Fix github page action (hopefully)

software/.github/workflows/pkgdown.yaml → .github/workflows/pkgdown.yaml

@@ -16,6 +16,10 @@ jobs:
   pkgdown:
     runs-on: ubuntu-latest
     # Only restrict concurrency for non-PR jobs
+    defaults:
+      run:
+        working-directory: software
+        # specification that the job is run inside the software folder where the excode package lives
     concurrency:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
@@ -33,6 +37,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          working-directory: software
           extra-packages: any::pkgdown, local::.
           needs: website
 
@@ -46,4 +51,4 @@ jobs:
         with:
           clean: false
           branch: gh-pages
-          folder: docs
+          folder: software/docs

Readme.md

@@ -3,6 +3,7 @@
 
 
 Documentation  
+
 # excode: Excess Count Detection in Epidemiological Time Series
 
 <br> 
@@ -57,7 +58,7 @@ surveillance.
 This is an R package. You can use `install_github()` from devtools to
 install this package.
 
-``` commandline
+```r
 library(devtools)
 install_github("robert-koch-institut/excode",subdir = "software")
 ```
@@ -103,7 +104,7 @@ The following code example illustrates how to fit a three-state model with
 sine/cosine functions ('Harmonic') to model seasonal and a natural cubic 
 spline with two knots to caputre long-term trends ('Spline2').
 
-``` commandline
+```r
 library(excode)
 data(mort_df_germany)
 sum_har_nb <- run_excode(surv_ts = mort_df_germany,
@@ -118,7 +119,7 @@ sum_har_nb <- run_excode(surv_ts = mort_df_germany,
 Results can be extracted using the `summary()` and plotted with the 
 `plot_excode_summary()` functions:
 
-``` commandline
+```r
 sum_har_nb <- summary(res_har_nb)
 plot_excode_summary(sum_har_nb)
 ```