Causal Mediation Analysis
Jie Zhou
2023-11-29
Last updated: 2024-06-09
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Knit directory:
madi-brussels-pertussis-thailand/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 8c46744 | Jie Zhou | 2024-06-03 | remove antigen elisa |
| html | 8c46744 | Jie Zhou | 2024-06-03 | remove antigen elisa |
| html | 2fd12dc | Jie Zhou | 2024-05-31 | start manuscript 2 |
| Rmd | 42c1edc | Jie Zhou | 2024-04-28 | double pca |
| html | 42c1edc | Jie Zhou | 2024-04-28 | double pca |
| Rmd | 17ca781 | Jie Zhou | 2024-04-07 | cleanup |
Attaching package: 'glue'The following object is masked from 'package:gdata':
trimhere() starts at C:/Users/Jie Zhou/Desktop/madi-brussels-pertussis-thailand0.1 Model description
[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+/-
### load PCA scores
library(tidyr)
load("./code/pca_scores_both_studies.RData")
index=which(pca_store$group %in% c("RClust1", "RClust2", "RClust3", "RClust4")
& pca_store$manuscript=="manuscript1"
& pca_store$visit_name=="vaccinated")
clusterdata=pca_store[index,]
cl1=clusterdata[which(clusterdata$group=="RClust1"),]
cl2=clusterdata[which(clusterdata$group=="RClust2"),]
cl3=clusterdata[which(clusterdata$group=="RClust3"),]
cl4=clusterdata[which(clusterdata$group=="RClust4"),]0.2.1 cluster 1
0.2.1.1 Direct causal effects
outcome mediator deffect dlower dupper dpvalue dfdr
1 PC2 ELISA_FHA_IgG -1.33364323 -2.285571 -0.4527285 0.002 0.012
2 PC2 ELISA_PRN_IgG -1.39596664 -2.322278 -0.4387961 0.006 0.018
3 PC2 ELISA_PT_IgG -1.33183009 -2.286999 -0.3912140 0.010 0.020
4 PC1 ELISA_PRN_IgG -0.18317077 -1.629314 1.1183415 0.822 0.984
5 PC1 ELISA_FHA_IgG -0.13712247 -1.490628 1.1832640 0.830 0.984
6 PC1 ELISA_PT_IgG -0.00570454 -1.412446 1.3864768 0.984 0.9840.2.1.2 Mediation causal effects
outcome mediator meffect mlower mupper mpvalue mfdr
1 PC2 ELISA_FHA_IgG -0.0900569387 -0.4044780 0.1081501 0.440 0.8784
2 PC2 ELISA_PT_IgG -0.0817426340 -0.3817395 0.1183038 0.446 0.8784
3 PC1 ELISA_PT_IgG -0.0814718563 -0.5017488 0.2331207 0.596 0.8784
4 PC1 ELISA_PRN_IgG 0.0658518784 -0.2176415 0.4599149 0.666 0.8784
5 PC1 ELISA_FHA_IgG 0.0465015288 -0.1838283 0.3744302 0.732 0.8784
6 PC2 ELISA_PRN_IgG -0.0004444533 -0.2075622 0.2128584 0.984 0.98400.2.1.3 Total effects
outcome mediator teffect tlower tupper tpvalue tfdr
1 PC2 ELISA_FHA_IgG -1.42370017 -2.368972 -0.4885919 0.000 0.000
2 PC2 ELISA_PRN_IgG -1.39641109 -2.315415 -0.5125377 0.000 0.000
3 PC2 ELISA_PT_IgG -1.41357272 -2.362192 -0.4705191 0.002 0.004
4 PC1 ELISA_FHA_IgG -0.09062094 -1.417274 1.2367720 0.866 0.898
5 PC1 ELISA_PRN_IgG -0.11731889 -1.532371 1.2359292 0.898 0.898
6 PC1 ELISA_PT_IgG -0.08717640 -1.462824 1.3303458 0.898 0.8980.2.2 cluster 2
0.2.2.1 Direct causal effects
