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Attaching package: 'data.table'
The following objects are masked from 'package:gdata':

    first, last
The following objects are masked from 'package:dplyr':

    between, first, last

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 Definitions

0.1.2 model

[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" 
[1] "The Proportion explained by the principal components: "
[1] 0.559 0.850 1.000

0.2 Results 1: matimm+/-

0.2.1 Direct causal effects

      outcome      deffect        dlower       dupper dpvalue       dfdr
1      PT_IgG -0.437796255 -0.6659503668 -0.163429562   0.000 0.00000000
2   TT_FcgR2a  0.256071844  0.1141989961  0.439205830   0.000 0.00000000
3   TT_FcgR3b  0.609550681  0.2990839307  1.022512968   0.000 0.00000000
4     TT_ADCD  0.433959242  0.2054953620  0.685466333   0.000 0.00000000
5     TT_ADCP  0.206383746  0.0840270499  0.341283338   0.002 0.02000000
6   DT_FcgR3b  0.572777510  0.0848840643  1.011729927   0.010 0.07142857
7     TT_IgG1  0.544240040  0.1174210760  1.005950479   0.010 0.07142857
8    FHA_ADCP -0.118206076 -0.1950125816 -0.025196657   0.012 0.07500000
9     TT_ADNP  0.157238616  0.0254691654  0.273075335   0.022 0.12222222
10    DT_IgG3  0.279411757  0.0200576270  0.469192581   0.030 0.15000000
11    PT_IgG1 -0.382916943 -0.7235185922 -0.010093490   0.034 0.15454545
12    FHA_IgG -0.228346582 -0.4028635116  0.004768727   0.044 0.17857143
13    TT_IgG3  0.224390667  0.0045782358  0.432396135   0.048 0.17857143
14   FHA_IgG2 -0.272631308 -0.5286583667  0.005080510   0.050 0.17857143
15   FHA_IgG4 -0.356565821 -0.7524476427  0.007706168   0.062 0.19411765
16 PRN_FcgR2a  0.296481345 -0.0285871243  0.595154990   0.066 0.19411765
17    PT_IgG3  0.212389576 -0.0073220772  0.430724573   0.066 0.19411765
18 FHA_FcgR2a  0.186418557 -0.0129937221  0.415121000   0.074 0.20555556
19  DT_FcgR2a  0.131280778  0.0004617927  0.333199467   0.082 0.21578947
20   FHA_ADNP  0.089810859 -0.0092439875  0.190050127   0.088 0.22000000
21     TT_IgG  0.155374324 -0.0333963585  0.349032516   0.120 0.27391304
22 FHA_FcgR3b  0.264294145 -0.0514374249  0.648671960   0.124 0.27391304
23    DT_ADCD  0.127481120 -0.0366039393  0.309472389   0.126 0.27391304
24 PRN_FcgR3b  0.399427711 -0.2101596901  0.890768124   0.176 0.36000000
25    PT_IgG2 -0.079612662 -0.2136540218  0.037060502   0.180 0.36000000
26     DT_IgG -0.145741215 -0.3565214066  0.079357770   0.198 0.36551724
27    DT_IgG4 -0.277152572 -0.7035625419  0.134357180   0.206 0.36551724
28   PRN_ADCD  0.159700911 -0.0806461494  0.409848142   0.212 0.36551724
29    PT_ADNP  0.105617489 -0.0495370828  0.283808934   0.212 0.36551724
30   PRN_IgG2  0.166336539 -0.1254750295  0.408818608   0.238 0.39666667
31   PRN_IgG1  0.272054363 -0.1751213107  0.730040726   0.256 0.41290323
32   PRN_ADNP  0.038385381 -0.0300736339  0.112144415   0.282 0.44062500
33    PT_ADCD  0.193109967 -0.1728385714  0.557190086   0.292 0.44242424
34   PRN_IgG3  0.164189691 -0.1333244931  0.460671080   0.306 0.45000000
35    PT_IgG4 -0.056306024 -0.1843457147  0.051375069   0.340 0.48571429
36   FHA_ADCD  0.092373678 -0.1675435972  0.325498320   0.456 0.62702703
37    TT_IgG2  0.045164861 -0.0881174050  0.177222282   0.464 0.62702703
38    DT_ADNP  0.015811015 -0.0382049698  0.072604126   0.516 0.66410256
39    DT_IgG2 -0.096476378 -0.3504110572  0.188005416   0.518 0.66410256
40    PRN_IgG -0.086525591 -0.3643006577  0.182001282   0.546 0.67804878
41   FHA_IgG3  0.101720076 -0.2304640131  0.403481978   0.556 0.67804878
42   PRN_IgG4  0.057299548 -0.2306736333  0.285087288   0.638 0.75952381
43   FHA_IgG1  0.066382412 -0.2430847626  0.364172736   0.654 0.76046512
44    TT_IgG4  0.047198392 -0.2420750976  0.307465551   0.694 0.78863636
45   PRN_ADCP -0.018251222 -0.1223102594  0.096856768   0.728 0.79565217
46    DT_IgG1  0.073993113 -0.3332654197  0.573146259   0.732 0.79565217
47  PT_FcgR3b -0.039853026 -0.2866512651  0.260311645   0.808 0.84166667
48    PT_ADCP -0.015272535 -0.1400979573  0.107621217   0.808 0.84166667
49    DT_ADCP -0.002280838 -0.0591040660  0.060352039   0.894 0.91224490
50  PT_FcgR2a -0.006686480 -0.3334244796  0.278623575   0.952 0.95200000

