Last updated: 2018-10-08

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✔ Session information: recorded

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✔ Repository version: 0d0b30d
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```
Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    Extra feature drafts/
    Ignored:    Shiny App Practice.R
    Ignored:    Shiny2.0/.DS_Store
    Ignored:    data/.DS_Store
    Ignored:    data/big_data/

Untracked files:
    Untracked:  pesticide_explorer-Sara’s MacBook Pro.Rproj

Unstaged changes:
    Modified:   analysis/California.Rmd
    Modified:   analysis/Data.Rmd
    Modified:   analysis/Tox_load_vig.Rmd
    Modified:   analysis/about_tox_load.Rmd
    Modified:   analysis/neonic_vig.Rmd
```
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

Expand here to see past versions:

File	Version	Author	Date	Message
Rmd	6d69e9e	ssoba	2018-08-09	Revised GitHub website for all typos
html	6d69e9e	ssoba	2018-08-09	Revised GitHub website for all typos
Rmd	e7d10a2	ssoba	2018-08-08	Revised CA vignette and facetted a plot in intensity vignette
html	e7d10a2	ssoba	2018-08-08	Revised CA vignette and facetted a plot in intensity vignette
Rmd	acb68e5	ssoba	2018-08-07	Added contact and oral toxic loads to Graphs tab and California Vignette. Also added a final graph to California vignette.
html	acb68e5	ssoba	2018-08-07	Added contact and oral toxic loads to Graphs tab and California Vignette. Also added a final graph to California vignette.
Rmd	f4ef47c	ssoba	2018-08-07	Forgot to wflow_build the last commit
html	f4ef47c	ssoba	2018-08-07	Forgot to wflow_build the last commit
Rmd	bb1bf40	ssoba	2018-08-06	Got rid of code in GitHub site. Wrote Limitations to Data section and broadened introduction. Moved descriptions in shiny and extended sidebar
html	bb1bf40	ssoba	2018-08-06	Got rid of code in GitHub site. Wrote Limitations to Data section and broadened introduction. Moved descriptions in shiny and extended sidebar
html	36cbc40	ssoba	2018-08-06	Build site.
Rmd	15a59b5	ssoba	2018-08-03	Spelling fixes
html	15a59b5	ssoba	2018-08-03	Spelling fixes
html	1d48d55	ssoba	2018-08-03	Build site.
Rmd	3ee9a38	ssoba	2018-08-02	Started neonicotinoid vignette!
html	3ee9a38	ssoba	2018-08-02	Started neonicotinoid vignette!
Rmd	dd313f8	ssoba	2018-08-01	Fixed all spelling mistakes and some formatting issues
html	dd313f8	ssoba	2018-08-01	Fixed all spelling mistakes and some formatting issues
html	8b09700	ssoba	2018-08-01	Build site.
Rmd	4b1a915	ssoba	2018-07-31	Added Vignette tab to nav bar, fixed California vignette to be insecticides not all pesticides. Cleaned up the Home page
html	4b1a915	ssoba	2018-07-31	Added Vignette tab to nav bar, fixed California vignette to be insecticides not all pesticides. Cleaned up the Home page
Rmd	ca7e234	ssoba	2018-07-27	Adding new tab to Shiny app and started toxic load per kg applied vignette
html	ca7e234	ssoba	2018-07-27	Adding new tab to Shiny app and started toxic load per kg applied vignette
html	00421e3	ssoba	2018-07-20	Fixed scale again
Rmd	20b481a	ssoba	2018-07-20	Fixed figure size in Data
html	20b481a	ssoba	2018-07-20	Fixed figure size in Data
Rmd	9531377	ssoba	2018-07-20	Added some new pages: the California story
html	9531377	ssoba	2018-07-20	Added some new pages: the California story
Rmd	672cebf	ssoba	2018-07-20	Added some new pages: the California story
html	672cebf	ssoba	2018-07-20	Added some new pages: the California story
Rmd	270f0bd	ssoba	2018-07-19	Added a dodged bar plot
html	270f0bd	ssoba	2018-07-19	Added a dodged bar plot
Rmd	0f02ee6	ssoba	2018-07-19	Fixed spelling errors
Rmd	c5246c6	ssoba	2018-07-19	Fixed spelling errors
html	c5246c6	ssoba	2018-07-19	Fixed spelling errors
html	68b56b2	ssoba	2018-07-19	fixed merge issue
Rmd	8a8f256	ssoba	2018-07-19	First graphs are up!
html	8a8f256	ssoba	2018-07-19	First graphs are up!
html	018607b	ssoba	2018-07-19	First graphs are up!

Introduction

This page contains some graphs summarizing trends in national insecticide use.

Total Toxic Load over Time (National)

Goal: This graph displays the Total Toxic Load for the Entire State-Crop combination change between 1997 and 2014, sorted by crop. In short, you should be able to see the total toxic load of each crop changing over time.

Expand here to see past versions of unnamed-chunk-4-1.png:

Version	Author	Date
e7d10a2	ssoba	2018-08-08
acb68e5	ssoba	2018-08-07
8a8f256	ssoba	2018-07-19

Note the different y-axis scales in the above plots.

