Dose-Response Assay Compilation
Last updated: 2021-06-02
Checks: 6 1
Knit directory: toxin_dose_responses/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | ab92e85 | sam-widmayer | 2021-06-02 | condensed build |
| Rmd | b8fd879 | sam-widmayer | 2021-06-02 | condensed build |
| Rmd | 70ab313 | sam-widmayer | 2021-06-01 | remove DRC metrics chunk |
| Rmd | 1e4a104 | sam-widmayer | 2021-06-01 | remove DRC metrics chunk |
| Rmd | bc88ae7 | sam-widmayer | 2021-06-01 | fix EC10 plotting…again |
| Rmd | 7dfdf40 | sam-widmayer | 2021-06-01 | weird nickel plotting |
| Rmd | 9028052 | sam-widmayer | 2021-06-01 | EC10 plotting with selected models |
| Rmd | e1f3a00 | sam-widmayer | 2021-06-01 | NIEHS meeting 06/03 update |
| Rmd | 45e214b | sam-widmayer | 2021-05-13 | may trip push |
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| Rmd | b1d3b74 | sam-widmayer | 2021-04-26 | fix chlorpyrifos |
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| Rmd | 26547e8 | sam-widmayer | 2021-04-19 | integrate toxin27A |
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| Rmd | ea23ad6 | sam-widmayer | 2021-04-09 | toxin26A and tx group analyses |
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| Rmd | 59b9a05 | sam-widmayer | 2021-04-07 | explicit DRC plotting |
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| Rmd | 0cc26e9 | sam-widmayer | 2021-04-07 | require ggbeeswarm |
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| Rmd | 3720d88 | sam-widmayer | 2021-03-29 | integrate toxin24A |
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| Rmd | f2b09cd | sam-widmayer | 2021-03-23 | EC plot and DRC evaluation updates |
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| Rmd | 32ad79a | sam-widmayer | 2021-03-21 | heatmap outputs |
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| Rmd | 01b3361 | sam-widmayer | 2021-03-21 | heatmap outputs |
| Rmd | 7eb07f1 | sam-widmayer | 2021-03-21 | toxin23 updates and Worm_Length filter for MDHD data |
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| Rmd | 3f4a99b | sam-widmayer | 2021-03-14 | integrate toxin22 results |
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| Rmd | 46c9647 | sam-widmayer | 2021-03-06 | static working directory |
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| Rmd | 0c9d312 | sam-widmayer | 2021-03-05 | initiate toxin DRC analysis repo |
Purpose:
- Compile past assay results.
- Provide dose-response curves for each toxin.
Analysis Date: June 02, 2021
Assay Summary
Metadata_Experiment bleach median cv.censor
1 toxin09A 1 0.3836145 0
2 toxin10A 1 0.4305145 0
3 toxin11A 1 0.4277093 0
4 toxin14A 1 0.3309190 0
5 toxin14A 2 0.6202207 1
6 toxin14A 3 0.3139512 0
7 toxin14B 1 0.3531075 0
8 toxin14B 2 0.6821373 1
9 toxin14B 3 0.4144394 0
10 toxin15A 1 0.3776043 0
11 toxin15A 2 0.3237794 0
12 toxin15A 3 0.5858180 1
13 toxin15B 1 0.3014705 0
14 toxin15B 2 0.3782805 0
15 toxin15B 3 0.5791055 1
16 toxin16A 1 0.3024091 0
17 toxin16A 2 0.6394078 1
18 toxin16A 3 0.6430524 1
19 toxin17A 1 0.3203867 0
20 toxin17A 2 0.5750981 1
21 toxin17A 3 0.3401813 0
22 toxin18A 1 0.3202607 0
23 toxin18A 2 0.3228881 0
24 toxin18A 3 0.3338709 0
25 toxin19A 1 0.3333869 0
26 toxin19A 2 0.3179010 0
27 toxin19A 3 0.3330344 0
28 toxin22A 1 0.2625332 0
29 toxin22A 2 0.2967801 0
30 toxin22A 3 0.2706957 0
31 toxin23A 1 0.3243216 0
32 toxin23A 2 0.3411546 0
33 toxin23A 3 0.2809086 0
34 toxin24A 1 0.2672445 0
35 toxin24A 2 0.3018825 0
36 toxin24A 3 0.3152494 0
37 toxin25A 1 0.3024884 0
38 toxin25A 2 0.2940015 0
39 toxin25A 3 0.3507315 0