0.2.2 Mediation causal effects

      outcome         meffect       mlower       mupper mpvalue  mfdr
1    FHA_IgG1 -0.075689516839 -0.236802000 0.0002190974   0.096 0.972
2    FHA_IgG2 -0.051119791084 -0.175516290 0.0047667498   0.154 0.972
3      TT_IgG -0.032180838391 -0.146588501 0.0013944285   0.154 0.972
4    FHA_ADNP -0.017780785324 -0.066997593 0.0026799186   0.166 0.972
5     FHA_IgG -0.030160367569 -0.096346950 0.0038051702   0.172 0.972
6    FHA_ADCP -0.013561595767 -0.042770206 0.0027023031   0.206 0.972
7     DT_ADCP  0.007459049766 -0.001242029 0.0338833166   0.214 0.972
8    FHA_IgG3 -0.047308939560 -0.183454346 0.0114101162   0.270 0.972
9     DT_IgG3 -0.031672097728 -0.115976773 0.0146934328   0.286 0.972
10    PT_IgG3 -0.026863507557 -0.132032351 0.0096157641   0.316 0.972
11    TT_IgG2  0.020335399096 -0.014389584 0.0744866612   0.334 0.972
12 FHA_FcgR2a -0.023352753799 -0.121338530 0.0109189617   0.344 0.972
13 FHA_FcgR3b -0.040204106466 -0.181044765 0.0205292166   0.356 0.972
14 PRN_FcgR3b  0.051265353584 -0.048018223 0.2629233962   0.404 0.972
15     DT_IgG -0.019117699448 -0.111913436 0.0102939226   0.406 0.972
16   PRN_ADCP  0.010532392655 -0.010069482 0.0444795689   0.412 0.972
17  TT_FcgR2a -0.014934156805 -0.114518334 0.0067660505   0.430 0.972
18    DT_IgG4 -0.038035469877 -0.209637531 0.0386701738   0.456 0.972
19    PT_ADCD  0.034885432340 -0.032226487 0.1741766056   0.458 0.972
20    TT_IgG3 -0.020316638035 -0.108374690 0.0229748660   0.462 0.972
21   FHA_ADCD -0.019462933572 -0.079933785 0.0243764404   0.500 0.972
22   PRN_IgG1  0.045124829744 -0.061632169 0.2482312631   0.510 0.972
23    PT_ADNP  0.013584324311 -0.019933323 0.0663214726   0.522 0.972
24  TT_FcgR3b -0.020195743714 -0.207616777 0.0241198644   0.562 0.972
25 PRN_FcgR2a  0.018761185451 -0.031736178 0.1143405589   0.576 0.972
26    TT_ADNP  0.007800509659 -0.017352101 0.0466144016   0.578 0.972
27   PRN_IgG3 -0.026665893329 -0.143718450 0.0581021318   0.580 0.972
28    TT_IgG4  0.030884202687 -0.049421497 0.1394571902   0.604 0.972
29  DT_FcgR3b -0.030976705888 -0.219047506 0.0637426040   0.610 0.972
30    TT_ADCD -0.011404988689 -0.115846083 0.0220653668   0.634 0.972
31  DT_FcgR2a -0.009850882547 -0.101049308 0.0139439645   0.646 0.972
32  PT_FcgR3b  0.014792231211 -0.042610224 0.1245712779   0.658 0.972
33   FHA_IgG4 -0.021799008971 -0.165726513 0.0709249699   0.662 0.972
34    TT_IgG1 -0.016547651402 -0.237692121 0.0594507348   0.674 0.972
35  PT_FcgR2a  0.015445521247 -0.063571741 0.1164317223   0.724 0.972
36   PRN_IgG2 -0.009749616288 -0.118451565 0.0412160288   0.726 0.972
37     PT_IgG  0.010876217604 -0.045540610 0.0914122885   0.750 0.972
38    PT_ADCP  0.004794060812 -0.030037436 0.0354236402   0.774 0.972
39    TT_ADCP -0.004356780099 -0.075856600 0.0150031585   0.792 0.972
40    PT_IgG2  0.002855577421 -0.019976788 0.0589008347   0.796 0.972
41    DT_ADNP  0.001348914574 -0.010690545 0.0218587596   0.826 0.972
42   PRN_IgG4 -0.001773783320 -0.094932127 0.0500552181   0.828 0.972
43    DT_IgG2 -0.000926649410 -0.144624035 0.0457107842   0.856 0.972
44    PT_IgG1  0.005284322225 -0.100837449 0.1011699604   0.896 0.972
45    DT_IgG1 -0.004110558204 -0.236509366 0.1217741224   0.910 0.972
46   PRN_ADNP -0.001179825633 -0.031424668 0.0169278087   0.922 0.972
47   PRN_ADCD  0.001046268738 -0.075739084 0.0468950406   0.940 0.972
48    PT_IgG4  0.001034985180 -0.049635779 0.0338484893   0.954 0.972
49    DT_ADCD  0.001504258512 -0.049684477 0.0342790173   0.964 0.972
50    PRN_IgG  0.000005552545 -0.054265981 0.0892570738   0.972 0.972

