraux et al. 1983 ind_counseling 23 140 no_contact 9 140 in-no gr-in-no
#> 4 4 3 Slama et al. 1990 ind_counseling 9 205 no_contact 2 106 in-no in-no
#> 5 5 4 Jamrozik et al. 1984 ind_counseling 237 1561 no_contact 58 549 in-no in-no
#> 6 6 5 Rabkin et al. 1984 ind_counseling 9 48 no_contact 0 33 in-no in-no
#> 7 7 6 Decker and Evans 1989 ind_counseling 16 43 self_help 20 49 in-se in-se
#> 8 8 7 Richmond et al. 1986 ind_counseling 31 98 no_contact 3 100 in-no in-no
#> 9 9 8 Leung 1991 ind_counseling 26 95 no_contact 1 31 in-no in-no
#> 10 10 9 Mothersill et al. 1988 grp_counseling 29 170 self_help 11 78 gr-se gr-in-se
#> 11 11 9 Mothersill et al. 1988 ind_counseling 12 85 self_help 11 78 in-se gr-in-se
#> 12 12 10 Langford et al. 1983 ind_counseling 17 77 no_contact 6 39 in-no in-no
#> 13 13 11 Gritz et al. 1992 self_help 77 694 no_contact 79 702 se-no se-no
#> 14 14 12 Campbell et al. 1986 self_help 21 535 no_contact 18 671 se-no se-no
#> 15 15 13 Sanders et al. 1989 ind_counseling 107 761 no_contact 64 642 in-no in-no
#> 16 16 14 Hilleman et al. 1993 grp_counseling 20 74 ind_counseling 12 76 gr-in gr-in
#> 17 17 15 Gillams et al. 1984 grp_counseling 3 26 ind_counseling 9 55 gr-in gr-in
#> 18 18 16 Mogielnicki et al. 1986 grp_counseling 32 127 self_help 7 66 gr-se gr-se
#> 19 19 17 Page et al. 1986 ind_counseling 8 90 no_contact 5 62 in-no in-no
#> 20 20 18 Vetter and Ford 1990 ind_counseling 34 237 no_contact 20 234 in-no in-no
#> 21 21 19 Williams and Hall 1988 grp_counseling 9 20 no_contact 0 20 gr-no gr-no
#> 22 22 20 Pallonen et al. 1994 self_help 19 149 no_contact 8 116 se-no se-no
#> 23 23 21 Russell et al. 1983 ind_counseling 143 1031 no_contact 95 1107 in-no in-no
#> 24 24 22 Stewart and Rosser 1982 ind_counseling 36 504 no_contact 15 187 in-no in-no
#> 25 25 23 Russell et al. 1979 ind_counseling 73 675 no_contact 78 584 in-no in-no
#> 26 26 24 Kendrick et al. 1995 ind_counseling 54 888 no_contact 69 1177 in-no in-no
#> grp ind sel no_
#> 1 0 1 0 -1
#> 2 1 0 0 -1
#> 3 0 1 0 -1
#> 4 0 1 0 -1
#> 5 0 1 0 -1
#> 6 0 1 0 -1
#> 7 0 1 -1 0
#> 8 0 1 0 -1
#> 9 0 1 0 -1
#> 10 1 0 -1 0
#> 11 0 1 -1 0
#> 12 0 1 0 -1
#> 13 0 0 1 -1
#> 14 0 0 1 -1
#> 15 0 1 0 -1
#> 16 1 -1 0 0
#> 17 1 -1 0 0
#> 18 1 0 -1 0
#> 19 0 1 0 -1
#> 20 0 1 0 -1
#> 21 1 0 0 -1
#> 22 0 0 1 -1
#> 23 0 1 0 -1
#> 24 0 1 0 -1
#> 25 0 1 0 -1
#> 26 0 1 0 -1