diff --git a/NAMESPACE b/NAMESPACE
index edc806f..90036e9 100644
--- 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
index f68d93a..a4cb615 100644
--- 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
index ba8f531..69c92e2 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -22,10 +22,6 @@ 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
@@ -33,6 +29,12 @@ navbar:
         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 b/inst/markdown/report_assessment.Rmd
similarity index 100%
rename from report_assessment.Rmd
rename to inst/markdown/report_assessment.Rmd
diff --git a/inst/markdown/report_assessment.css b/inst/markdown/report_assessment.css
new file mode 100644
index 0000000..886bfd9
--- /dev/null
+++ b/inst/markdown/report_assessment.css
@@ -0,0 +1,3 @@
+li.gap {
+    margin-bottom: 3pt;
+}
diff --git a/report_assessment_status.Rmd b/inst/markdown/report_assessment_status.Rmd
similarity index 100%
rename from report_assessment_status.Rmd
rename to inst/markdown/report_assessment_status.Rmd
diff --git a/report_assessment_status_imposex.Rmd b/inst/markdown/report_assessment_status_imposex.Rmd
similarity index 100%
rename from report_assessment_status_imposex.Rmd
rename to inst/markdown/report_assessment_status_imposex.Rmd
diff --git a/report_assessment_trend.Rmd b/inst/markdown/report_assessment_trend.Rmd
similarity index 100%
rename from report_assessment_trend.Rmd
rename to inst/markdown/report_assessment_trend.Rmd
diff --git a/report_assessment_trend_imposex.Rmd b/inst/markdown/report_assessment_trend_imposex.Rmd
similarity index 100%
rename from report_assessment_trend_imposex.Rmd
rename to inst/markdown/report_assessment_trend_imposex.Rmd
diff --git a/man/apply_subset.Rd b/man/apply_subset.Rd
new file mode 100644
index 0000000..11ebd26
--- /dev/null
+++ b/man/apply_subset.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/graphics_functions.R
+\name{apply_subset}
+\alias{apply_subset}
+\title{Apply subsetting to a time series}
+\usage{
+apply_subset(timeSeries, subset, env = parent.frame())
+}
+\arguments{
+\item{timeSeries}{a time series data frame}
+
+\item{subset}{(default \code{NULL}) either \code{NULL}, which selects all entries, or a logical,
+which \code{TRUE} selects all entries and \code{FALSE} none of them, or an expression, which
+will be evaluated in the context of the dataframe to generate a subsetting vector.}
+
+\item{env}{the calling environment for variable values.}
+}
+\description{
+This is an internal function that applies a subsetting function to a timeseries.
+It is somewhat complex, due to way it is designed to be called. The subset is designed
+to be passed either as a value (\code{NULL} or  logical), as a expression, or as a variable
+holding an expression. When it is an expression, it is applied in the context of the
+timeseries data frame to generate a vector of booleans for subsetting. The complexity
+comes from the way this implements lazy evaluation, so we cannot evaluate the expression
+in the normal calling context.
+
+The function also removes row names, and converts the series column to row names.
+}
diff --git a/man/report_assessment.Rd b/man/report_assessment.Rd
new file mode 100644
index 0000000..41a2311
--- /dev/null
+++ b/man/report_assessment.Rd
@@ -0,0 +1,39 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/reporting_functions.R
+\name{report_assessment}
+\alias{report_assessment}
+\title{Reports the assessment of individual time series}
+\usage{
+report_assessment(
+  assessment_obj,
+  subset = NULL,
+  output_dir = ".",
+  max_report = 100L
+)
+}
+\arguments{
+\item{assessment_obj}{An assessment object resulting from a call to
+run_assessment}
+
+\item{subset}{An optional vector specifying which timeseries are to be
+reported. An expression will be evaluated in the timeSeries component of
+assessment_obj; use 'series' to identify individual timeseries.}
+
+\item{output_dir}{The output directory for the assessment plots (possibly
+supplied using 'file.path'). The default is the working directory. The
+output directory must already exist.}
+
+\item{max_report}{The maximum number of reports that will be generated.
+Defaults to 100. Each report is about 1MB in size and takes a few seconds
+to run, so this prevents a ridiculous number of reports being created.}
+}
+\value{
+A series of html files with, for each time series, meta data,
+plots of the data with the fitted assessment model, statistical summaries,
+and a simple interpretation of the fitted model.
+}
+\description{
+Generates a series of html reports with, for each time series, meta data,
+plots of the data with the fitted assessment model, statistical summaries,
+and a simple interpretation of the fitted model.
