Merge pull request #393 from morungos/markdown-reports

Add support for report generation
osparcomm · Dec 12, 2023 · 95d95a4 · 95d95a4
2 parents f53d93e + 8455070
commit 95d95a4
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Showing 16 changed files with 410 additions and 24 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -41,6 +41,7 @@ export(normalise_sediment_OSPAR)
 export(plot_assessment)
 export(read_contaminants)
 export(read_data)
+export(report_assessment)
 export(run_assessment)
 export(subset_assessment)
 export(tidy_data)

diff --git a/R/reporting_functions.R b/R/reporting_functions.R
@@ -817,14 +817,13 @@ report_assessment <- function(
 
 
   info <- assessment_obj$info
-  timeSeries <- assessment_obj$timeSeries 
-
+  timeSeries <- assessment_obj$timeSeries   
 
   # set up time series information:
   # - merge with station information
   # - add in additional useful variables 
   # - subset if necessary
-  
+
   timeSeries <- tibble::rownames_to_column(timeSeries, "series")
 
   timeSeries <- dplyr::left_join(
@@ -851,13 +850,7 @@ report_assessment <- function(
     timeSeries$matrix <- "WT"
   }
 
-  if (!is.null(substitute(subset))) {
-    ok <- eval(substitute(subset), timeSeries, parent.frame())
-    timeSeries <- timeSeries[ok, ]
-    row.names(timeSeries) <- NULL
-  }
-
-  timeSeries <- tibble::column_to_rownames(timeSeries, "series")
+  timeSeries <- apply_subset(timeSeries, subset, parent.frame())
 
   series_id <- row.names(timeSeries)
 
@@ -904,8 +897,12 @@ report_assessment <- function(
     output_id <- gsub("\\", " ", output_id, fixed = TRUE)
 
 
+    package_dir = system.file(package = "harsat")
+    template_dir = file.path(package_dir, "markdown")
+    report_file <- file.path(template_dir, "report_assessment.Rmd")
+
     rmarkdown::render(
-      "report_assessment.Rmd", 
+      report_file, 
       params = list(
         assessment_object = assessment_obj, 
         series = id
@@ -916,8 +913,7 @@ report_assessment <- function(
   })
 
   invisible() 
-}  
-
+}
 
 
 

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -22,17 +22,19 @@ navbar:
       - text: External file format
         href: articles/external-file-format.html
       - text: -------
-      - text: "Resources"
-      - text: Datasets
-        href: articles/datasets.html
-      - text: -------
       - text: "Examples"
       - text: HELCOM (read first)
         href: articles/example_HELCOM.html
       - text: OSPAR
         href: articles/example_OSPAR.html
       - text: AMAP external data
         href: articles/example_external_data.html
+      - text: -------
+      - text: "Additional resources"
+      - text: Datasets
+        href: articles/datasets.html
+      - text: Report template
+        href: articles/report-template.html
 
 reference:
 - title: Primary functions

diff --git a/report_assessment.Rmd → inst/markdown/report_assessment.Rmd b/report_assessment.Rmd → inst/markdown/report_assessment.Rmd
diff --git a/inst/markdown/report_assessment.css b/inst/markdown/report_assessment.css
@@ -0,0 +1,3 @@
+li.gap {
+    margin-bottom: 3pt;
+}
diff --git a/report_assessment_status.Rmd → inst/markdown/report_assessment_status.Rmd b/report_assessment_status.Rmd → inst/markdown/report_assessment_status.Rmd
diff --git a/report_assessment_status_imposex.Rmd → ...down/report_assessment_status_imposex.Rmd b/report_assessment_status_imposex.Rmd → ...down/report_assessment_status_imposex.Rmd
diff --git a/report_assessment_trend.Rmd → inst/markdown/report_assessment_trend.Rmd b/report_assessment_trend.Rmd → inst/markdown/report_assessment_trend.Rmd
diff --git a/report_assessment_trend_imposex.Rmd → ...kdown/report_assessment_trend_imposex.Rmd b/report_assessment_trend_imposex.Rmd → ...kdown/report_assessment_trend_imposex.Rmd
diff --git a/man/apply_subset.Rd b/man/apply_subset.Rd
diff --git a/man/report_assessment.Rd b/man/report_assessment.Rd
diff --git a/report_assessment.css b/report_assessment.css