In LEEF-UZH/LEEF.analysis: Access Functions, Tests and Basic Analysis of the RRD Data from the LEEF Project

if (!exists("params")) {
  params <- rmarkdown::yaml_front_matter("~/git/0.RPackages/LEEF/analysis/LEEF.analysis/inst/LEEF-2/DiagnosticReport.Rmd")$params
}

knitr::opts_chunk$set(echo = TRUE)
library(LEEF.analysis)

options(RRDarrow = params$parquet_dir)

Invocation from commandline

The report can be generated from the command line by using

```{bash info_invocation, eval = FALSE} Rscript -e "library(LEEF.analysis); LEEF_2_report_diagnostic(db = 'DATABASE PATH', template = 'LEEF_2', format = 'html', lastDays = 7);"

\pagebreak

## Response  variable in the last timestap

```r
LEEF_2_plot_response_incubator(params$db, arrow = params$arrow)

\pagebreak

Check Bottles per Measurement per Timestep

This plot shows, if a bottle is present for the measurement for the timestamps analysed. Each measurement is a panes. Missing dots indicate missing datapoints for the bottle at the measurement for the timestamp.

LEEF_2_plot_bottles_per_timestamp(params$db, lastDays = params$lastDays, arrow = params$arrow)

\pagebreak

Density of Species per bottle as measured by measurement over time

\pagebreak

Bemovi Magnification 16

LEEF_2_plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = FALSE, 
  measurement = "bemovi_mag_16",
  species_set_id = NULL, 
  arrow = params$arrow
)

\pagebreak

Bemovi Magnification 25

LEEF_2_plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = FALSE, 
  measurement = "bemovi_mag_25",
  species_set_id = NULL, 
  arrow = params$arrow
)

\pagebreak

Bemovi Magnification 25 cropped

LEEF_2_plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = FALSE, 
  measurement = "bemovi_mag_25_cropped",
  species_set_id = NULL, 
  arrow = params$arrow
)

\pagebreak

Flowcam Everything

LEEF_2_plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = FALSE, 
  measurement = "flowcam",
  species_set_id = NULL, 
  arrow = params$arrow
)

\pagebreak

Flowcam Algae

LEEF_2_plot_density_species_per_bottle_per_timestamp(
  params$db,
  transform_density_4throot = FALSE,
  measurement = "flowcam",
  species_set_id = "LEEF_2_flowcam_algae",
  arrow = params$arrow
)

` \pagebreak

Flowcam Rest

LEEF_2_plot_density_species_per_bottle_per_timestamp(
  params$db,
  transform_density_4throot = FALSE,
  measurement = "flowcam",
  species_set_id = "LEEF_2_flowcam_rest",
  arrow = params$arrow
)

\pagebreak

Flowcytometer

LEEF_2_plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = FALSE, 
  measurement = "flowcytometer",
  species_set_id = NULL,
  arrow = params$arrow
)

\pagebreak

Manualcount

LEEF_2_plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = FALSE, 
  measurement = "manualcount",
  species_set_id = NULL,
  arrow = params$arrow
)

\pagebreak

Percent O~2~

LEEF_2_plot_o2s_per_bottle_per_timestamp(
  params$db,
  arrow = params$arrow
)

\pagebreak

Conductivity

LEEF_2_plot_conductivity_per_bottle_per_timestamp(
  params$db,
  arrow = params$arrow
)

\pagebreak

TOC and TC

LEEF_2_plot_tocs_per_bottle_per_timestamp(
  params$db,
  type = c("TOC", "TC"),
  arrow = params$arrow
)

\pagebreak

IC and TN

LEEF_2_plot_tocs_per_bottle_per_timestamp(
  params$db,
  type = c("IC", "TN"),
  arrow = params$arrow
)

4^th^ root Density of Species per bottle as measured by measurement over time

\pagebreak

Bemovi Magnification 16

LEEF_2_plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = TRUE, 
  measurement = "bemovi_mag_16",
  species_set_id = NULL,
  arrow = params$arrow
)

\pagebreak

Bemovi Magnification 25

LEEF_2_plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = TRUE, 
  measurement = "bemovi_mag_25",
  species_set_id = NULL,
  arrow = params$arrow
)

\pagebreak

Bemovi Magnification 25 cropped

LEEF_2_plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = TRUE, 
  measurement = "bemovi_mag_25_cropped",
  species_set_id = NULL,
  arrow = params$arrow
)

\pagebreak

Flowcam Algae

LEEF_2_plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = TRUE, 
  measurement = "flowcam",
  species_set_id = "LEEF_2_flowcam_algae",
  arrow = params$arrow
)

\pagebreak

Flowcam Rest

LEEF_2_plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = TRUE, 
  measurement = "flowcam",
  species_set_id = "LEEF_flowcam_rest",
  arrow = params$arrow
)

\pagebreak

Flowcytometer

LEEF_2_plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = TRUE, 
  measurement = "flowcytometer",
  species_set_id = NULL,
  arrow = params$arrow
)

\pagebreak

Manualcount

LEEF_2_plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = TRUE, 
  measurement = "manualcount",
  species_set_id = NULL,
  arrow = params$arrow
)

\pagebreak

Percent O~2~

LEEF_2_plot_o2s_per_bottle_per_timestamp(
  params$db,
  arrow = params$arrow
)

\pagebreak

Conductivity

LEEF_2_plot_conductivity_per_bottle_per_timestamp(
  params$db,
  arrow = params$arrow
)

\pagebreak

TOC and TC

LEEF_2_plot_tocs_per_bottle_per_timestamp(
  params$db,
  type = c("TOC", "TC"),
  arrow = params$arrow
)

\pagebreak

IC and TN

LEEF_2_plot_tocs_per_bottle_per_timestamp(
  params$db,
  type = c("IC", "TN"),
  arrow = params$arrow
)

LEEF-UZH/LEEF.analysis documentation built on Feb. 8, 2025, 11:18 a.m.