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      "body": "Thank for the interesting post. This is certainly a great concept but will need a lots of work to be applicable for clinical settings. Detection limit of 10^6 CFU/ml is very high given that sepsis patients might have 5-100 CFU/ml bacterial load in their blood.",
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      "title": "The rise of antibiotic resistance rates in Escherichia coli  in Europe",
      "body": "@@ -840,16 +840,120 @@\n ible. %0A%0A\n+The final product of this post is this image:%0A%0A!%5B%5D(https://s5.postimg.org/sw6cbfcpj/ecdc_res_map.gif)%0A%0A%0A\n ### 1. T\n",
      "json_metadata": "{\"tags\":[\"dataviz\",\"steemstem\",\"antibiotic\",\"rprogramming\",\"microbiology\"],\"image\":[\"https://s5.postimg.org/sw6cbfcpj/ecdc_res_map.gif\",\"https://s5.postimg.org/ff9dska3r/unnamed-chunk-8-1.png\",\"https://s5.postimg.org/cl68f4fnb/unnamed-chunk-9-1.png\"],\"links\":[\"https://www.blog.cultureofinsight.com/2017/09/animated-choropleth-maps-in-r/\",\"https://steemit.com/steemstem/@jepper/escherichia-coli-friend-or-foe-microbiology-4\",\"https://ecdc.europa.eu/en/antimicrobial-resistance/surveillance-and-disease-data/data-ecdc\",\"https://www.dropbox.com/s/i3vu8guefq2tcbx/ECDC_surveillance_data_Antimicrobial_resistance.csv.zip?dl=0\",\"#notes\",\"http://www.naturalearthdata.com/\",\"http://www.imagemagick.org/script/index.php\",\"http://www.graphicsmagick.org/\"],\"app\":\"steemit/0.1\",\"format\":\"markdown\"}"
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      "title": "The rise of antibiotic resistance rates in *Escherichia coli*  in Europe",
      "body": "I have always been fasciated with using animated graphs to visualise data. It is an attractive way to add another dimension, usually time, to the plot. Animated choropleth map is an effective and only way to present time-series data on a map. \n\nI have no previous experience in making animated plots and would like to start learning/experimenting on them. I do work with R and ggplot2 so making animation based on ggplot2 would be a good start for me. After a bit of research on google, I decided to follow the instructions from this [blog](https://www.blog.cultureofinsight.com/2017/09/animated-choropleth-maps-in-r/) as it seems to be most up-to-date and uses many packages I am familiar with.\n\nHere I documented the steps I have taken to make my first animated choropleth map using R. I hope you'll find these codes helpful and reproducible. \n\n### 1. The data\n\nA major focus of my research is on antibiotic resistance of bacteria, especially [Escherichia coli](https://steemit.com/steemstem/@jepper/escherichia-coli-friend-or-foe-microbiology-4). So as a practice for my animiated choroplath map, I dedided to download data from ECDC, showing the average proportion of resistance isolates from European countries every year since 2010 to 2016.\n\nI don't know how to download this data set directly from R so I described here how I downloaded data from ECDC website in a point'n'click way. If you know how to do this in R, please comment to let me know - I would love to learn from you.\n\n- Go to ECDC data [website](https://ecdc.europa.eu/en/antimicrobial-resistance/surveillance-and-disease-data/data-ecdc):  \n- Click on download icon\n- Select: (1) All time periods, (2) All regions, (3) All indicators, (4) CSV file\n- Click Export to download .csv file (8.7MB)\n\nAlternatively, you can download this csv file [here](https://www.dropbox.com/s/i3vu8guefq2tcbx/ECDC_surveillance_data_Antimicrobial_resistance.csv.zip?dl=0)\n\n### 2. Required packages\n\nThe following packages are required for my codes to work. Please note that `ggplot2` and `gganimate` require developer version. See my [Extra notes](#notes) at the bottom for other requirements.