0.2.3 Total effects

      outcome      teffect       tlower      tupper tpvalue       tfdr
1      PT_IgG -0.426920037 -0.653541754 -0.17079027   0.000 0.00000000
2   TT_FcgR2a  0.241137688  0.112672135  0.39658401   0.000 0.00000000
3   TT_FcgR3b  0.589354937  0.286580684  0.96287633   0.000 0.00000000
4     TT_ADCD  0.422554253  0.207049865  0.67251212   0.000 0.00000000
5     TT_ADCP  0.202026966  0.082678188  0.32276265   0.000 0.00000000
6     TT_ADNP  0.165039126  0.043148212  0.26717823   0.002 0.01666667
7    FHA_ADCP -0.131767672 -0.210631927 -0.03967033   0.006 0.04285714
8   DT_FcgR3b  0.541800804  0.113682724  0.96152150   0.008 0.05000000
9     TT_IgG1  0.527692388  0.104098056  0.93921965   0.010 0.05555556
10   FHA_IgG2 -0.323751099 -0.549761177 -0.04007584   0.018 0.09000000
11   FHA_IgG4 -0.378364830 -0.712448821 -0.05124104   0.020 0.09090909
12    FHA_IgG -0.258506950 -0.418234923 -0.02121004   0.024 0.10000000
13    PT_IgG1 -0.377632621 -0.742275776 -0.02110133   0.036 0.13846154
14    DT_IgG3  0.247739659 -0.002742856  0.44069838   0.048 0.17142857
15 PRN_FcgR2a  0.315242530 -0.005205230  0.60871583   0.052 0.17333333
16    TT_IgG3  0.204074029 -0.002667692  0.42353459   0.068 0.21250000
17  DT_FcgR2a  0.121429896 -0.002527717  0.28321970   0.076 0.22352941
18 FHA_FcgR2a  0.163065803 -0.012169028  0.37889210   0.082 0.22777778
19    PT_IgG3  0.185526068 -0.033588380  0.41153944   0.098 0.25000000
20    DT_ADCD  0.128985379 -0.022376023  0.30278383   0.102 0.25000000
21 PRN_FcgR3b  0.450693065 -0.131731065  0.93495094   0.108 0.25000000
22    DT_IgG4 -0.315188042 -0.732436848  0.04657734   0.110 0.25000000
23     DT_IgG -0.164858914 -0.347968355  0.03850453   0.120 0.26086957
24   FHA_ADNP  0.072030074 -0.018004534  0.17264912   0.150 0.30000000
25    PT_ADNP  0.119201813 -0.041417684  0.27319357   0.150 0.30000000
26   PRN_IgG1  0.317179192 -0.118224593  0.78166994   0.162 0.31153846
27 FHA_FcgR3b  0.224090039 -0.076937737  0.57417555   0.176 0.31428571
28   PRN_ADCD  0.160747179 -0.058455909  0.37462946   0.176 0.31428571
29    PT_IgG2 -0.076757084 -0.196197377  0.03995595   0.198 0.34137931
30     TT_IgG  0.123193486 -0.065330111  0.29580930   0.224 0.36129032
31    PT_ADCD  0.227995399 -0.138264040  0.56996167   0.224 0.36129032
32    PT_IgG4 -0.055271039 -0.156165749  0.03474189   0.238 0.36969697
33   PRN_IgG2  0.156586922 -0.128357277  0.39426554   0.244 0.36969697
34   PRN_ADNP  0.037205555 -0.029172947  0.10630082   0.272 0.40000000
35    TT_IgG2  0.065500260 -0.064554712  0.20141165   0.300 0.42857143
36   PRN_IgG3  0.137523797 -0.150732732  0.45182472   0.398 0.54324324
37    DT_IgG2 -0.097403027 -0.325925112  0.14959872   0.402 0.54324324
38    DT_ADNP  0.017159929 -0.034576403  0.07194845   0.484 0.63684211
39    PRN_IgG -0.086520039 -0.349284060  0.15606738   0.528 0.67692308
40   FHA_ADCD  0.072910744 -0.169273190  0.32104635   0.546 0.67804878
41    TT_IgG4  0.078082594 -0.155089542  0.33799040   0.556 0.67804878
42   PRN_IgG4  0.055525765 -0.199296474  0.23930106   0.600 0.71428571
43   FHA_IgG3  0.054411136 -0.259839704  0.33886449   0.732 0.85116279
44    DT_IgG1  0.069882555 -0.341157934  0.53216366   0.750 0.85227273
45    PT_ADCP -0.010478474 -0.130952146  0.10331083   0.844 0.92173913
46   PRN_ADCP -0.007718830 -0.117880274  0.10176049   0.848 0.92173913
47    DT_ADCP  0.005178212 -0.050916202  0.06485176   0.880 0.93617021
48  PT_FcgR3b -0.025060794 -0.275378988  0.26689601   0.914 0.95208333
49   FHA_IgG1 -0.009307104 -0.320998145  0.26535682   0.956 0.97551020
50  PT_FcgR2a  0.008759042 -0.317150230  0.27533538   0.982 0.98200000