+}
diff --git a/report_assessment.css b/report_assessment.css
deleted file mode 100644
index 2a3a8f5..0000000
--- a/report_assessment.css
+++ /dev/null
@@ -1,7 +0,0 @@
-li.gap {margin-bottom: 3pt;}
-
-l
-
-
-
-
diff --git a/tests/datasets/external-1/data/EXTERNAL_FO_PW_DATA_TINY.csv b/tests/datasets/external-1/data/EXTERNAL_FO_PW_DATA_TINY.csv
new file mode 100644
index 0000000..3571b51
--- /dev/null
+++ b/tests/datasets/external-1/data/EXTERNAL_FO_PW_DATA_TINY.csv
@@ -0,0 +1,133 @@
+country,station_code,station_name,year,date,latitude,longitude,dephu,purpm,species,sex,subseries,n_individual,determinand,matrix,basis,value,unit,limit_detection,limit_quantification,uncertainty,unit_uncertainty,censoring,method_analysis,sample
+Denmark,A902,Føroyskar hvalvágir ,2011,02/09/2011,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.1,ng/g,,,,,<,UPLC-MS-MS,4310175
+Denmark,A902,Føroyskar hvalvágir ,2011,09/02/2011,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.1,ng/g,,,,,<,UPLC-MS-MS,4310171
+Denmark,A902,Føroyskar hvalvágir ,2011,09/02/2011,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.1,ng/g,,,,,,UPLC-MS-MS,4310171
+Denmark,A902,Føroyskar hvalvágir ,2011,02/09/2011,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.5,ng/g,,,,,,UPLC-MS-MS,4310175
+Denmark,A902,Føroyskar hvalvágir ,2011,02/09/2011,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.3,ng/g,,,,,,UPLC-MS-MS,4310175
+Denmark,A902,Føroyskar hvalvágir ,2012,10/07/2012,62.224293,-6.571586,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.4,ng/g,,,,,,UPLC-MS-MS,4310167
+Denmark,A902,Føroyskar hvalvágir ,2012,09/08/2012,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.7,ng/g,,,,,,UPLC-MS-MS,4310168
+Denmark,A902,Føroyskar hvalvágir ,2012,09/08/2012,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.3,ng/g,,,,,,UPLC-MS-MS,4310168
+Denmark,A902,Føroyskar hvalvágir ,2012,09/08/2012,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.5,ng/g,,,,,,UPLC-MS-MS,4310168
+Denmark,A902,Føroyskar hvalvágir ,2013,08/08/2013,62.05149,-7.155315,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.5,ng/g,,,,,<,UPLC-MS-MS,4310161
+Denmark,A902,Føroyskar hvalvágir ,2013,08/08/2013,62.05149,-7.155315,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.5,ng/g,,,,,<,UPLC-MS-MS,4310161
+Denmark,A902,Føroyskar hvalvágir ,2013,08/08/2013,62.05149,-7.155315,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.5,ng/g,,,,,<,UPLC-MS-MS,4310161
+Denmark,A902,Føroyskar hvalvágir ,2013,30/07/2013,62.23875,-6.810065,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.2,ng/g,,,,,,UPLC-MS-MS,4310160
+Denmark,A902,Føroyskar hvalvágir ,2013,30/07/2013,62.23875,-6.810065,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.5,ng/g,,,,,<,UPLC-MS-MS,4310160
+Denmark,A902,Føroyskar hvalvágir ,2013,30/07/2013,62.23875,-6.810065,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.5,ng/g,,,,,<,UPLC-MS-MS,4310160
+Denmark,A902,Føroyskar hvalvágir ,2013,30/07/2013,62.23875,-6.810065,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.1,ng/g,,,,,,UPLC-MS-MS,4310160
+Denmark,A902,Føroyskar hvalvágir ,2015,06/06/2015,62.04664,-7.186415,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.2,ng/g,,,,,,UPLC-MS-MS,4309941
+Denmark,A902,Føroyskar hvalvágir ,2015,06/06/2015,62.04664,-7.186415,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.7,ng/g,,,,,,UPLC-MS-MS,4309941
+Denmark,A902,Føroyskar hvalvágir ,2015,06/06/2015,62.04664,-7.186415,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.1,ng/g,,,,,<,UPLC-MS-MS,4309941
+Denmark,A902,Føroyskar hvalvágir ,2015,29/06/2015,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.2,ng/g,,,,,,UPLC-MS-MS,4309942
+Denmark,A902,Føroyskar hvalvágir ,2015,29/06/2015,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.4,ng/g,,,,,,UPLC-MS-MS,4309942
+Denmark,A902,Føroyskar hvalvágir ,2016,07/11/2016,62.1155,-7.04508,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.1,ng/g,,,,,<,UPLC-MS-MS,4308911