\n\n\n```r\nlibrary(tidyverse) # dev ggplot version required:  devtools::install_github(\"hadley/ggplot2\")\nlibrary(sf)\nlibrary(readxl)\nlibrary(gganimate) # devtools::install_github(\"dgrtwo/gganimate\")\n```\n\n### 3. Load csv file downloaded in step 1 to R\n\nI saved the csv file from step 1 here in my computer:\n\n\n```r\ndatafile <- \"../ECDC_data/ECDC_surveillance_data_Antimicrobial_resistance.csv\"\n```\n\nLoad data file with `read_csv()`, then split column `Population` into two columns `Organisms` and `Antibiotic` using `|` as a separator. \n\nNotice that I specify the data types for each column in the csv file. This was done by first load the data with `read_csv()` and let it automatically decide on the data type, review the detected data type and change the `read_csv()` parameters to proper data type (for example `NumValue` column will be detected as `col_character()` and here I changed it to `col_double()`)\n\n\n```r\nd <- read_csv(datafile, \n              col_types = cols(\n                  HealthTopic = col_character(),\n                  Population = col_character(),\n                  Indicator = col_character(),\n                  Unit = col_character(),\n                  Time = col_integer(),\n                  RegionCode = col_character(),\n                  RegionName = col_character(),\n                  NumValue = col_double(),\n                  TxtValue = col_character()), \n              na = \"-\") %>%\n    separate(col = Population, into = c(\"Organism\",\"Antibiotics\"), sep = \"\\\\|\") \n```\n\nThe countries included in this data set are:\n\n\n```r\ncountry.name <- unique(d$RegionName)\ncountry.name\n```\n\n```\n##  [1] \"Austria\"        \"Belgium\"        \"Bulgaria\"       \"Cyprus\"        \n##  [5] \"Czech Republic\" \"Germany\"        \"Denmark\"        \"Estonia\"       \n##  [9] \"Greece\"         \"Spain\"          \"Finland\"        \"France\"        \n## [13] \"Croatia\"        \"Hungary\"        \"Ireland\"        \"Iceland\"       \n## [17] \"Italy\"          \"Lithuania\"      \"Luxembourg\"     \"Latvia\"        \n## [21] \"Malta\"          \"Netherlands\"    \"Norway\"         \"Poland\"        \n## [25] \"Portugal\"       \"Romania\"        \"Sweden\"         \"Slovenia\"      \n## [29] \"Slovakia\"       \"United Kingdom\"\n```\n\n### 4. Reduce the data set\n\nIn this map, I only want to focus on *E. coli* so I will filter the data to keep only *E. coli*. The indicator I would like to display is `Resistant (R) isolates proportion` so I'll also get rid of other indicators. Several unused columns will also be removed. \n\n\n```r\n# I created this abname object to replace the value in the data with the new value, which are shorter and fit the plot.\nabname <- tribble(~current, ~new,\n                  \"Aminoglycosides\", \"Aminoglycosides\",\n                  \"Aminopenicillins\", \"Aminopenicillins\",\n                  \"Carbapenems\", \"Carbapenems\",\n                  \"Combined resistance (third-generation cephalosporin, fluoroquinolones and aminoglycoside)\", \"3rdgen-cep/FQ/AMG\",\n                  \"Fluoroquinolones\", \"Fluoroquinolones\",\n                  \"Third-generation cephalosporins\", \"3rdgen cep\")\n\n# reduce data set\nclean_dat <- d %>%\n    filter(Organism == \"Escherichia coli\", Indicator == \"Resistant (R) isolates proportion\") %>%\n    left_join(abname, by = c(\"Antibiotics\"= \"current\")) %>%\n    select(-HealthTopic, -Unit, -TxtValue, -Antibiotics) %>%\n    rename(Antibiotics = new) \n```\n\n### 5. Download the country shapefile from [Natural Earth](http://www.naturalearthdata.com/)\n\nThe shapefiles from Natural Earth are freely available. There are many versions but I find this version contains all the countries in this data set.\n\n\n```r\nshapefile <- \"ne_10m_admin_0_countries.shp\"\n\nif (!file.exists(shapefile)) {\n    # download the natural earth shapefile we need into the working directory\n    URL <- \"http://www.naturalearthdata.com/http//www.naturalearthdata.com/download/10m/cultural/ne_10m_admin_0_countries.zip\"\n    temp <- tempfile()\n    download.file(URL, temp)\n    unzip(temp)\n    unlink(temp)\n}\n```\n\n### 6. Load shape file into R with `st_read()`\n\nNext I read the shape file into R as in `sf` object and set the projection. I have to admit I do you understand much about the `st_transform()` function and the syntax for `crs = \"+proj=longlat +datum=WGS84\"`.\n\n\n```r\nworld <- st_read(shapefile) %>% \n    st_transform(crs = \"+proj=longlat +datum=WGS84\") %>%\n    select(NAME, NAME_LONG, geometry) # keep only the fields needed\n```\n\n```\n## Reading layer `ne_10m_admin_0_countries' from data source `/Users/uqmphan1/MyWork/Post-doc/Labbooks/Bioinformatics/ABR_mapviz/ECDC_mapviz/ne_10m_admin_0_countries.shp' using driver `ESRI Shapefile'\n## Simple feature collection with 255 features and 71 fields\n## geometry type:  MULTIPOLYGON\n## dimension:      XY\n## bbox:           xmin: -180 ymin: -90 xmax: 180 ymax: 83.6341\n## epsg (SRID):    4326\n## proj4string:    +proj=longlat +datum=WGS84 +no_defs\n```\n\nBecause `sf` library works with base plot, we can do a quick check with base `plot()` function to make sure we have successfully download the shapes.