From 7244ab4f2dff6d22f8a86a0662aef4d513ff1ec5 Mon Sep 17 00:00:00 2001 From: Paul Oldham Date: Mon, 27 Feb 2017 21:00:17 +0000 Subject: [PATCH] tidying bullets --- mapgbif.Rmd | 36 ++++++++++++++++++------------------ mapgbif.html | 25 ++++++++++++++++++++++--- 2 files changed, 40 insertions(+), 21 deletions(-) diff --git a/mapgbif.Rmd b/mapgbif.Rmd index 159c8a9..731d992 100644 --- a/mapgbif.Rmd +++ b/mapgbif.Rmd @@ -217,7 +217,7 @@ Next, and optionally, run the test files below (generating a lot of returns and source(system.file("tests","testing.R", package="geonames"), echo=TRUE) ``` -To get the boundaries for a country we need to access the country info. The data that we are after is on this [page](http://api.geonames.org/countryInfo?username=demo) +To get the boundaries for a country we need to access the country info. The data that we are after is on this [page](http://api.geonames.org/countryInfo?username=demo). To access that information with the geonames package we use the two letter [country code from here](http://www.geonames.org/countries/) or, if you are planning to do a lot of work with country codes, see the useful [countrycode](https://github.com/vincentarelbundock/countrycode) package: @@ -475,28 +475,28 @@ ColorBrewer contains three types of palette: It is the qualitative (categorical) palettes that we want, to give distinct colors to our kingdoms. The qualitative palettes are: -Accent 8 -Dark2 8 -Paired 12 -Pastel1 9 -Pastel2 8 -Set1 9 -Set2 8 -Set3 12 +- Accent 8 +- Dark2 8 +- Paired 12 +- Pastel1 9 +- Pastel2 8 +- Set1 9 +- Set2 8 +- Set3 12 If we visit the color brewer website we can test out the colors across the three types. The name of the palette appears in the URL based on your choices, for example: [http://colorbrewer2.org/#type=qualitative&scheme=Paired&n=7](http://colorbrewer2.org/#type=qualitative&scheme=Paired&n=7) We need to define the categories that will be used for the colours. In this case we will want to colour by kingdom. But bear in mind that an individual dataset may not include all of the kingdoms used in the [GBIF taxomony](http://www.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c). The Kingdoms used in GBIF are: -Animalia -Archaea -Bacteria -Chromista -Fungi -incertae sedis -Plantae -Protozoa -Viruses +- Animalia +- Archaea +- Bacteria +- Chromista +- Fungi +- incertae sedis +- Plantae +- Protozoa +- Viruses So, for use across multiple datasets we will want 9 colour categories. A colour will be allocated to NA (Not Available) by default and so we do not need to worry about that. diff --git a/mapgbif.html b/mapgbif.html index 8d40e6c..f56309a 100644 --- a/mapgbif.html +++ b/mapgbif.html @@ -522,7 +522,7 @@

Narrowing the Map using boundaries

options(geonamesUsername = "yourusername")

Next, and optionally, run the test files below (generating a lot of returns and not shown) to check that you can access the service.

source(system.file("tests", "testing.R", package = "geonames"), echo = TRUE)
-

To get the boundaries for a country we need to access the country info. The data that we are after is on this page

+

To get the boundaries for a country we need to access the country info. The data that we are after is on this page.

To access that information with the geonames package we use the two letter country code from here or, if you are planning to do a lot of work with country codes, see the useful countrycode package:

kenya_geonames_info <- GNcountryInfo(country = "KE")
 kenya_geonames_info
@@ -697,10 +697,29 @@

Using Colours for Categories

  • Qualitative

    • It is the qualitative (categorical) palettes that we want, to give distinct colors to our kingdoms. The qualitative palettes are:

    -

    Accent 8 Dark2 8 Paired 12 Pastel1 9 Pastel2 8 Set1 9 Set2 8 Set3 12

    +

    If we visit the color brewer website we can test out the colors across the three types. The name of the palette appears in the URL based on your choices, for example: http://colorbrewer2.org/#type=qualitative&scheme=Paired&n=7

    We need to define the categories that will be used for the colours. In this case we will want to colour by kingdom. But bear in mind that an individual dataset may not include all of the kingdoms used in the GBIF taxomony. The Kingdoms used in GBIF are:

    -

    Animalia Archaea Bacteria Chromista Fungi incertae sedis Plantae Protozoa Viruses

    +

    So, for use across multiple datasets we will want 9 colour categories. A colour will be allocated to NA (Not Available) by default and so we do not need to worry about that.

    With leaflet we can preview the colours we want to apply to our categorical data. This works better run in the console than in an Rmarkdown document.

    library(RColorBrewer)