+Denmark,A902,Føroyskar hvalvágir ,2016,26/07/2016,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.4,ng/g,,,,,,UPLC-MS-MS,4308908
+Denmark,A902,Føroyskar hvalvágir ,2016,26/07/2016,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.3,ng/g,,,,,,UPLC-MS-MS,4308908
+Denmark,A902,Føroyskar hvalvágir ,2016,26/07/2016,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.8,ng/g,,,,,,UPLC-MS-MS,4308908
+Denmark,A902,Føroyskar hvalvágir ,2016,26/07/2016,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.3,ng/g,,,,,,UPLC-MS-MS,4308908
+Denmark,A902,Føroyskar hvalvágir ,2017,16/06/2017,62.00031,-6.77677,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,BB,W,0.04,ng/g,,,,,<,UPLC-MS-MS,4310328
+Denmark,A902,Føroyskar hvalvágir ,2017,16/06/2017,62.00031,-6.77677,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,BB,W,0.36,ng/g,,,19,%,,UPLC-MS-MS,4310328
+Denmark,A902,Føroyskar hvalvágir ,2017,26/06/2017,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,BB,W,0.04,ng/g,,,,,<,UPLC-MS-MS,4310329
+Denmark,A902,Føroyskar hvalvágir ,2017,26/06/2017,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,BB,W,0.04,ng/g,,,,,<,UPLC-MS-MS,4310329
+Denmark,A902,Føroyskar hvalvágir ,2017,29/06/2017,62.29236,-7.143775,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,BB,W,0.04,ng/g,,,,,<,UPLC-MS-MS,4310330
+Denmark,A902,Føroyskar hvalvágir ,2018,24/07/2018,62.00031,-6.77677,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,BB,W,0.4,ng/g,,,,,<,UPLC-MS-MS,4310342
+Denmark,A902,Føroyskar hvalvágir ,2018,24/07/2018,62.00031,-6.77677,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,BB,W,0.4,ng/g,,,,,<,UPLC-MS-MS,4310342
+Denmark,A902,Føroyskar hvalvágir ,2018,22/05/2018,62.185916,-6.753463,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,BB,W,0.49,ng/g,,,19,%,,UPLC-MS-MS,4310339
+Denmark,A902,Føroyskar hvalvágir ,2018,22/05/2018,62.185916,-6.753463,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,BB,W,0.83,ng/g,,,19,%,,UPLC-MS-MS,4310339
+Denmark,A902,Føroyskar hvalvágir ,2018,22/05/2018,62.185916,-6.753463,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,BB,W,0.43,ng/g,,,19,%,,UPLC-MS-MS,4310339
+Denmark,A902,Føroyskar hvalvágir ,2019,29/05/2019,62.00031,-6.77677,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.53,ng/g,,,9,%,,UPLC-MS-MS,4310347
+Denmark,A902,Føroyskar hvalvágir ,2019,27/08/2019,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.17,ng/g,,,9,%,,UPLC-MS-MS,4310350
+Denmark,A902,Føroyskar hvalvágir ,2019,27/08/2019,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.13,ng/g,,,9,%,,UPLC-MS-MS,4310350
+Denmark,A902,Føroyskar hvalvágir ,2019,27/08/2019,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.15,ng/g,,,9,%,,UPLC-MS-MS,4310350
+Denmark,A902,Føroyskar hvalvágir ,2019,02/08/2019,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.835,ng/g,,,9,%,,UPLC-MS-MS,4310349
+Denmark,A902,Føroyskar hvalvágir ,2020,16/10/2020,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.05,ng/g,,,9,%,,UPLC-MS-MS,4310358
+Denmark,A902,Føroyskar hvalvágir ,2020,16/10/2020,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.05,ng/g,,,9,%,,UPLC-MS-MS,4310358
+Denmark,A902,Føroyskar hvalvágir ,2020,16/10/2020,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.07,ng/g,,,9,%,,UPLC-MS-MS,4310358
+Denmark,A902,Føroyskar hvalvágir ,2020,16/10/2020,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.08,ng/g,,,9,%,,UPLC-MS-MS,4310358
+Denmark,A902,Føroyskar hvalvágir ,2020,16/10/2020,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOA,LI,W,0.07,ng/g,,,9,%,,UPLC-MS-MS,4310358
+Denmark,A902,Føroyskar hvalvágir ,2011,02/09/2011,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,25.4,ng/g,,,,,,UPLC-MS-MS,4310175
+Denmark,A902,Føroyskar hvalvágir ,2011,09/02/2011,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,53.4,ng/g,,,,,,UPLC-MS-MS,4310171
+Denmark,A902,Føroyskar hvalvágir ,2011,09/02/2011,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,44.7,ng/g,,,,,,UPLC-MS-MS,4310171