\n\n\n```r\nplot(world$geometry)\n```\n\n![](https://s5.postimg.org/ff9dska3r/unnamed-chunk-8-1.png)\n\nWe can also do a quick plot in ggplot2 to check using a new geom: `geom_sf` (dev ggplot2 version required). Here we set `coord_sf(xlim = c(-20,35), ylim = c(35,70))` to view only Europe.\n\n\n```r\neu_map <- ggplot() +\n  geom_sf(data = world, colour = \"#ffffff20\", fill = \"#2d2d2d60\", size = .5) +\n    coord_sf(xlim = c(-20,35), ylim = c(35,70))\neu_map\n```\n\n![](https://s5.postimg.org/cl68f4fnb/unnamed-chunk-9-1.png)\n\n### 7. Combine resistance data with shape data\n\nBefore binding resistance data to map data, it is a good idea to check whether the country names in resistance data matched with the country names used in shape data (if you don't use the exact shape file as I do).\n\n\n```r\nmatch(country.name, world$NAME)\n```\n\n```\n##  [1]  17  20  24  60  NA  62  65  73  91  72  75  78 100 102 108 111 113\n## [18] 137 138 139 151 169 170 183 186 191 216 215 214  82\n```\n\n\n```r\nmatch(country.name, world$NAME_LONG)\n```\n\n```\n##  [1]  17  20  24  60  61  62  65  73  91  72  75  78 100 102 108 111 113\n## [18] 137 138 139 151 169 170 183 186 191 216 215 214  82\n```\n\nThe following name Czech Republic does not match with `world$NAME`. We'll have to use the `world$NAME_LONG` column to match with country names in resistance data.\n\n\n```r\necdc_dat <- merge(world, clean_dat, by.x = \"NAME_LONG\", by.y = \"RegionName\")\n```\n\nChange `Antibiotics` column into factors to control the order of facets in the final plot.\n\n\n```r\necdc_dat$Antibiotics <- factor(ecdc_dat$Antibiotics, levels = c(\"Aminopenicillins\", \"Aminoglycosides\", \"Fluoroquinolones\", \"3rdgen cep\", \"Carbapenems\", \"3rdgen-cep/FQ/AMG\"))\n```\n\n### 8. Create plot with ggplot\n\nFirst, I repeat the europe map as in step 6 with `geom_sf` to set the first layer with background country shapes. Then I added another `geom_sf` with resistance data (`ecdc_dat`), connecting `fill = NumValue`, and to prepare for the animation, I needed to add two more parameters: `frame = Time` and `cumulative = FALSE`. These two parameters are not recognised by `ggplot2` and thus I expected a warning message from `ggplot2`.\n\nI also use `facet_wrap` to separate the data by `Antibiotics`.\n\n\n```r\necdc_res_map <- ggplot() +\n    geom_sf(data = world, colour = \"#ffffff20\", fill = \"#2d2d2d60\", size = .5) +\n    geom_sf(data = ecdc_dat, aes(fill = NumValue, frame = Time, cumulative = FALSE)) +\n    scale_fill_gradient(name = \"Resistance %\", low = \"green\", high = \"red\", na.value = \"#ffffff20\") +\n    coord_sf(xlim = c(-20,35), ylim = c(35,70)) +\n    facet_wrap(~Antibiotics, ncol = 3) +\n    theme_light()\n```\n\n```\n## Warning: Ignoring unknown aesthetics: frame, cumulative\n```\n\n### 9. Make animated map\n\nI used `gganimate` to make animated map and saved it to a gif file. See my [Extra notes](#notes) on `convert` parameter. I set the delay between frame at `interval = 0.5`. The `title_frame = TRUE` is set to allow the display of the year corresponding to each frame.\n\n\n```r\nanimation::ani.options(interval = 0.5)\ngganimate(ecdc_res_map, ani.width =  800, ani.height = 600, filename = \"ecdc_res_map.gif\", title_frame = TRUE, convert = \"gm convert\")\n```\n\n```\n## Executing: \n## gm convert -loop 0 -delay 50 Rplot1.png Rplot2.png Rplot3.png\n##     Rplot4.png Rplot5.png Rplot6.png Rplot7.png Rplot8.png\n##     Rplot9.png Rplot10.png Rplot11.png Rplot12.png Rplot13.png\n##     Rplot14.png Rplot15.png Rplot16.png Rplot17.png\n##     'ecdc_res_map.gif'\n```\n\n```\n## Output at: ecdc_res_map.gif\n```\n\n![](https://s5.postimg.org/sw6cbfcpj/ecdc_res_map.gif)\n\nWith this map, we can see the increasing resistance rates in European countries over time. The map is quite basic. If you have any suggestion to make it look better, please comment below.\n\n### Extra notes {#notes}\n\nTo make animated plots and export to gif format, you'll need to install either [ImageMagick](http://www.imagemagick.org/script/index.php) or [GraphicsMagick](http://www.graphicsmagick.org/) to your system. \n\nFor ImageMagick, use `convert = \"convert\"` in `gganimate()`. For GraphicsMagick, use `convert = \"gm convert\"`.