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iobis · Jan 18, 2024 · bbd1fd7 · bbd1fd7
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diff --git a/README.md b/README.md
@@ -3,10 +3,15 @@
 This is a workflow for processing eDNA results from the [eDNA Expeditions project](https://www.unesco.org/en/edna-expeditions) into an integrated dataset. Source data are fetched from [pacman-pipeline-results](https://github.com/iobis/pacman-pipeline-results) and [edna-tracker-data](https://github.com/iobis/edna-tracker-data).
 
 ## How to read this dataset
-
 ### Download the dataset
 
-Download the zipped dataset from <https://obis-edna-results.s3.amazonaws.com/output.zip>.
+Download the zipped dataset from <https://obis-edna-results.s3.amazonaws.com/output.zip> and extract.
+
+```bash
+rm -r output output.zip
+wget https://obis-edna-results.s3.amazonaws.com/output.zip
+unzip output.zip
+```
 
 ### Read the dataset using R
 

diff --git a/docs/read.Rmd b/docs/read.Rmd
@@ -16,8 +16,8 @@ library(dplyr)
 library(stringr)
 library(purrr)
 
-dna_files <- list.files("./data", "*DNADerivedData*", full.names = TRUE)
-occurrence_files <- list.files("./data", "*Occurrence*", full.names = TRUE)
+dna_files <- list.files("../output", "*DNADerivedData*", full.names = TRUE)
+occurrence_files <- list.files("../output", "*Occurrence*", full.names = TRUE)
 
 dna <- map(dna_files, read.table, sep = "\t", quote = "", header = TRUE) %>%
   bind_rows() %>%

diff --git a/docs/read.md b/docs/read.md
@@ -8,8 +8,8 @@ Read the individual Occurrence and DNADerivedData files, and join them:
     library(stringr)
     library(purrr)
 
-    dna_files <- list.files("./data", "*DNADerivedData*", full.names = TRUE)
-    occurrence_files <- list.files("./data", "*Occurrence*", full.names = TRUE)
+    dna_files <- list.files("../output", "*DNADerivedData*", full.names = TRUE)
+    occurrence_files <- list.files("../output", "*Occurrence*", full.names = TRUE)
 
     dna <- map(dna_files, read.table, sep = "\t", quote = "", header = TRUE) %>%
       bind_rows() %>%
@@ -89,52 +89,52 @@ Inspect updated names:
 <tr class="odd">
 <td style="text-align: left;">Animalia</td>
 <td style="text-align: left;">Metazoa</td>
-<td style="text-align: right;">293593</td>
+<td style="text-align: right;">607990</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">Bellerochea polymorpha</td>
 <td style="text-align: left;">Minutocellus polymorphus</td>
-<td style="text-align: right;">858</td>
+<td style="text-align: right;">1649</td>
 </tr>
 <tr class="odd">
+<td style="text-align: left;">Azurina atrilobata</td>
+<td style="text-align: left;">Chromis atrilobata</td>
+<td style="text-align: right;">931</td>
+</tr>
+<tr class="even">
 <td style="text-align: left;">Callyspongia (Cladochalina) plicifera</td>
 <td style="text-align: left;">Callyspongia plicifera</td>
-<td style="text-align: right;">493</td>
+<td style="text-align: right;">640</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td style="text-align: left;">Neoparamoeba aestuarina</td>
 <td style="text-align: left;">Paramoeba aestuarina</td>
-<td style="text-align: right;">315</td>
-</tr>
-<tr class="odd">
-<td style="text-align: left;">Azurina atrilobata</td>
-<td style="text-align: left;">Chromis atrilobata</td>
-<td style="text-align: right;">260</td>
+<td style="text-align: right;">584</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">Coscinodiscophycidae</td>
 <td style="text-align: left;">Coscinodiscophyceae</td>
-<td style="text-align: right;">226</td>
+<td style="text-align: right;">510</td>
 </tr>
 <tr class="odd">
 <td style="text-align: left;">Platybelone argalus</td>
 <td style="text-align: left;">Platybelone argala</td>
-<td style="text-align: right;">203</td>
+<td style="text-align: right;">428</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">Acartia (Acanthacartia) tonsa</td>
 <td style="text-align: left;">Acartia tonsa</td>
-<td style="text-align: right;">160</td>
+<td style="text-align: right;">386</td>
 </tr>
 <tr class="odd">
-<td style="text-align: left;">Eucampia striata</td>
-<td style="text-align: left;">Guinardia striata</td>
-<td style="text-align: right;">143</td>
+<td style="text-align: left;">Istiblennius edentulus</td>
+<td style="text-align: left;">Istiblennius enosimae</td>
+<td style="text-align: right;">336</td>
 </tr>
 <tr class="even">
 <td style="text-align: left;">Sundstroemia setigera</td>
 <td style="text-align: left;">Rhizosolenia setigera</td>
-<td style="text-align: right;">137</td>
+<td style="text-align: right;">314</td>
 </tr>
 </tbody>
 </table>

diff --git a/docs/read_files/figure-markdown_strict/exploration-1.png b/docs/read_files/figure-markdown_strict/exploration-1.png