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Rmd 532d320 Jie Zhou 2024-02-21 madi meeting
html 532d320 Jie Zhou 2024-02-21 madi meeting 

Attaching package: 'glue'
The following object is masked from 'package:gdata':

    trim
here() starts at C:/Users/Jie Zhou/Desktop/madi-brussels-pertussis-thailand

0.1 Model description

0.1.1 Definition

Let \(a\) be the treatment whit \(a=0\) for no maternal vaccination and \(a=1\) for maternal vaccination. \(M\) represents mediator,i.e, maternal antibodies, and \(Y\) the outcome, i.e., infant antibodies.

Causal direct effects of maternal vaccination on infant antibodies are defined as \[\tau_i=Y_i(1,M_i(a))-Y_i(0,M_i(a));\] while causal mediation effects of maternal antibodies on infant antibodies are defined as \[\alpha_i=Y_i(a,M_i(1))-Y_i(a,M_i(0))\]

0.1.2 model

For mediators, we have

\[M_{i1}=\gamma_{01}+\gamma_{11}a_i+e_{mi1}\]

\[M_{i2}=\gamma_{02}+\gamma_{12}a_i+e_{mi2}\]

\[M_{i3}=\gamma_{03}+\gamma_{13}a_i+e_{mi3}\] For outcome, we have

\[Y_i=\beta_0+\beta_1M_{i1}+\beta_2M_{i2}+\beta_3M_{i3}+\beta_{4}a_i+e_{yi}\]

[1] "All the outcome (infant antibodies) considered: "
 [1] "DT_FcgR2a"  "DT_FcgR3b"  "DT_IgG"     "DT_IgG1"    "DT_IgG2"   
 [6] "DT_IgG3"    "DT_IgG4"    "FHA_FcgR2a" "FHA_FcgR3b" "FHA_IgG"   
[11] "FHA_IgG1"   "FHA_IgG2"   "FHA_IgG3"   "FHA_IgG4"   "PRN_FcgR2a"
[16] "PRN_FcgR3b" "PRN_IgG"    "PRN_IgG1"   "PRN_IgG2"   "PRN_IgG3"  
[21] "PRN_IgG4"   "PT_FcgR2a"  "PT_FcgR3b"  "PT_IgG"     "PT_IgG1"   
[26] "PT_IgG2"    "PT_IgG3"    "PT_IgG4"    "TT_FcgR2a"  "TT_FcgR3b" 
[31] "TT_IgG"     "TT_IgG1"    "TT_IgG2"    "TT_IgG3"    "TT_IgG4"   
[36] "DT_ADCD"    "FHA_ADCD"   "PRN_ADCD"   "PT_ADCD"    "TT_ADCD"   
[41] "DT_ADCP"    "FHA_ADCP"   "PRN_ADCP"   "PT_ADCP"    "TT_ADCP"   
[46] "DT_ADNP"    "FHA_ADNP"   "PRN_ADNP"   "PT_ADNP"    "TT_ADNP"   
[1] "All the mediators (maternal cord blood total igg): "
[1] "ELISA_FHA_IgG" "ELISA_PRN_IgG" "ELISA_PT_IgG"

