README.md

chmi_tools

Package to manage and obtain results from CHMI Study contains. results of CHMI study. demo to understand the coefficient in linear mixed model (LMM). * demo to understand the Simultaneous Tests for General Linear Hypotheses (GLHT).

demo to understand aim3

All examples have been done with the IgG istoype & AMA1_3D71 antigen.

summary() for the gr_hbs with 3 levels in LMM.

Linear mixed model fit by REML. t-tests use Satterthwaite's method ['lmerModLmerTest']
Formula: log10_mfi ~ t2_point_lm * gr_hbs + (t2_point_lm | original_id)
   Data: .x

REML criterion at convergence: 152.6

Scaled residuals:
    Min      1Q  Median      3Q     Max
-2.3791 -0.3007  0.0408  0.3286  3.1782

Random effects:
 Groups      Name        Variance  Std.Dev. Corr
 original_id (Intercept) 1.0655633 1.03226       
             t2_point_lm 0.0006115 0.02473  -0.73
 Residual                0.0601413 0.24524       
Number of obs: 111, groups:  original_id, 25

Fixed effects:
                     Estimate Std. Error       df t value Pr(>|t|)    
(Intercept)           4.48319    0.46975 21.95865   9.544 2.86e-09 ***
t2_point_lm           0.04272    0.01293 18.47458   3.305  0.00383 **
gr_hbsAA              2.99953    0.56645 21.94396   5.295 2.61e-05 ***
gr_hbsAS              3.63161    0.58712 22.11956   6.186 3.09e-06 ***
t2_point_lm:gr_hbsAA -0.01839    0.01542 18.20749  -1.192  0.24854    
t2_point_lm:gr_hbsAS -0.03487    0.01595 18.27883  -2.186  0.04207 *  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Correlation of Fixed Effects:
            (Intr) t2_pn_ gr_hAA gr_hAS t2__:_AA
t2_point_lm -0.677                              
gr_hbsAA    -0.829  0.562                       
gr_hbsAS    -0.800  0.542  0.664                
t2_pnt_:_AA  0.568 -0.838 -0.685 -0.454         
t2_pnt_:_AS  0.549 -0.810 -0.455 -0.690  0.679

summary() for the gr_hbs with 3 levels in glht()

 Simultaneous Tests for General Linear Hypotheses

Fit: lmer(formula = as.formula(.y), data = .x)

Linear Hypotheses:
              Estimate Std. Error z value Pr(>|z|)    
t2_point_lm == 0  0.04272    0.01293   3.305  0.00095 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Adjusted p values reported -- single-step method)

Bibliography

See nexts tutorials to obtain more information about the interpretation of the interaction terms in categorical and continuous data. tutorial_01 tutotial_02



mvazquezs/chmitools documentation built on March 24, 2019, 5:20 p.m.