+Denmark,A902,Føroyskar hvalvágir ,2011,02/09/2011,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,69.8,ng/g,,,,,,UPLC-MS-MS,4310175
+Denmark,A902,Føroyskar hvalvágir ,2011,02/09/2011,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,171.9,ng/g,,,,,,UPLC-MS-MS,4310175
+Denmark,A902,Føroyskar hvalvágir ,2012,10/07/2012,62.224293,-6.571586,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,79.8,ng/g,,,,,,UPLC-MS-MS,4310167
+Denmark,A902,Føroyskar hvalvágir ,2012,09/08/2012,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,100.7,ng/g,,,,,,UPLC-MS-MS,4310168
+Denmark,A902,Føroyskar hvalvágir ,2012,09/08/2012,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,82.8,ng/g,,,,,,UPLC-MS-MS,4310168
+Denmark,A902,Føroyskar hvalvágir ,2012,09/08/2012,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,86.7,ng/g,,,,,,UPLC-MS-MS,4310168
+Denmark,A902,Føroyskar hvalvágir ,2013,08/08/2013,62.05149,-7.155315,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,31.7,ng/g,,,,,,UPLC-MS-MS,4310161
+Denmark,A902,Føroyskar hvalvágir ,2013,08/08/2013,62.05149,-7.155315,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,282,ng/g,,,,,,UPLC-MS-MS,4310161
+Denmark,A902,Føroyskar hvalvágir ,2013,08/08/2013,62.05149,-7.155315,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,74.6,ng/g,,,,,,UPLC-MS-MS,4310161
+Denmark,A902,Føroyskar hvalvágir ,2013,30/07/2013,62.23875,-6.810065,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,68.4,ng/g,,,,,,UPLC-MS-MS,4310160
+Denmark,A902,Føroyskar hvalvágir ,2013,30/07/2013,62.23875,-6.810065,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,23.1,ng/g,,,,,,UPLC-MS-MS,4310160
+Denmark,A902,Føroyskar hvalvágir ,2013,30/07/2013,62.23875,-6.810065,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,26.6,ng/g,,,,,,UPLC-MS-MS,4310160
+Denmark,A902,Føroyskar hvalvágir ,2013,30/07/2013,62.23875,-6.810065,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,58.4,ng/g,,,,,,UPLC-MS-MS,4310160
+Denmark,A902,Føroyskar hvalvágir ,2015,06/06/2015,62.04664,-7.186415,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,51.7,ng/g,,,,,,UPLC-MS-MS,4309941
+Denmark,A902,Føroyskar hvalvágir ,2015,06/06/2015,62.04664,-7.186415,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,121.8,ng/g,,,,,,UPLC-MS-MS,4309941
+Denmark,A902,Føroyskar hvalvágir ,2015,06/06/2015,62.04664,-7.186415,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,28.9,ng/g,,,,,,UPLC-MS-MS,4309941
+Denmark,A902,Føroyskar hvalvágir ,2015,29/06/2015,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,64.1,ng/g,,,,,,UPLC-MS-MS,4309942
+Denmark,A902,Føroyskar hvalvágir ,2015,29/06/2015,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,110.7,ng/g,,,,,,UPLC-MS-MS,4309942
+Denmark,A902,Føroyskar hvalvágir ,2016,07/11/2016,62.1155,-7.04508,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,16.5,ng/g,,,,,,UPLC-MS-MS,4308911
+Denmark,A902,Føroyskar hvalvágir ,2016,26/07/2016,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,42.2,ng/g,,,,,,UPLC-MS-MS,4308908
+Denmark,A902,Føroyskar hvalvágir ,2016,26/07/2016,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,73.1,ng/g,,,,,,UPLC-MS-MS,4308908
+Denmark,A902,Føroyskar hvalvágir ,2016,26/07/2016,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,120.6,ng/g,,,,,,UPLC-MS-MS,4308908
+Denmark,A902,Føroyskar hvalvágir ,2016,26/07/2016,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,66.5,ng/g,,,,,,UPLC-MS-MS,4308908
+Denmark,A902,Føroyskar hvalvágir ,2017,16/06/2017,62.00031,-6.77677,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,BB,W,16.03,ng/g,,,24,%,,UPLC-MS-MS,4310328
+Denmark,A902,Føroyskar hvalvágir ,2017,16/06/2017,62.00031,-6.77677,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,BB,W,24.26,ng/g,,,24,%,,UPLC-MS-MS,4310328
+Denmark,A902,Føroyskar hvalvágir ,2017,26/06/2017,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,BB,W,13.54,ng/g,,,24,%,,UPLC-MS-MS,4310329
