Last updated: 2021-11-22
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Knit directory: proxyMR/
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Untracked files:
Untracked: Rplots.pdf
Unstaged changes:
Modified: analysis/AM_MR_summary.Rmd
Modified: analysis/couple_selection.Rmd
Modified: output/tables/define_Neale_categories.csv
Modified: output/tables/define_Neale_categories_filled.csv
Modified: renv.lock
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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/update_meeting_11_11_2021.Rmd
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File | Version | Author | Date | Message |
---|---|---|---|---|
Rmd | 810aae7 | Jenny Sjaarda | 2021-11-22 | wflow_publish("analysis/update_meeting_11_11_2021.Rmd") |
Rmd | 9845a87 | jennysjaarda | 2021-11-11 | add update meeting 11-11-21 |
html | 9845a87 | jennysjaarda | 2021-11-11 | add update meeting 11-11-21 |
# r reverse_MR_threshold
, corresponding to the reverse_MR_threshold
in the code below.reverse_t_threshold = stats::qnorm(reverse_MR_threshold)
dat_filter <- dat %>%
mutate(z_score.exposure = beta.exposure / se.exposure) %>%
mutate(z_score.outcome = beta.outcome / se.outcome) %>%
mutate(std_beta.exposure = z_score.exposure / sqrt(samplesize.exposure)) %>%
mutate(std_beta.outcome = z_score.outcome / sqrt(samplesize.outcome)) %>%
mutate(std_se.exposure = 1 / sqrt(samplesize.exposure)) %>%
mutate(std_se.outcome = 1 / sqrt(samplesize.outcome)) %>%
mutate(std_t_stat = (abs(std_beta.exposure) - abs(std_beta.outcome)) /
sqrt(std_se.exposure^2 + std_se.outcome^2)) %>%
filter(std_t_stat > reverse_t_threshold)
As a recap, the model is below.
Version | Author | Date |
---|---|---|
529020f | jennysjaarda | 2021-09-24 |
A summary of the regressions between \(\omega\), \(\rho\) and \(\gamma\) is below.
Call:
lm(formula = rho_beta ~ omega_beta + 0, data = data)
Residuals:
Min 1Q Median 3Q Max
-0.59720 -0.02468 0.00983 0.04595 0.36472
Coefficients:
Estimate Std. Error t value Pr(>|t|)
omega_beta 0.445129 0.009718 45.8 <0.0000000000000002 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Residual standard error: 0.06695 on 929 degrees of freedom
Multiple R-squared: 0.6931, Adjusted R-squared: 0.6928
F-statistic: 2098 on 1 and 929 DF, p-value: < 0.00000000000000022
Call:
lm(formula = gam_beta ~ omega_beta + 0, data = data)
Residuals:
Min 1Q Median 3Q Max
-0.75402 -0.02179 0.01994 0.04937 1.10864
Coefficients:
Estimate Std. Error t value Pr(>|t|)
omega_beta 0.62689 0.01225 51.18 <0.0000000000000002 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Residual standard error: 0.08438 on 929 degrees of freedom
Multiple R-squared: 0.7382, Adjusted R-squared: 0.7379
F-statistic: 2620 on 1 and 929 DF, p-value: < 0.00000000000000022
Call:
lm(formula = gam_rho_beta ~ omega_beta + 0, data = data)
Residuals:
Min 1Q Median 3Q Max
-1.18334 -0.02240 0.02567 0.07289 1.45454
Coefficients:
Estimate Std. Error t value Pr(>|t|)
omega_beta 1.07202 0.01664 64.42 <0.0000000000000002 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Residual standard error: 0.1147 on 929 degrees of freedom
Multiple R-squared: 0.8171, Adjusted R-squared: 0.8169
F-statistic: 4149 on 1 and 929 DF, p-value: < 0.00000000000000022
Call:
lm(formula = gam_rho_resid ~ omega_beta + 0, data = data)
Residuals:
Min 1Q Median 3Q Max
-0.76873 -0.02561 0.01144 0.04716 0.85106
Coefficients:
Estimate Std. Error t value Pr(>|t|)
omega_beta 0.72646 0.01171 62.02 <0.0000000000000002 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Residual standard error: 0.0807 on 929 degrees of freedom
Multiple R-squared: 0.8054, Adjusted R-squared: 0.8052
F-statistic: 3846 on 1 and 929 DF, p-value: < 0.00000000000000022
sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /data/sgg2/jenny/bin/R-4.1.0/lib64/R/lib/libRblas.so
LAPACK: /data/sgg2/jenny/bin/R-4.1.0/lib64/R/lib/libRlapack.so
locale:
[1] en_CA.UTF-8
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] cowplot_1.1.1 kableExtra_1.3.4 knitr_1.33 DT_0.18.1
[5] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4
[9] readr_1.4.0 tidyr_1.1.3 tibble_3.1.2 ggplot2_3.3.4
[13] tidyverse_1.3.1 targets_0.5.0.9001 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] httr_1.4.2 sass_0.4.0 splines_4.1.0 jsonlite_1.7.2
[5] viridisLite_0.4.0 modelr_0.1.8 bslib_0.3.0 assertthat_0.2.1
[9] highr_0.9 renv_0.13.2-62 cellranger_1.1.0 yaml_2.2.1
[13] lattice_0.20-44 pillar_1.6.1 backports_1.2.1 glue_1.4.2
[17] digest_0.6.27 promises_1.2.0.1 rvest_1.0.0 colorspace_2.0-1
[21] Matrix_1.3-3 htmltools_0.5.2 httpuv_1.6.1 pkgconfig_2.0.3
[25] broom_0.7.7 haven_2.4.1 scales_1.1.1 webshot_0.5.2
[29] processx_3.5.2 svglite_2.0.0 whisker_0.4 later_1.2.0
[33] git2r_0.28.0 mgcv_1.8-35 farver_2.1.0 generics_0.1.0
[37] ellipsis_0.3.2 withr_2.4.2 cli_2.5.0 magrittr_2.0.1
[41] crayon_1.4.1 readxl_1.3.1 evaluate_0.14 ps_1.6.0
[45] fs_1.5.0 fansi_0.5.0 nlme_3.1-152 xml2_1.3.2
[49] tools_4.1.0 data.table_1.14.0 hms_1.1.0 lifecycle_1.0.0
[53] munsell_0.5.0 reprex_2.0.0 callr_3.7.0 compiler_4.1.0
[57] jquerylib_0.1.4 systemfonts_1.0.2 rlang_0.4.11 grid_4.1.0
[61] rstudioapi_0.13 htmlwidgets_1.5.3 igraph_1.2.6 rmarkdown_2.11.2
[65] gtable_0.3.0 codetools_0.2-18 DBI_1.1.1 R6_2.5.0
[69] lubridate_1.7.10 fastmap_1.1.0 utf8_1.2.1 rprojroot_2.0.2
[73] stringi_1.6.2 Rcpp_1.0.6 vctrs_0.3.8 dbplyr_2.1.1
[77] tidyselect_1.1.1 xfun_0.24