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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 528d126 | Jie Zhou | 2024-01-23 | added pls and pca based mediation analysis |
| html | 528d126 | Jie Zhou | 2024-01-23 | added pls and pca based mediation analysis |
| html | 7e12be2 | Jie Zhou | 2024-01-15 | added pls mediation analysis |
| Rmd | 30792a7 | Jie Zhou | 2024-01-13 | added pls mediation analysis |
| html | 30792a7 | Jie Zhou | 2024-01-13 | added pls mediation analysis |
Attaching package: 'glue'The following object is masked from 'package:gdata':
trimhere() starts at C:/Users/Jie Zhou/Desktop/madi-brussels-pertussis-thailand[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 with ELISA): "[1] "ELISA_FHA_IgG" "ELISA_PRN_IgG" "ELISA_PT_IgG" outcome deffect dlower dupper dpvalue dfdr
1 PT_IgG -0.4194867626 -0.646005041 -0.146839004 0.000 0.00000000
2 TT_FcgR2a 0.2519224842 0.108219438 0.405794985 0.000 0.00000000
3 TT_FcgR3b 0.5969227363 0.286236439 0.997289595 0.000 0.00000000
4 TT_ADCD 0.4155610970 0.191761694 0.654806774 0.000 0.00000000
5 TT_ADCP 0.2011831741 0.080606654 0.321791702 0.000 0.00000000
6 TT_IgG1 0.5355682895 0.132385986 0.973455718 0.008 0.06666667
7 DT_FcgR3b 0.5365543432 0.093365552 0.949627465 0.010 0.07142857
8 FHA_ADCP -0.1191948205 -0.196103658 -0.026843019 0.014 0.08750000
9 TT_ADNP 0.1570412465 0.023967062 0.269939092 0.020 0.11111111
10 DT_IgG3 0.2917482953 0.042252329 0.486646412 0.024 0.12000000
11 FHA_IgG -0.2323643505 -0.404853044 -0.007319695 0.032 0.14545455
12 PT_IgG3 0.2191228311 0.003324850 0.422863925 0.040 0.16153846
13 PT_IgG1 -0.3610174346 -0.711316789 -0.016809777 0.042 0.16153846
14 TT_IgG3 0.2240585553 0.002877598 0.441323685 0.052 0.18571429
15 FHA_IgG2 -0.2505785493 -0.493252434 0.009358586 0.056 0.18666667
16 FHA_FcgR2a 0.1858684610 0.001771516 0.413076455 0.064 0.18823529
17 FHA_IgG4 -0.3388279640 -0.685055966 0.009523665 0.064 0.18823529
18 PRN_FcgR2a 0.2883685679 -0.037375364 0.581512538 0.068 0.18888889
19 FHA_ADNP 0.0919768316 -0.007306544 0.194813333 0.076 0.20000000
20 DT_FcgR2a 0.1286960335 -0.006509772 0.318666277 0.092 0.23000000
21 FHA_FcgR3b 0.2644471361 -0.068863780 0.642291150 0.106 0.25238095
22 TT_IgG 0.1472988667 -0.048242957 0.322483588 0.144 0.32727273
23 PRN_FcgR3b 0.4054539158 -0.199998928 0.877851375 0.172 0.37391304
24 PRN_ADCD 0.1506924955 -0.072849863 0.358013015 0.190 0.37931034
25 DT_ADCD 0.0995824264 -0.047309145 0.248449280 0.202 0.37931034
26 PT_IgG2 -0.0752337491 -0.195812183 0.043135773 0.206 0.37931034
27 PT_ADNP 0.1052672386 -0.050671480 0.275431383 0.208 0.37931034
28 DT_IgG4 -0.2565092828 -0.684379368 0.129867784 0.218 0.37931034
29 DT_IgG -0.1410915135 -0.353223154 0.081569167 0.220 0.37931034
30 PRN_IgG2 0.1584620126 -0.126248198 0.384584183 0.252 0.39696970
31 PRN_IgG1 0.2794602125 -0.167968664 0.732165002 0.258 0.39696970
32 PT_IgG4 -0.0552628819 -0.168748023 0.038278742 0.262 0.39696970
33 PRN_ADNP 0.0397604828 -0.030898593 0.109605260 0.262 0.39696970
34 PRN_IgG3 0.1699961951 -0.114406591 0.469937059 0.274 0.40294118
35 PT_ADCD 0.1698935931 -0.198947364 0.526121421 0.372 0.53142857
36 DT_IgG2 -0.1004507254 -0.344236004 0.139063339 0.394 0.54722222
37 TT_IgG2 0.0484467367 -0.084078511 0.178739853 0.446 0.60270270
38 FHA_ADCD 0.0881184515 -0.165915964 0.335542643 0.482 0.63421053
39 FHA_IgG3 0.1029681950 -0.230562102 0.410499111 0.548 0.70256410
40 DT_ADNP 0.0137511603 -0.037979899 0.066229931 0.566 0.70750000
41 PRN_IgG -0.0740126631 -0.350470534 0.189953322 0.604 0.73571429
42 PRN_IgG4 0.0499452724 -0.223750514 0.237602487 0.618 0.73571429
43 PRN_ADCP -0.0197120317 -0.123540454 0.092049952 0.686 0.79545455
44 TT_IgG4 0.0540463429 -0.211795064 0.296006026 0.700 0.79545455
45 FHA_IgG1 0.0528474066 -0.256068880 0.354446774 0.728 0.80888889
46 PT_ADCP -0.0153444397 -0.139672842 0.107901294 0.808 0.86595745