40 toxin26A 1 0.3178134 0
41 toxin26A 2 0.2864734 0
42 toxin26A 3 0.2638100 0
43 toxin27 1 0.3471797 0
44 toxin27 2 0.3083537 0
45 toxin27 3 0.3159872 0 Df Sum Sq Mean Sq F value Pr(>F)
assay 16 2.5484 0.15928 19.149 < 2e-16 ***
as.factor(bleach) 2 0.4302 0.21509 25.859 4.3e-11 ***
strain 7 0.0979 0.01399 1.682 0.113
assay:as.factor(bleach) 26 2.0940 0.08054 9.683 < 2e-16 ***
Residuals 302 2.5120 0.00832
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Silver
Cadmium
Copper
Nickel
Paraquat
Zinc
Pyraclostrobin
Aldicarb
Chlorfenapyr
| Version | Author | Date |
|---|---|---|
| 8529055 | sam-widmayer | 2021-04-19 |
| bc5c5b5 | sam-widmayer | 2021-04-09 |
| 1f8d045 | sam-widmayer | 2021-04-07 |
| 0a1d24d | sam-widmayer | 2021-04-07 |
| 0e83f2b | sam-widmayer | 2021-03-24 |
| 02a633e | sam-widmayer | 2021-03-24 |
| deb1df5 | sam-widmayer | 2021-03-21 |
| 7ae886c | sam-widmayer | 2021-03-14 |
| cb6e132 | sam-widmayer | 2021-03-06 |
Methomyl
Methyl Mercury
Triphenyl phosphate
Arsenic trioxide
Carbaryl
Carboxin
Chlorpyrifos
[1] "Excluding toxin17A: No Response"
Lead (II) nitrate
%20nitrate-1.png)
%20nitrate-2.png)
%20nitrate-3.png)
Atrazine
[1] "Excluding toxin16A: Inaccurate Dilution Series"
2,4-D
Malathion
Chlorothalonil
Deltamethrin
Error in optim(startVec, opfct, hessian = TRUE, method = optMethod, control = list(maxit = maxIt, :
non-finite finite-difference value [3]
[1] "Unable to optimize model"
[1] "Unable to optimize model"
Manganese dichloride
Propoxur
Mancozeb
EC Estimates
EC10
EC50
EC90
Summary Tables
Toxicant Classes
sessionInfo()R version 4.0.4 (2021-02-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggrepel_0.9.1 ggbeeswarm_0.6.0 cowplot_1.1.1 RColorBrewer_1.1-2
[5] RCurl_1.98-1.2 ddpcr_1.15 kableExtra_1.3.4 knitr_1.31
[9] drc_3.0-1 MASS_7.3-53 easyXpress_0.1.0 forcats_0.5.1
[13] stringr_1.4.0 dplyr_1.0.4 purrr_0.3.4 readr_1.4.0
[17] tidyr_1.1.2 tibble_3.1.0 ggplot2_3.3.3 tidyverse_1.3.0
[21] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] TH.data_1.0-10 colorspace_2.0-0 ellipsis_0.3.1
[4] rio_0.5.16 rprojroot_2.0.2 fs_1.5.0
[7] rstudioapi_0.13 farver_2.0.3 audio_0.1-7
[10] fansi_0.4.2 mvtnorm_1.1-1 lubridate_1.7.9.2
[13] xml2_1.3.2 codetools_0.2-18 splines_4.0.4
[16] readbitmap_0.1.5 jsonlite_1.7.2 broom_0.7.5
[19] dbplyr_2.1.0 png_0.1-7 compiler_4.0.4
[22] httr_1.4.2 backports_1.2.1 assertthat_0.2.1
[25] bmp_0.3 Matrix_1.3-2 cli_2.3.1
[28] beepr_1.3 later_1.1.0.1 htmltools_0.5.1.1
[31] tools_4.0.4 igraph_1.2.6 gtable_0.3.0
[34] glue_1.4.2 rebus.base_0.0-3 Rcpp_1.0.6
[37] carData_3.0-4 cellranger_1.1.0 jquerylib_0.1.3
[40] vctrs_0.3.6 svglite_2.0.0 xfun_0.21
[43] rebus.datetimes_0.0-1 openxlsx_4.2.3 rvest_0.3.6
[46] lifecycle_1.0.0 rebus.numbers_0.0-1 gtools_3.8.2
[49] zoo_1.8-8 scales_1.1.1 hms_1.0.0
[52] promises_1.2.0.1 sandwich_3.0-0 yaml_2.2.1
[55] curl_4.3 sass_0.3.1 stringi_1.5.3
[58] imager_0.42.7 highr_0.8 plotrix_3.8-1
[61] tiff_0.1-6 zip_2.1.1 bitops_1.0-6
[64] rlang_0.4.10 pkgconfig_2.0.3 systemfonts_1.0.1
[67] evaluate_0.14 lattice_0.20-41 labeling_0.4.2
[70] tidyselect_1.1.0 magrittr_2.0.1 R6_2.5.0
[73] generics_0.1.0 multcomp_1.4-16 DBI_1.1.1
[76] pillar_1.5.0 haven_2.3.1 whisker_0.4
[79] foreign_0.8-81 withr_2.4.1 rebus_0.1-3
[82] survival_3.2-7 abind_1.4-5 rebus.unicode_0.0-2
[85] modelr_0.1.8 crayon_1.4.1 car_3.0-10
[88] utf8_1.1.4 rmarkdown_2.7 jpeg_0.1-8.1
[91] grid_4.0.4 readxl_1.3.1 data.table_1.14.0
[94] git2r_0.28.0 reprex_1.0.0 digest_0.6.27
[97] webshot_0.5.2 httpuv_1.5.5 munsell_0.5.0
[100] beeswarm_0.2.3 viridisLite_0.3.0 vipor_0.4.5
[103] bslib_0.2.4