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

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

Invocation from commandline

The report can be generated from the command line by using

```{bash info_invocation, eval = FALSE} Rscript -e "library(LEEF.analysis); db <- '~/Desktop/9.backend/LEEF.RRD.sqlite'; report_interactive();"

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## Response  variable in the last timestap

```r
plot_response_incubator(params$db)

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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.

plot_bottles_per_timestamp(params$db, lastDays = params$lastDays)

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Number of Species per timestamp

This plot shows the

plot_no_species_per_bottle_per_timestamp(params$db)

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Species per timestamp and measurement

Measurements are colour coded and in the order as in the legend on the right.

plot_species_per_timestamp_per_measure(params$db)

Density of Species per bottle as measured by measurement over time

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Bemovi Magnification 16

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

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Bemovi Magnification 25

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

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Bemovi Magnification 25 non_cropped

plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = FALSE, 
  measurement = "bemovi_mag_25_non_cropped",
  species_set_id = NULL
)

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Bemovi Magnification 25 cropped

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

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Flowcam Algae

plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = FALSE, 
  measurement = "flowcam",
  species_set_id = "flowcam_algae"
)

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Flowcam Ciliates

plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = FALSE, 
  measurement = "flowcam",
  species_set_id = "flowcam_ciliates"
)

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Flowcam Rest

plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = FALSE, 
  measurement = "flowcam",
  species_set_id = "flowcam_rest"
)

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Flowcytometer

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

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Manualcount

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

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Percent O~2~

plot_o2s_per_bottle_per_timestamp(
  params$db
)

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TOC and TC

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

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IC and TN

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

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

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Bemovi Magnification 16

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

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Bemovi Magnification 25

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

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Bemovi Magnification 25 non cropped

plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = TRUE, 
  measurement = "bemovi_mag_25_non_cropped",
  species_set_id = NULL
)

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Bemovi Magnification 25 cropped

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

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Flowcam Algae

plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = TRUE, 
  measurement = "flowcam",
  species_set_id = "flowcam_algae"
)

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Flowcam Ciliates

plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = TRUE, 
  measurement = "flowcam",
  species_set_id = "flowcam_ciliates"
)

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Flowcam Rest

plot_density_species_per_bottle_per_timestamp(
  params$db, 
  transform_density_4throot = TRUE, 
  measurement = "flowcam",
  species_set_id = "flowcam_rest"
)

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Flowcytometer

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

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Manualcount

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

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Percent O~2~

plot_o2s_per_bottle_per_timestamp(
  params$db
)

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TOC and TC

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

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IC and TN

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

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