Trying out a second plot: standardizing the height of each bar, effectively showing which crops account for which proportions of the total contact toxic load for each year.

Expand here to see past versions of unnamed-chunk-5-1.png:

Version	Author	Date
e7d10a2	ssoba	2018-08-08
acb68e5	ssoba	2018-08-07
3ee9a38	ssoba	2018-08-02
8b09700	ssoba	2018-08-01
4b1a915	ssoba	2018-07-31
ca7e234	ssoba	2018-07-27
9531377	ssoba	2018-07-20
8b46fc8	ssoba	2018-07-19
8a8f256	ssoba	2018-07-19

The plots below display the same information as the one above, just as line graphs facetted by crop instead of a bar graph. These plots allow you to easily compare between different crop groups.

Total Contact Toxic Load

Expand here to see past versions of unnamed-chunk-6-1.png:

Version	Author	Date
e7d10a2	ssoba	2018-08-08
acb68e5	ssoba	2018-08-07
36cbc40	ssoba	2018-08-06
3ee9a38	ssoba	2018-08-02
8b09700	ssoba	2018-08-01
4b1a915	ssoba	2018-07-31
9531377	ssoba	2018-07-20
672cebf	ssoba	2018-07-20
270f0bd	ssoba	2018-07-19
8b46fc8	ssoba	2018-07-19
8a8f256	ssoba	2018-07-19

Total Oral Toxic Load

Expand here to see past versions of unnamed-chunk-7-1.png:

Version	Author	Date
e7d10a2	ssoba	2018-08-08
acb68e5	ssoba	2018-08-07
36cbc40	ssoba	2018-08-06
3ee9a38	ssoba	2018-08-02
8b09700	ssoba	2018-08-01
4b1a915	ssoba	2018-07-31
9531377	ssoba	2018-07-20
270f0bd	ssoba	2018-07-19
8b46fc8	ssoba	2018-07-19
8a8f256	ssoba	2018-07-19

A Closer Look at Corn

Let’s just look at corn (accounted for the largest proportion of both contact and oral toxic load)

Expand here to see past versions of unnamed-chunk-9-1.png:

Version	Author	Date
e7d10a2	ssoba	2018-08-08
acb68e5	ssoba	2018-08-07
36cbc40	ssoba	2018-08-06
3ee9a38	ssoba	2018-08-02
8b09700	ssoba	2018-08-01
4b1a915	ssoba	2018-07-31
ca7e234	ssoba	2018-07-27
9531377	ssoba	2018-07-20
8b46fc8	ssoba	2018-07-19
8a8f256	ssoba	2018-07-19

Toxicity by State

Contact Toxicity by State for 2014

Expand here to see past versions of unnamed-chunk-13-1.png:

Version	Author	Date
36cbc40	ssoba	2018-08-06
3ee9a38	ssoba	2018-08-02
8b09700	ssoba	2018-08-01
4b1a915	ssoba	2018-07-31
ca7e234	ssoba	2018-07-27
9531377	ssoba	2018-07-20
8b46fc8	ssoba	2018-07-19
8a8f256	ssoba	2018-07-19

NOTE: Keep in mind that the states are all different sizes, so the bars are not fully comparable. However, there are still some interesting patterns to be found (i.e. California)

Wow! California is a high risk place for bees, even when you account for the state’s size (just compare California to another large state like Texas). Why is California’s toxic load so high? Let’s find out more here

Oral Toxicity by State for 2014

Expand here to see past versions of unnamed-chunk-15-1.png:

Version	Author	Date
e7d10a2	ssoba	2018-08-08
acb68e5	ssoba	2018-08-07

NOTE: Keep in mind that the states are all different sizes, so the bars are not fully comparable.

Interesting! Looks like Iowa and Illinois are tied for highest total oral toxic load, leaving California near the bottom rankings. Let’s find out why here.

Session information

sessionInfo()

R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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] bindrcpp_0.2.2  gridExtra_2.3   scales_0.5.0    forcats_0.3.0  
 [5] stringr_1.3.1   purrr_0.2.5     tidyr_0.8.1     tibble_1.4.2   
 [9] tidyverse_1.2.1 ggplot2_2.2.1   dplyr_0.7.5     readr_1.1.1    

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.4  reshape2_1.4.3    haven_1.1.1      
 [4] lattice_0.20-35   colorspace_1.3-2  htmltools_0.3.6  
 [7] yaml_2.1.19       utf8_1.1.4        rlang_0.2.1      
[10] R.oo_1.22.0       pillar_1.2.3      foreign_0.8-70   
[13] glue_1.2.0        R.utils_2.6.0     modelr_0.1.2     
[16] readxl_1.1.0      bindr_0.1.1       plyr_1.8.4       
[19] munsell_0.5.0     gtable_0.2.0      workflowr_1.1.1  
[22] cellranger_1.1.0  rvest_0.3.2       R.methodsS3_1.7.1
[25] psych_1.8.4       evaluate_0.10.1   labeling_0.3     
[28] knitr_1.20        parallel_3.5.0    broom_0.4.4      
[31] Rcpp_0.12.17      backports_1.1.2   jsonlite_1.5     
[34] mnormt_1.5-5      hms_0.4.2         digest_0.6.15    
[37] stringi_1.2.3     grid_3.5.0        rprojroot_1.3-2  
[40] cli_1.0.0         tools_3.5.0       magrittr_1.5     
[43] lazyeval_0.2.1    crayon_1.3.4      whisker_0.3-2    
[46] pkgconfig_2.0.1   xml2_1.2.0        lubridate_1.7.4  
[49] rstudioapi_0.7    assertthat_0.2.0  rmarkdown_1.10   
[52] httr_1.3.1        R6_2.2.2          nlme_3.1-137     
[55] git2r_0.22.1      compiler_3.5.0

This reproducible R Markdown analysis was created with workflowr 1.1.1

Graphs

Sara Soba

2018-07-19