\n\n### Session Info\n\n\n```r\nsessionInfo()\n```\n\n```\n## R version 3.4.3 (2017-11-30)\n## Platform: x86_64-apple-darwin15.6.0 (64-bit)\n## Running under: macOS High Sierra 10.13.3\n## \n## Matrix products: default\n## BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib\n## LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib\n## \n## locale:\n## [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8\n## \n## attached base packages:\n## [1] stats     graphics  grDevices utils     datasets  methods   base     \n## \n## other attached packages:\n##  [1] bindrcpp_0.2         gganimate_0.1.0.9000 readxl_1.0.0        \n##  [4] sf_0.6-0             forcats_0.3.0        stringr_1.3.0       \n##  [7] dplyr_0.7.4          purrr_0.2.4          readr_1.1.1         \n## [10] tidyr_0.8.0          tibble_1.4.2         ggplot2_2.2.1.9000  \n## [13] tidyverse_1.2.1     \n## \n## loaded via a namespace (and not attached):\n##  [1] tidyselect_0.2.4  reshape2_1.4.3    haven_1.1.1      \n##  [4] lattice_0.20-35   colorspace_1.3-2  htmltools_0.3.6  \n##  [7] base64enc_0.1-3   yaml_2.1.17       rlang_0.2.0.9000 \n## [10] e1071_1.6-8       pillar_1.2.1      foreign_0.8-69   \n## [13] glue_1.2.0        withr_2.1.1.9000  DBI_0.7          \n## [16] modelr_0.1.1      bindr_0.1         plyr_1.8.4       \n## [19] munsell_0.4.3     gtable_0.2.0      cellranger_1.1.0 \n## [22] rvest_0.3.2       psych_1.7.8       evaluate_0.10.1  \n## [25] labeling_0.3      knitr_1.20        class_7.3-14     \n## [28] parallel_3.4.3    broom_0.4.3       Rcpp_0.12.15     \n## [31] udunits2_0.13     scales_0.5.0.9000 backports_1.1.2  \n## [34] classInt_0.1-24   jsonlite_1.5      mnormt_1.5-5     \n## [37] hms_0.4.1         digest_0.6.15     stringi_1.1.6    \n## [40] animation_2.5     grid_3.4.3        rprojroot_1.3-2  \n## [43] cli_1.0.0         tools_3.4.3       magrittr_1.5     \n## [46] lazyeval_0.2.1    crayon_1.3.4      pkgconfig_2.0.1  \n## [49] xml2_1.2.0        lubridate_1.7.3   assertthat_0.2.0 \n## [52] rmarkdown_1.8     httr_1.3.1        rstudioapi_0.7   \n## [55] R6_2.2.2          units_0.5-1       nlme_3.1-131.1   \n## [58] compiler_3.4.3\n```",
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      "body": "Thanks man! I will try to upload some impressive cherry pics later.",
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      "body": "Wow! Thanks for the link, going to check it in the morning (night here), didnt know that we have such tech already.",
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      "body": "It's not hypothetical, several markers in blood have been associated with either bacterial or viral infections, one of them is human neutrophil lipocalin (HNL). I think the test based on HNL is coming: see [here](https://horizon-magazine.eu/article/finger-prick-test-wins-eur-1-million-fight-antibiotic-resistance_en.html)",
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      "body": "Thanks for your tutorial. Very well explained. In my opinion, this should be lesson 2 right after the bitfinex set up.",
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      "body": "I am happy that you liked the article @pmduy!\n\nYes, such technology would be amazing! However, I have no idea how to create it, but will keep thinking. Great inspiration for future article btw :D hypothetical technology that could diagnose it in short time.",
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      "title": "",
      "body": "Thanks for writing on another topic very close to my heart. Great article. I think making doctors aware of the correct use of antibiotics can only go so far as reducing misuse cases a bit. What needed, and so far non-existence, is a point-of-care diagnostic test (think pregnancy test) that can tell the doctor on the spot what antibiotic is safe to use for a particular infection. Or, even in a simplest cases, confirm to the doctor that it is indeed a bacterial, not viral, infection and therefore the use of antibiotic is needed.",
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      "body": "Thanks for writing on another topic very close to my heart. Great article. I think making doctors aware of the correct use of antibiotics can only go so far as reducing misuse cases a bit. What needed, and so far non-existence, is a point-of-care diagnostic test (think pregnancy test) that can tell the doctor on the spot what antibiotic is safe to use for a particular infection. Or, even in a simplest cases, confirm to the doctor that it is indeed a bacterial, not viral, infection and therefore the use of antibiotic is needed.",
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