+Denmark,A902,Føroyskar hvalvágir ,2017,26/06/2017,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,BB,W,19.37,ng/g,,,24,%,,UPLC-MS-MS,4310329
+Denmark,A902,Føroyskar hvalvágir ,2017,29/06/2017,62.29236,-7.143775,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,BB,W,18.31,ng/g,,,24,%,,UPLC-MS-MS,4310330
+Denmark,A902,Føroyskar hvalvágir ,2018,24/07/2018,62.00031,-6.77677,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,BB,W,104,ng/g,,,24,%,,UPLC-MS-MS,4310342
+Denmark,A902,Føroyskar hvalvágir ,2018,24/07/2018,62.00031,-6.77677,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,BB,W,59.8,ng/g,,,24,%,,UPLC-MS-MS,4310342
+Denmark,A902,Føroyskar hvalvágir ,2018,22/05/2018,62.185916,-6.753463,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,BB,W,102,ng/g,,,24,%,,UPLC-MS-MS,4310339
+Denmark,A902,Føroyskar hvalvágir ,2018,22/05/2018,62.185916,-6.753463,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,BB,W,105,ng/g,,,24,%,,UPLC-MS-MS,4310339
+Denmark,A902,Føroyskar hvalvágir ,2018,22/05/2018,62.185916,-6.753463,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,BB,W,129,ng/g,,,24,%,,UPLC-MS-MS,4310339
+Denmark,A902,Føroyskar hvalvágir ,2019,29/05/2019,62.00031,-6.77677,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,120,ng/g,,,8,%,,UPLC-MS-MS,4310347
+Denmark,A902,Føroyskar hvalvágir ,2019,27/08/2019,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,35,ng/g,,,8,%,,UPLC-MS-MS,4310350
+Denmark,A902,Føroyskar hvalvágir ,2019,27/08/2019,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,63,ng/g,,,8,%,,UPLC-MS-MS,4310350
+Denmark,A902,Føroyskar hvalvágir ,2019,27/08/2019,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,17,ng/g,,,8,%,,UPLC-MS-MS,4310350
+Denmark,A902,Føroyskar hvalvágir ,2019,02/08/2019,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,134.5,ng/g,,,8,%,,UPLC-MS-MS,4310349
+Denmark,A902,Føroyskar hvalvágir ,2020,16/10/2020,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,9.2,ng/g,,,8,%,,UPLC-MS-MS,4310358
+Denmark,A902,Føroyskar hvalvágir ,2020,16/10/2020,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,11.6,ng/g,,,8,%,,UPLC-MS-MS,4310358
+Denmark,A902,Føroyskar hvalvágir ,2020,16/10/2020,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,27.46,ng/g,,,8,%,,UPLC-MS-MS,4310358
+Denmark,A902,Føroyskar hvalvágir ,2020,16/10/2020,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,20.13,ng/g,,,8,%,,UPLC-MS-MS,4310358
+Denmark,A902,Føroyskar hvalvágir ,2020,16/10/2020,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOS,LI,W,9.9,ng/g,,,8,%,,UPLC-MS-MS,4310358
+Denmark,A902,Føroyskar hvalvágir ,2011,09/02/2011,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,12.3,ng/g,,,,,,UPLC-MS-MS,4310171
+Denmark,A902,Føroyskar hvalvágir ,2011,09/02/2011,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,17.5,ng/g,,,,,,UPLC-MS-MS,4310171
+Denmark,A902,Føroyskar hvalvágir ,2011,02/09/2011,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,17.7,ng/g,,,,,,UPLC-MS-MS,4310175
+Denmark,A902,Føroyskar hvalvágir ,2011,02/09/2011,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,19.1,ng/g,,,,,,UPLC-MS-MS,4310175
+Denmark,A902,Føroyskar hvalvágir ,2011,02/09/2011,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,13.5,ng/g,,,,,,UPLC-MS-MS,4310175
+Denmark,A902,Føroyskar hvalvágir ,2012,10/07/2012,62.224293,-6.571586,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,13.1,ng/g,,,,,,UPLC-MS-MS,4310167
+Denmark,A902,Føroyskar hvalvágir ,2012,09/08/2012,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,10.4,ng/g,,,,,,UPLC-MS-MS,4310168
+Denmark,A902,Føroyskar hvalvágir ,2012,09/08/2012,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,8,ng/g,,,,,,UPLC-MS-MS,4310168
+Denmark,A902,Føroyskar hvalvágir ,2012,09/08/2012,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,8.2,ng/g,,,,,,UPLC-MS-MS,4310168
+Denmark,A902,Føroyskar hvalvágir ,2013,08/08/2013,62.05149,-7.155315,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,18.3,ng/g,,,,,,UPLC-MS-MS,4310161
