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Packages

# Load rmarkdown package
library(rmarkdown)
# Load knitr package
library(knitr)
# Load tidyverse package
library(tidyverse)
## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr     1.1.4     ✔ readr     2.1.5
## ✔ forcats   1.0.0     ✔ stringr   1.5.1
## ✔ ggplot2   3.5.0     ✔ tibble    3.2.1
## ✔ lubridate 1.9.3     ✔ tidyr     1.3.1
## ✔ purrr     1.0.2     
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag()    masks stats::lag()
## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

Data

data(CO2)
str(CO2)
## Classes 'nfnGroupedData', 'nfGroupedData', 'groupedData' and 'data.frame':   84 obs. of  5 variables:
##  $ Plant    : Ord.factor w/ 12 levels "Qn1"<"Qn2"<"Qn3"<..: 1 1 1 1 1 1 1 2 2 2 ...
##  $ Type     : Factor w/ 2 levels "Quebec","Mississippi": 1 1 1 1 1 1 1 1 1 1 ...
##  $ Treatment: Factor w/ 2 levels "nonchilled","chilled": 1 1 1 1 1 1 1 1 1 1 ...
##  $ conc     : num  95 175 250 350 500 675 1000 95 175 250 ...
##  $ uptake   : num  16 30.4 34.8 37.2 35.3 39.2 39.7 13.6 27.3 37.1 ...
##  - attr(*, "formula")=Class 'formula'  language uptake ~ conc | Plant
##   .. ..- attr(*, ".Environment")=<environment: R_EmptyEnv> 
##  - attr(*, "outer")=Class 'formula'  language ~Treatment * Type
##   .. ..- attr(*, ".Environment")=<environment: R_EmptyEnv> 
##  - attr(*, "labels")=List of 2
##   ..$ x: chr "Ambient carbon dioxide concentration"
##   ..$ y: chr "CO2 uptake rate"
##  - attr(*, "units")=List of 2
##   ..$ x: chr "(uL/L)"
##   ..$ y: chr "(umol/m^2 s)"
summary(CO2)
##      Plant             Type         Treatment       conc          uptake     
##  Qn1    : 7   Quebec     :42   nonchilled:42   Min.   :  95   Min.   : 7.70  
##  Qn2    : 7   Mississippi:42   chilled   :42   1st Qu.: 175   1st Qu.:17.90  
##  Qn3    : 7                                    Median : 350   Median :28.30  
##  Qc1    : 7                                    Mean   : 435   Mean   :27.21  
##  Qc3    : 7                                    3rd Qu.: 675   3rd Qu.:37.12  
##  Qc2    : 7                                    Max.   :1000   Max.   :45.50  
##  (Other):42
Variable <- c("Plant", "Type", "Treatment", "conc", "uptake")
Description <- c("an ordered factor with levels Qn1 < Qn2 <...< Mc1 giving a unique identifier for each plant",
                 "a factor with levels Quebec Mississippi giving the origin of the plant",
                 "a factor with levels nonchilled chilled",
                 "a numeric vector of ambient carbon dioxide concentrations (mL/L)",
                 "a numeric vector of carbon dioxide uptake rates (umol/m^2 sec)")
metadata <- data.frame(Variable, Description)
kable(metadata)
Variable Description
Plant an ordered factor with levels Qn1 < Qn2 <…< Mc1 giving a unique identifier for each plant
Type a factor with levels Quebec Mississippi giving the origin of the plant
Treatment a factor with levels nonchilled chilled
conc a numeric vector of ambient carbon dioxide concentrations (mL/L)
uptake a numeric vector of carbon dioxide uptake rates (umol/m^2 sec) 
metadata2 <- read.csv("metadata.csv")
Description <- c("an ordered factor with levels Qn1 < Qn2 <...< Mc1 giving a unique identifier for each plant",
                 "a factor with levels Quebec Mississippi giving the origin of the plant",
                 "a factor with levels nonchilled chilled",
                 "a numeric vector of ambient carbon dioxide concentrations (mL/L)",
                 "a numeric vector of carbon dioxide uptake rates (umol/m^2 sec)")

Fig. 1 Echinochloa crus-galli, common name barnyardgrass. Source: Wikimedia commons. \(v = V_{max}\frac{[CO_{2}]}{[CO_{2}]_{k}+[CO_{2}]}\)

Hypothesis

Even if there is any amount of CO2 available, there is a max uptake of CO2 and a saturation level where no more CO2 can be absorbed.

Results

# Create dataframe of chilled plants from Mississippi
MS_chilled <- CO2[CO2$Type == "Mississippi" & CO2$Treatment == "chilled",]

# Plot relationship for replicate plants
qplot(x = conc,
      y = uptake,
      data = MS_chilled,
      facets = ~Plant,
      geom = "line",
      xlab = "CO2 Concentration (ppm)",
      ylab = "CO2 Uptake Rate (umol/m^2/s)")
## Warning: `qplot()` was deprecated in ggplot2 3.4.0.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

Relationship between ambient CO2 and CO2 uptake for plants collected from Mississippi and chilled prior to measurement

# Create dataframe of chilled plants from Mississippi
QN_chilled <- CO2[CO2$Type == "Quebec" & CO2$Treatment == "chilled",]

# Plot relationship for replicate plants
qplot(x = conc,
      y = uptake,
      data = QN_chilled,
      facets = ~Plant,
      geom = "line",
      xlab = "CO2 Concentration (ppm)",
      ylab = "CO2 Uptake Rate (umol/m^2/s)")

Relationship between ambient CO2 and CO2 uptake for plants collected from Quebec and chilled prior to measurement