47 DT_IgG1 0.0539887218 -0.386831768 0.518107530 0.814 0.86595745
48 PT_FcgR3b -0.0316205359 -0.274930041 0.273297716 0.874 0.91041667
49 PT_FcgR2a -0.0008826274 -0.319366013 0.267602678 0.950 0.96400000
50 DT_ADCP -0.0009174507 -0.054439239 0.060452539 0.964 0.96400000 outcome meffect mlower mupper mpvalue mfdr
1 FHA_IgG2 -0.073172549584 -0.201583280 0.0024346907 0.108 0.9340909
2 FHA_ADNP -0.019946757708 -0.073810329 0.0005820076 0.118 0.9340909
3 FHA_IgG1 -0.062154510939 -0.220487139 0.0033081516 0.136 0.9340909
4 DT_IgG3 -0.044008636043 -0.145458945 0.0066480265 0.156 0.9340909
5 FHA_ADCP -0.012572851168 -0.042846312 0.0028584794 0.230 0.9340909
6 PT_ADCD 0.058101806308 -0.010226127 0.2310065531 0.232 0.9340909
7 FHA_IgG -0.026142599277 -0.093054523 0.0071187200 0.236 0.9340909
8 FHA_IgG3 -0.048557058861 -0.198344965 0.0079341576 0.258 0.9340909
9 PRN_ADCP 0.011993201947 -0.003936427 0.0499245598 0.276 0.9340909
10 TT_IgG -0.024105381002 -0.096749036 0.0066423861 0.282 0.9340909
11 DT_IgG -0.023767400511 -0.126920104 0.0072524254 0.312 0.9340909
12 PT_IgG3 -0.033596762617 -0.129533754 0.0219412393 0.312 0.9340909
13 FHA_FcgR3b -0.040357097535 -0.204043963 0.0173757164 0.320 0.9340909
14 DT_ADCD 0.029402952418 -0.008425990 0.1587532049 0.350 0.9340909
15 DT_IgG4 -0.058678758762 -0.276504854 0.0186577938 0.354 0.9340909
16 FHA_FcgR2a -0.022802657658 -0.108907020 0.0095520000 0.366 0.9340909
17 DT_ADCP 0.006095662905 -0.003318502 0.0251941015 0.376 0.9340909
18 PRN_FcgR2a 0.026873962406 -0.011555119 0.1499793813 0.384 0.9340909
19 PRN_FcgR3b 0.045239148881 -0.024185177 0.2989431822 0.398 0.9340909
20 TT_IgG2 0.017053523380 -0.013631448 0.0704778708 0.402 0.9340909
21 FHA_IgG4 -0.039536865792 -0.267034911 0.0192498117 0.426 0.9340909
22 TT_IgG3 -0.019984526745 -0.103839191 0.0212084840 0.428 0.9340909
23 PRN_IgG3 -0.032472397842 -0.180846944 0.0306178785 0.430 0.9340909
24 TT_IgG4 0.024036251476 -0.014780563 0.1675479447 0.482 0.9340909
25 PRN_IgG1 0.037718979703 -0.025208786 0.2667427055 0.490 0.9340909
26 PT_ADNP 0.013934574417 -0.012994459 0.0689806404 0.490 0.9340909
27 DT_ADNP 0.003408768889 -0.002492729 0.0317201199 0.532 0.9340909
28 TT_ADNP 0.007997879330 -0.013941219 0.0540228455 0.558 0.9340909
29 FHA_ADCD -0.015207707299 -0.080690812 0.0142772709 0.584 0.9340909
30 PT_IgG1 -0.016615185965 -0.141772581 0.0164652156 0.612 0.9340909
31 TT_FcgR2a -0.010784796560 -0.065307452 0.0157213442 0.620 0.9340909
32 PRN_ADCD 0.010054683910 -0.013783375 0.1029336484 0.628 0.9340909
33 DT_IgG1 0.015893832877 -0.015891080 0.2431585142 0.640 0.9340909
34 PRN_IgG -0.012507375652 -0.096263200 0.0228440857 0.690 0.9340909
35 PRN_ADNP -0.002554927774 -0.032771722 0.0048008132 0.708 0.9340909
36 TT_ADCD 0.006993155935 -0.009905301 0.0924091831 0.722 0.9340909
37 PT_FcgR2a 0.009641668935 -0.017074252 0.1526248913 0.728 0.9340909
38 PT_IgG -0.007433274838 -0.117571227 0.0161828432 0.754 0.9340909
39 PT_ADCP 0.004865965938 -0.029233304 0.0364812142 0.764 0.9340909
40 DT_FcgR3b 0.005246460967 -0.020595587 0.1884751207 0.792 0.9340909
41 PT_FcgR3b 0.006559741551 -0.024789099 0.0933435673 0.806 0.9340909
42 TT_IgG1 -0.007875901040 -0.224872405 0.0515854148 0.808 0.9340909
43 PRN_IgG4 0.005580492812 -0.049332672 0.0906586185 0.818 0.9340909
44 DT_IgG2 0.003047697980 -0.017377542 0.0969960252 0.822 0.9340909
45 TT_FcgR3b -0.007567799289 -0.100447282 0.0550882482 0.854 0.9478261
46 TT_ADCP 0.000843792155 -0.013886552 0.0432641543 0.872 0.9478261
47 PT_IgG2 -0.001523335077 -0.033698990 0.0141338138 0.892 0.9489362
48 DT_FcgR2a -0.007266137885 -0.080823962 0.0265782573 0.932 0.9530612
49 PRN_IgG2 -0.001875090362 -0.025062324 0.0624745821 0.934 0.9530612
50 PT_IgG4 -0.000008157036 -0.015008320 0.0320748436 0.956 0.9560000
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