+Denmark,A902,Føroyskar hvalvágir ,2013,08/08/2013,62.05149,-7.155315,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,29.3,ng/g,,,,,,UPLC-MS-MS,4310161
+Denmark,A902,Føroyskar hvalvágir ,2013,08/08/2013,62.05149,-7.155315,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,13.7,ng/g,,,,,,UPLC-MS-MS,4310161
+Denmark,A902,Føroyskar hvalvágir ,2013,30/07/2013,62.23875,-6.810065,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,7.7,ng/g,,,,,,UPLC-MS-MS,4310160
+Denmark,A902,Føroyskar hvalvágir ,2013,30/07/2013,62.23875,-6.810065,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,8.5,ng/g,,,,,,UPLC-MS-MS,4310160
+Denmark,A902,Føroyskar hvalvágir ,2013,30/07/2013,62.23875,-6.810065,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,23,ng/g,,,,,,UPLC-MS-MS,4310160
+Denmark,A902,Føroyskar hvalvágir ,2013,30/07/2013,62.23875,-6.810065,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,12.8,ng/g,,,,,,UPLC-MS-MS,4310160
+Denmark,A902,Føroyskar hvalvágir ,2015,06/06/2015,62.04664,-7.186415,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,9.4,ng/g,,,,,,UPLC-MS-MS,4309941
+Denmark,A902,Føroyskar hvalvágir ,2015,06/06/2015,62.04664,-7.186415,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,7.5,ng/g,,,,,,UPLC-MS-MS,4309941
+Denmark,A902,Føroyskar hvalvágir ,2015,06/06/2015,62.04664,-7.186415,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,20.5,ng/g,,,,,,UPLC-MS-MS,4309941
+Denmark,A902,Føroyskar hvalvágir ,2015,29/06/2015,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,4.3,ng/g,,,,,,UPLC-MS-MS,4309942
+Denmark,A902,Føroyskar hvalvágir ,2015,29/06/2015,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,5,ng/g,,,,,,UPLC-MS-MS,4309942
+Denmark,A902,Føroyskar hvalvágir ,2016,07/11/2016,62.1155,-7.04508,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,6.9,ng/g,,,,,,UPLC-MS-MS,4308911
+Denmark,A902,Føroyskar hvalvágir ,2016,26/07/2016,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,6.1,ng/g,,,,,,UPLC-MS-MS,4308908
+Denmark,A902,Føroyskar hvalvágir ,2016,26/07/2016,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,15.9,ng/g,,,,,,UPLC-MS-MS,4308908
+Denmark,A902,Føroyskar hvalvágir ,2016,26/07/2016,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,13.4,ng/g,,,,,,UPLC-MS-MS,4308908
+Denmark,A902,Føroyskar hvalvágir ,2016,26/07/2016,62.30033,-6.523,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,7.3,ng/g,,,,,,UPLC-MS-MS,4308908
+Denmark,A902,Føroyskar hvalvágir ,2018,24/07/2018,62.00031,-6.77677,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,BB,W,13.2,ng/g,,,40,%,,UPLC-MS-MS,4310342
+Denmark,A902,Føroyskar hvalvágir ,2018,24/07/2018,62.00031,-6.77677,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,BB,W,31.8,ng/g,,,40,%,,UPLC-MS-MS,4310342
+Denmark,A902,Føroyskar hvalvágir ,2018,22/05/2018,62.185916,-6.753463,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,BB,W,17.3,ng/g,,,40,%,,UPLC-MS-MS,4310339
+Denmark,A902,Føroyskar hvalvágir ,2018,22/05/2018,62.185916,-6.753463,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,BB,W,17.7,ng/g,,,40,%,,UPLC-MS-MS,4310339
+Denmark,A902,Føroyskar hvalvágir ,2018,22/05/2018,62.185916,-6.753463,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,BB,W,17.7,ng/g,,,40,%,,UPLC-MS-MS,4310339
+Denmark,A902,Føroyskar hvalvágir ,2019,29/05/2019,62.00031,-6.77677,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,15,ng/g,,,1,%,,UPLC-MS-MS,4310347
+Denmark,A902,Føroyskar hvalvágir ,2019,27/08/2019,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,4.9,ng/g,,,1,%,,UPLC-MS-MS,4310350
+Denmark,A902,Føroyskar hvalvágir ,2019,27/08/2019,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,12,ng/g,,,1,%,,UPLC-MS-MS,4310350
+Denmark,A902,Føroyskar hvalvágir ,2019,27/08/2019,62.15383,-7.15983,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,11,ng/g,,,1,%,,UPLC-MS-MS,4310350
+Denmark,A902,Føroyskar hvalvágir ,2019,02/08/2019,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,7.8,ng/g,,,1,%,,UPLC-MS-MS,4310349
