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 ```
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
```

- Interpretation of
`fixed effects`

`Intercept`

shows base mean of`log10_mfi`

for the base level (naive) of the`gr_hbs`

group, for the average of`t2_point_lm`

.`t2_point_lm`

shows increase or decrease in`log10_mfi`

to naive group for every 1-unit increase in`t2_point_lm`

.`gr_hbsAA`

or`gr_hbsAS`

shows increase or decrease in`log10_mfi`

in comparison to`naive`

group, for the average of`t2_point_lm`

.-
`t2_point_lm:gr_hbsAA`

or`t2_point_lm:gr_hbsAS`

shows increase or decrease in`log10_mfi`

(in AA or AS groups) in comparison to naive group for every 1-unit increase in`t2_point_lm`

. To have this interpretation, we have to add up the`interaction`

term plus`t2_point_lm`

. -
Interpretation of

`fixed effects`

(example) `Intercept`

tells us that the naive group will have 4.48`log10_mfi`

, for an average`t2_point_lm`

.`t2_point_lm`

naive group will increase in 0.04`lo10_mfi`

, for every 1-unit increase in`t2_point_lm`

.`gr_hbsAA`

or`gr_hbsAS`

would expect to have 2.99 or 3.63`log10_mfi`

more than the naive group, for an average`t2_point_lm`

.-
`t2_point_lm:gr_hbsAA`

or`t2_point_lm:gr_hbsAS`

AA or AS groups will increase in (0.04 + (-0.01)) or (0.04 + (-0.03))`log10_mfi`

, in comparison to naive group for every 1-unit increase in`t2_point_lm`

. -
General interpretation

- The increase in
`log10_mfi`

for having a higher`t2_point_lm`

differs among groups.

`summary()`

for the `gr_hbs`

with `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)
```

- General interpretation
- The slope
`t2_point_lm`

(corresponding to`naive`

group) is significantly different from zero. - The test interpretation for the
`t2_point_lm:gr_hbsAA`

&`t2_point_lm:gr_hbsAA`

interactions is likewise.

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.

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