0.2 Results 1: matimm+/-

      outcome     direffect     medeffect  pvalue_dir    fdr_dir
1      PT_IgG -0.4499575258  0.0230374883 0.002170220 0.04007240
2   TT_FcgR2a  0.2533187242 -0.0121810366 0.002722835 0.04007240
3   TT_FcgR3b  0.6093153152 -0.0199603782 0.003201791 0.04007240
4     TT_ADCD  0.4258765874 -0.0033223344 0.003205792 0.04007240
5     TT_ADCP  0.2042313633 -0.0022043970 0.006566089 0.06566089
6     TT_ADNP  0.1600088555  0.0050302703 0.012963856 0.09493358
7    FHA_ADCP -0.1160743117 -0.0156933599 0.013290701 0.09493358
8   DT_FcgR3b  0.5842478944 -0.0424470902 0.018420608 0.10469266
9     DT_IgG3  0.2898259986 -0.0420863393 0.019336441 0.10469266
10    TT_IgG1  0.5422755995 -0.0145832111 0.020938533 0.10469266
11    FHA_IgG -0.2255506499 -0.0329562999 0.027256353 0.12389251
12   FHA_IgG2 -0.2649364929 -0.0588146060 0.036597309 0.15248879
13    PT_IgG1 -0.4009131978  0.0232805773 0.052664146 0.18212300
14    TT_IgG3  0.2288896521 -0.0248156236 0.054477580 0.18212300
15 PRN_FcgR2a  0.3062615152  0.0089810151 0.060004736 0.18212300
16    PT_IgG3  0.2225464697 -0.0370204012 0.060455970 0.18212300
17   FHA_IgG4 -0.3421763673 -0.0361884625 0.061921820 0.18212300
18   FHA_ADNP  0.0933205845 -0.0212905106 0.071997929 0.19999425
19 FHA_FcgR2a  0.1929955433 -0.0299297399 0.095775365 0.25204044
20  DT_FcgR2a  0.1307850883 -0.0093551928 0.118483437 0.29620859
21     TT_IgG  0.1541213846 -0.0309278988 0.142297719 0.33880409
22 PRN_FcgR3b  0.4156414045  0.0350516602 0.152794220 0.34285034
23 FHA_FcgR3b  0.2760421780 -0.0519521394 0.157711158 0.34285034
24   PRN_IgG2  0.1726181910 -0.0160312688 0.199806336 0.38169050
25     DT_IgG -0.1414461008 -0.0234128132 0.201080962 0.38169050
26    DT_ADCD  0.1154117504  0.0135736284 0.213845909 0.38169050
27    DT_IgG4 -0.2662554542 -0.0489325873 0.215050060 0.38169050
28    PT_ADNP  0.1085680096  0.0106338034 0.233716418 0.38169050
29   PRN_ADCD  0.1478524994  0.0128946800 0.236045518 0.38169050
30    PT_IgG2 -0.0788299441  0.0020728599 0.240032585 0.38169050
31   PRN_IgG3  0.1861963696 -0.0486725723 0.244277704 0.38169050
32   PRN_IgG1  0.2805928995  0.0365862927 0.244281921 0.38169050
33    PT_IgG4 -0.0562492281  0.0009781891 0.268695789 0.40265429
34   PRN_ADNP  0.0391632891 -0.0019577340 0.273804915 0.40265429
35    PT_ADCD  0.1752123956  0.0527830038 0.388879009 0.55554144
36    DT_IgG2 -0.0986487891  0.0012457617 0.467369115 0.64912377
37   FHA_IgG3  0.1126140111 -0.0582028750 0.487828486 0.65846979
38    TT_IgG2  0.0447426349  0.0207576252 0.512568493 0.65846979
39   FHA_ADCD  0.0877271239 -0.0148163798 0.513606437 0.65846979
40    DT_ADNP  0.0179837415 -0.0008238124 0.546986004 0.67107795
41   PRN_IgG4  0.0728321280 -0.0173063628 0.550283922 0.67107795
42    PRN_IgG -0.0798857105 -0.0066343282 0.568320586 0.67657213
43   FHA_IgG1  0.0692670775 -0.0785741819 0.661796030 0.76953027
44    TT_IgG4  0.0515032538  0.0265793405 0.701589110 0.79726035
45    DT_IgG1  0.0792252213 -0.0093426665 0.749766991 0.81947570
46  PT_FcgR3b -0.0467719676  0.0217111733 0.753917641 0.81947570
47   PRN_ADCP -0.0158204877  0.0081016579 0.774155410 0.82356959
48    PT_ADCP -0.0155166795  0.0050382057 0.811596327 0.84541284
49  PT_FcgR2a -0.0188736221  0.0276326636 0.911370131 0.92996952
50    DT_ADCP -0.0005439078  0.0057221199 0.986134924 0.98613492

sessionInfo()
R version 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] RColorBrewer_1.1-3 here_1.0.1         glue_1.7.0         RPostgres_1.4.6   
 [5] DT_0.33            DBI_1.2.2          pls_2.8-3          mediation_4.5.0   
 [9] sandwich_3.1-0     mvtnorm_1.2-4      Matrix_1.7-0       MASS_7.3-60.2     
[13] ggpubr_0.6.0       ggExtra_0.10.1     e1071_1.7-14       ggfortify_0.4.17  
[17] rmarkdown_2.26     knitr_1.46         ggplot2_3.5.1      gdata_3.0.0       
[21] tidyr_1.3.1        tidyquery_0.2.4    dplyr_1.1.4       

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.1  blob_1.2.4        fastmap_1.1.1     promises_1.3.0   
 [5] digest_0.6.35     rpart_4.1.23      timechange_0.3.0  mime_0.12        
 [9] lifecycle_1.0.4   cluster_2.1.6     magrittr_2.0.3    compiler_4.4.0   
[13] rlang_1.1.3       Hmisc_5.1-2       sass_0.4.9        tools_4.4.0      
[17] utf8_1.2.4        yaml_2.3.8        data.table_1.15.4 ggsignif_0.6.4   
[21] htmlwidgets_1.6.4 bit_4.0.5         abind_1.4-5       miniUI_0.1.1.1   
[25] workflowr_1.7.1   withr_3.0.0       foreign_0.8-86    purrr_1.0.2      
[29] nnet_7.3-19       grid_4.4.0        fansi_1.0.6       git2r_0.33.0     
[33] xtable_1.8-4      colorspace_2.1-0  scales_1.3.0      gtools_3.9.5     
[37] cli_3.6.2         generics_0.1.3    rstudioapi_0.16.0 minqa_1.2.6      
[41] cachem_1.0.8      proxy_0.4-27      stringr_1.5.1     splines_4.4.0    
[45] base64enc_0.1-3   vctrs_0.6.5       boot_1.3-30       jsonlite_1.8.8   
[49] carData_3.0-5     queryparser_0.3.2 car_3.1-2         hms_1.1.3        
[53] bit64_4.0.5       rstatix_0.7.2     Formula_1.2-5     htmlTable_2.4.2  
[57] jquerylib_0.1.4   nloptr_2.0.3      lubridate_1.9.3   stringi_1.8.3    
[61] gtable_0.3.5      later_1.3.2       lme4_1.1-35.3     munsell_0.5.1    
[65] tibble_3.2.1      pillar_1.9.0      htmltools_0.5.8.1 R6_2.5.1         
[69] rprojroot_2.0.4   lpSolve_5.6.20    evaluate_0.23     shiny_1.8.1.1    
[73] lattice_0.22-6    backports_1.4.1   broom_1.0.5       httpuv_1.6.15    
[77] bslib_0.7.0       class_7.3-22      Rcpp_1.0.12       nlme_3.1-164     
[81] gridExtra_2.3     checkmate_2.3.1   whisker_0.4.1     xfun_0.43        
[85] fs_1.6.4          zoo_1.8-12        pkgconfig_2.0.3