+Denmark,A902,Føroyskar hvalvágir ,2020,16/10/2020,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,19,ng/g,,,1,%,,UPLC-MS-MS,4310358
+Denmark,A902,Føroyskar hvalvágir ,2020,16/10/2020,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,11.49,ng/g,,,1,%,,UPLC-MS-MS,4310358
+Denmark,A902,Føroyskar hvalvágir ,2020,16/10/2020,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,5.08,ng/g,,,1,%,,UPLC-MS-MS,4310358
+Denmark,A902,Føroyskar hvalvágir ,2020,16/10/2020,62.18833,-7.02733,,B~T~S~R,Globicephala melas,M,JV,1,PFOSD,LI,W,12.07,ng/g,,,1,%,,UPLC-MS-MS,4310358
\ No newline at end of file
diff --git a/tests/testthat/test-markdown.R b/tests/testthat/test-markdown.R
new file mode 100644
index 0000000..d301a0d
--- /dev/null
+++ b/tests/testthat/test-markdown.R
@@ -0,0 +1,77 @@
+library(rprojroot)
+working_directory <- is_testthat$find_file()
+
+data_dir = file.path(working_directory, "..", "datasets", "external-1", "data")
+info_dir = file.path(working_directory, "..", "datasets", "external-1", "information")
+
+library(rmarkdown)
+
+package_dir = system.file(package = "harsat")
+template_dir = file.path(package_dir, "markdown")
+
+output_dir <- file.path(tempdir(), 'report-tests')
+dir.create(output_dir, showWarnings = FALSE)
+
+call_read_data <- function(compartment = "biota", data_format = "external", purpose = "AMAP",
+                           contaminants = "EXTERNAL_FO_PW_DATA_TINY.csv") {
+  read_data(
+    compartment = compartment,
+    purpose = purpose,
+    contaminants = contaminants,
+    stations = "EXTERNAL_AMAP_STATIONS.csv",
+    data_dir = data_dir,
+    data_format = data_format,
+    info_dir = info_dir
+  )
+}
+
+test_that('markdown reporting works', {
+
+  biota_data <- call_read_data()
+  biota_data <- tidy_data(biota_data)
+  biota_timeseries <- create_timeseries(biota_data, get_basis = get_basis_most_common)
+  biota_assessment <- run_assessment(biota_timeseries)
+
+  report_file <- file.path(template_dir, "report_assessment.Rmd")
+  output_file <- tempfile("plot", tmpdir = output_dir, fileext = c(".htm"))
+
+  params = list(
+    assessment_object = biota_assessment,
+    series = 'A902 PFOA Globicephala melas LI JV'
+  )
+
+  rmarkdown::render(
+    report_file,
+    output_file = output_file,
+    params = params,
+    envir = new.env()
+  )
+
+  file.body <- readr::read_file(output_file)
+  
+  expect_true(base::grepl('Perfluorooctanoic', file.body, fixed = TRUE))
+  expect_true(base::grepl('long-finned pilot whale', file.body, fixed = TRUE))
+  expect_true(base::grepl('liver', file.body, fixed = TRUE))
+  expect_true(base::grepl('Føroyskar hvalvágir', file.body, fixed = TRUE))
+
+  expect_true(base::grepl('Timeseries metadata', file.body, fixed = TRUE))
+  expect_true(base::grepl('Assessment plot', file.body, fixed = TRUE))
+  expect_true(base::grepl('Trend with data', file.body, fixed = TRUE))
+  expect_true(base::grepl('Statistical analysis', file.body, fixed = TRUE))
+
+  ## In addition, we should also be able to run `report_assessment`
+
+  report_assessment(
+    biota_assessment,
+    subset = NULL,
+    output_dir = output_dir
+  )
+
+  report.files <- list.files(output_dir, pattern = '\\.html$')
+  expect_setequal(report.files, c(
+    "A902 Faroe Islands Føroyskar hvalvágir PFOA Globicephala melas BB JV.html",
+    "A902 Faroe Islands Føroyskar hvalvágir PFOA Globicephala melas LI JV.html",
+    "A902 Faroe Islands Føroyskar hvalvágir PFOS Globicephala melas BB JV.html",
+    "A902 Faroe Islands Føroyskar hvalvágir PFOS Globicephala melas LI JV.html"
+  ))
+})
diff --git a/tests/testthat/test-run-assessment.R b/tests/testthat/test-run-assessment.R
new file mode 100644
index 0000000..6717e3d
--- /dev/null
+++ b/tests/testthat/test-run-assessment.R
@@ -0,0 +1,34 @@
+library(rprojroot)
+working_directory <- is_testthat$find_file()
+
+data_dir = file.path(working_directory, "..", "datasets", "external-1", "data")
