cglmm.md
In GLMMcosinor: Fit a Cosinor Model Using a Generalized Mixed Modeling Framework

model returns accurate parameters

Code
  f_round(object$coefficients)
Output
  [1]  1.0030 -0.4966  2.0122  0.9948  3.0115  0.3175

Code
  f_round(object$coefficients)
Output
  [1]  1.0089 -0.5004  1.9969  1.0107  3.0064  0.2923

Code
  f_round(object$coefficients)
Output
  [1]  1.0029 -0.5142  2.0043  0.9982  2.9990  0.2893

Code
  f_round(object$coefficients)
Output
  [1]  1.0115 -0.5103  2.0101  1.0149  2.9986  0.2806

Code
  f_round(object$coefficients)
Output
  [1]  0.9411 -0.4453  1.9462  1.0356  3.0154  0.3083

model output is class cglmm

Code
  print(object, digits = 2)
Output

   Conditional Model

   Raw formula: 
  vit_d ~ X + X:main_rrr1 + X:main_sss1

   Raw Coefficients: 
               Estimate
  (Intercept)      29.7
  X1                1.9
  X0:main_rrr1      0.8
  X1:main_rrr1      6.5
  X0:main_sss1      6.1
  X1:main_sss1      4.8

   Transformed Coefficients: 
              Estimate
  (Intercept)     29.7
  [X=1]            1.9
  [X=0]:amp        6.2
  [X=1]:amp        8.1
  [X=0]:acr        1.4
  [X=1]:acr        0.6

  ***********************

   Dispersion Model

   Raw  Formula: 
  ~X:disp_rrr1 + X:disp_sss1 - 1

   Raw  Coefficients: 
               Estimate
  X0:disp_rrr1      0.3
  X1:disp_rrr1     -0.1
  X0:disp_sss1      0.0
  X1:disp_sss1      0.0

   Transformed  Coefficients: 
            Estimate
  [X=0]:amp      0.3
  [X=1]:amp      0.1
  [X=0]:acr      0.0
  [X=1]:acr     -2.6

  ***********************

   Zero-Inflation Model

   Raw  Formula: 
  ~X:zi_rrr1 + X:zi_sss1 - 1

   Raw  Coefficients: 
             Estimate
  X0:zi_rrr1     -0.2
  X1:zi_rrr1      0.1
  X0:zi_sss1      0.1
  X1:zi_sss1      0.2

   Transformed  Coefficients: 
            Estimate
  [X=0]:amp      0.2
  [X=1]:amp      0.2
  [X=0]:acr      2.6
  [X=1]:acr      1.3

Code
  print(object, digits = 2)
Output

   Conditional Model

   Raw formula: 
  Y ~ group + group:main_rrr1 + group:main_sss1 + group:main_rrr2 +      group:main_sss2 + (0 + main_rrr2 + main_sss2 | group)

   Raw Coefficients: 
                   Estimate
  (Intercept)           5.0
  group1               -3.0
  group0:main_rrr1      0.1
  group1:main_rrr1      0.0
  group0:main_sss1      0.9
  group1:main_sss1      1.0
  group0:main_rrr2      1.1
  group1:main_rrr2      1.1
  group0:main_sss2      1.7
  group1:main_sss2      1.7

   Transformed Coefficients: 
                 Estimate
  (Intercept)         5.0
  [group=1]          -3.0
  [group=0]:amp1      0.9
  [group=1]:amp1      1.0
  [group=0]:amp2      2.0
  [group=1]:amp2      2.0
  [group=0]:acr1      1.5
  [group=1]:acr1      1.6
  [group=0]:acr2      1.0
  [group=1]:acr2      1.0

specifying no amp_acro term works

Code
  f()
Output

   Conditional Model

   Raw formula: 
  vit_d ~ X + X:main_rrr1 + X:main_sss1

   Raw Coefficients: 
               Estimate
  (Intercept)  29.69639
  X1            1.86497
  X0:main_rrr1  0.96645
  X1:main_rrr1  6.43236
  X0:main_sss1  6.27112
  X1:main_sss1  4.79989

   Transformed Coefficients: 
              Estimate
  (Intercept) 29.69639
  [X=1]        1.86497
  [X=0]:amp    6.34516
  [X=1]:amp    8.02584
  [X=0]:acr    1.41789
  [X=1]:acr    0.64107

  ***********************

   Dispersion Model

   Raw  Formula: 
  ~X

   Raw  Coefficients: 
              Estimate
  (Intercept)  1.63602
  X1           0.09579

Code
  f()
Output

   Conditional Model

   Raw formula: 
  vit_d ~ X + X:main_rrr1 + X:main_sss1

   Raw Coefficients: 
               Estimate
  (Intercept)  29.69639
  X1            1.86497
  X0:main_rrr1  0.96645
  X1:main_rrr1  6.43236
  X0:main_sss1  6.27114
  X1:main_sss1  4.79989

   Transformed Coefficients: 
              Estimate
  (Intercept) 29.69639
  [X=1]        1.86497
  [X=0]:amp    6.34517
  [X=1]:amp    8.02585
  [X=0]:acr    1.41789
  [X=1]:acr    0.64107

  ***********************

   Zero-Inflation Model

   Raw  Formula: 
  NULL

   Raw  Coefficients: 
               Estimate
  (Intercept) -15.07683
  X1           -1.30260

Code
  f()
Output

   Conditional Model

   Raw formula: 
  vit_d ~ X + X:main_rrr1 + X:main_sss1

   Raw Coefficients: 
               Estimate
  (Intercept)  29.69639
  X1            1.86498
  X0:main_rrr1  0.96645
  X1:main_rrr1  6.43236
  X0:main_sss1  6.27113
  X1:main_sss1  4.79989

   Transformed Coefficients: 
              Estimate
  (Intercept) 29.69639
  [X=1]        1.86498
  [X=0]:amp    6.34517
  [X=1]:amp    8.02584
  [X=0]:acr    1.41789
  [X=1]:acr    0.64107

  ***********************

   Dispersion Model

   Raw  Formula: 
  ~X

   Raw  Coefficients: 
              Estimate
  (Intercept)  1.63602
  X1           0.09579

  ***********************

   Zero-Inflation Model

   Raw  Formula: 
  NULL

   Raw  Coefficients: 
               Estimate
  (Intercept) -21.51196
  X1          -13.25923