outcome mediator deffect dlower dupper dpvalue dfdr
1 PC1 ELISA_PT_IgG 1.9630587 0.5345413 3.462975 0.012 0.0480
2 PC1 ELISA_PRN_IgG 1.9192500 0.3824428 3.367074 0.016 0.0480
3 PC1 ELISA_FHA_IgG 1.7779105 0.1810343 3.302970 0.028 0.0560
4 PC2 ELISA_PRN_IgG 0.5122989 -0.1999695 1.257762 0.160 0.2400
5 PC2 ELISA_FHA_IgG 0.4870020 -0.2543515 1.277551 0.212 0.2544
6 PC2 ELISA_PT_IgG 0.4117045 -0.3430096 1.134905 0.304 0.30400.2.2.2 Mediation causal effects
outcome mediator meffect mlower mupper mpvalue mfdr
1 PC2 ELISA_PT_IgG 0.135497089 -0.04313602 0.4079518 0.176 0.855
2 PC1 ELISA_PT_IgG -0.190745271 -0.69613816 0.1234275 0.300 0.855
3 PC1 ELISA_PRN_IgG -0.107981143 -0.56590047 0.1677196 0.506 0.855
4 PC2 ELISA_FHA_IgG 0.044701674 -0.08492599 0.2599039 0.570 0.855
5 PC2 ELISA_PRN_IgG 0.012496199 -0.12218534 0.1980211 0.866 0.986
6 PC1 ELISA_FHA_IgG 0.002276055 -0.37890251 0.3241301 0.986 0.9860.2.2.3 Total effects
outcome mediator teffect tlower tupper tpvalue tfdr
1 PC1 ELISA_PT_IgG 1.7723134 0.3056033 3.203446 0.018 0.060
2 PC1 ELISA_PRN_IgG 1.8112688 0.2532304 3.251029 0.020 0.060
3 PC1 ELISA_FHA_IgG 1.7801866 0.1711000 3.303233 0.032 0.064
4 PC2 ELISA_PRN_IgG 0.5247951 -0.1938216 1.231579 0.152 0.182
5 PC2 ELISA_FHA_IgG 0.5317037 -0.2157883 1.322118 0.170 0.182
6 PC2 ELISA_PT_IgG 0.5472016 -0.2216279 1.278463 0.182 0.1820.2.3 cluster 3
0.2.3.1 Direct causal effects
outcome mediator deffect dlower dupper dpvalue dfdr
1 PC2 ELISA_PRN_IgG 1.42579764 0.2864403 2.397460 0.004 0.0240
2 PC2 ELISA_FHA_IgG 1.49781195 0.4836739 2.568917 0.008 0.0240
3 PC2 ELISA_PT_IgG 1.51878647 0.4618136 2.514459 0.012 0.0240
4 PC1 ELISA_PRN_IgG 0.28230579 -1.1192842 1.719964 0.690 0.8976
5 PC1 ELISA_FHA_IgG 0.27676964 -1.2070390 1.767124 0.748 0.8976
6 PC1 ELISA_PT_IgG 0.07314142 -1.5253284 1.609204 0.916 0.91600.2.3.2 Mediation causal effects
outcome mediator meffect mlower mupper mpvalue mfdr
1 PC1 ELISA_PT_IgG 0.13007741 -0.2022499 0.6181570 0.470 0.946
2 PC2 ELISA_PT_IgG -0.09044620 -0.4215620 0.1494247 0.488 0.946
3 PC2 ELISA_FHA_IgG -0.04950298 -0.3347248 0.1561648 0.686 0.946
4 PC1 ELISA_PRN_IgG -0.05012777 -0.4104483 0.2095281 0.758 0.946
5 PC1 ELISA_FHA_IgG -0.02064108 -0.3280140 0.2609410 0.852 0.946
6 PC2 ELISA_PRN_IgG -0.01103198 -0.2652956 0.1872902 0.946 0.9460.2.3.3 Total effects
outcome mediator teffect tlower tupper tpvalue tfdr
1 PC2 ELISA_PRN_IgG 1.4147657 0.3228873 2.415478 0.002 0.012
2 PC2 ELISA_FHA_IgG 1.4483090 0.4138235 2.542958 0.008 0.016
3 PC2 ELISA_PT_IgG 1.4283403 0.3166595 2.423078 0.008 0.016
4 PC1 ELISA_PRN_IgG 0.2321780 -1.2343321 1.630743 0.744 0.782
5 PC1 ELISA_FHA_IgG 0.2561286 -1.2193489 1.694458 0.766 0.782
6 PC1 ELISA_PT_IgG 0.2032188 -1.3728811 1.644870 0.782 0.782
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