+info_dir = file.path(working_directory, "..", "datasets", "external-1", "information")
+
+call_read_data <- function(compartment = "biota", data_format = "external", purpose = "AMAP",
+                           contaminants = "EXTERNAL_FO_PW_DATA_TINY.csv") {
+  read_data(
+    compartment = compartment,
+    purpose = purpose,
+    contaminants = contaminants,
+    stations = "EXTERNAL_AMAP_STATIONS.csv",
+    data_dir = data_dir,
+    data_format = data_format,
+    info_dir = info_dir
+  )
+}
+
+test_that('run_assessment works', {
+    biota_data <- call_read_data()
+    biota_data <- tidy_data(biota_data)
+    biota_timeseries <- create_timeseries(biota_data, get_basis = get_basis_most_common)
+    biota_assessment <- run_assessment(biota_timeseries)
+
+    expect_equal(biota_assessment$info$compartment, 'biota')
+    expect_type(biota_assessment$timeSeries, 'list')
+    expect_type(biota_assessment$assessment, 'list')
+    expect_type(biota_assessment$assessment$`A902 PFOA Globicephala melas LI JV`, 'list')
+    expect_equal(biota_assessment$assessment$`A902 PFOA Globicephala melas LI JV`$method, 'linear')
+    expect_equal(biota_assessment$assessment$`A902 PFOA Globicephala melas LI JV`$convergence, 0)
+    expect_equal(biota_assessment$assessment$`A902 PFOA Globicephala melas BB JV`$method, 'none')
+    expect_equal(biota_assessment$assessment$`A902 PFOA Globicephala melas BB JV`$convergence, 0)
+})
diff --git a/vignettes/report-template.Rmd b/vignettes/report-template.Rmd
new file mode 100644
index 0000000..7f5f532
--- /dev/null
+++ b/vignettes/report-template.Rmd
@@ -0,0 +1,80 @@
+---
+title: "Report template usage"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Report template usage}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+The package includes a report template that may help you generate a 
+report for a given assessment. This is installed as a file `report_assessment.Rmd`
+in a directory `markdown`, so to use it, you'll need to use `system.file()` to 
+find the template file.
+
+You can use this report tempate in two different ways:
+
+## Through `report_assessment`
+
+The easiest way to generate reports is in bulk, as follows:
+
+```r
+## Do whatever you need to get the assessment object
+...
+assessment <- run_assessment(timeseries)
+
+report_assessment(
+  biota_assessment,
+  subset = NULL,
+  output_dir = my_output_dir
+)
+```
+
+This will generate all the reports, although you can pass a subsetting
+expression (just like with `plot_assessment`) to select which 
+individual assessments you want reports on. The reports are written 
+as HTML files into the given output directory.
+
+## Directly through R Markdown
+
+In this case, your usage will typically look a bit like this:
+
+```r
+library(rmarkdown)
+
+
+## Do whatever you need to get the assessment object
+...
+assessment <- run_assessment(timeseries)
+
+## Locate the report file
+package_dir = system.file(package = "harsat")
+template_dir = file.path(package_dir, "markdown")
+report_file <- file.path(template_dir, "report_assessment.Rmd")
+
+## Create a new filename for the output file, here we just
+## put it in a temporary file, but you'll usually want something
+## more persistent.
+output_file <- tempfile("plot", fileext = c(".htm"))
+
+## Choose what you want to report. Pick the series you want to
+## report like this.
+params = list(
+  assessment_object = assessment,
+  series = 'A902 PFOA Globicephala melas LI JV'
+)
+
+## Generate the report -- note the use of `new.env()` to make a 
+## nice clean enviroment containing only the parameters you pass,
+## as above. 
+rmarkdown::render(
+  report_file,
+  output_file = output_file,
+  params = params,
+  envir = new.env()
+)
+```
+
+Note that because this is R Markdown, you can do this as a child
+document from another template. You can also control the output
+format, generating PDF, for example.