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 broom_1.0.5        here_1.0.1         glue_1.7.0        
 [5] RPostgres_1.4.6    DT_0.33            data.table_1.15.4  DBI_1.2.2         
 [9] pls_2.8-3          mediation_4.5.0    sandwich_3.1-0     mvtnorm_1.2-4     
[13] Matrix_1.7-0       MASS_7.3-60.2      ggpubr_0.6.0       ggExtra_0.10.1    
[17] e1071_1.7-14       ggfortify_0.4.17   rmarkdown_2.26     knitr_1.46        
[21] ggplot2_3.5.1      gdata_3.0.0        tidyr_1.3.1        tidyquery_0.2.4   
[25] 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        ggsignif_0.6.4    htmlwidgets_1.6.4
[21] bit_4.0.5         abind_1.4-5       miniUI_0.1.1.1    workflowr_1.7.1  
[25] withr_3.0.0       foreign_0.8-86    purrr_1.0.2       nnet_7.3-19      
[29] grid_4.4.0        fansi_1.0.6       git2r_0.33.0      xtable_1.8-4     
[33] colorspace_2.1-0  scales_1.3.0      gtools_3.9.5      cli_3.6.2        
[37] generics_0.1.3    rstudioapi_0.16.0 minqa_1.2.6       cachem_1.0.8     
[41] proxy_0.4-27      stringr_1.5.1     splines_4.4.0     base64enc_0.1-3  
[45] vctrs_0.6.5       boot_1.3-30       jsonlite_1.8.8    carData_3.0-5    
[49] queryparser_0.3.2 car_3.1-2         hms_1.1.3         bit64_4.0.5      
[53] rstatix_0.7.2     Formula_1.2-5     htmlTable_2.4.2   jquerylib_0.1.4  
[57] nloptr_2.0.3      lubridate_1.9.3   stringi_1.8.3     gtable_0.3.5     
[61] later_1.3.2       lme4_1.1-35.3     munsell_0.5.1     tibble_3.2.1     
[65] pillar_1.9.0      htmltools_0.5.8.1 R6_2.5.1          rprojroot_2.0.4  
[69] lpSolve_5.6.20    evaluate_0.23     shiny_1.8.1.1     lattice_0.22-6   
[73] backports_1.4.1   httpuv_1.6.15     bslib_0.7.0       class_7.3-22     
[77] Rcpp_1.0.12       nlme_3.1-164      gridExtra_2.3     checkmate_2.3.1  
[81] whisker_0.4.1     xfun_0.43         fs_1.6.4          zoo_1.8-12       
[85] pkgconfig_2.0.3