CO2: Carbon Dioxide uptake in grass plants

In MEMSS: Data sets from Mixed-effects Models in S

Description

The CO2 data frame has 84 rows and 5 columns of data from an experiment on the cold tolerance of the grass species Echinochloa crus-galli.

Usage

CO2

Format

This data frame contains the following columns:

Plant

an factor 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).

Details

The CO2 uptake of six plants from Quebec and six plants from Mississippi was measured at several levels of ambient CO2 concentration. Half the plants of each type were chilled overnight before the experiment was conducted.

Source

Potvin, C., Lechowicz, M. J. and Tardif, S. (1990) “The statistical analysis of ecophysiological response curves obtained from experiments involving repeated measures”, Ecology, 71, 1389–1400.

Pinheiro, J. C. and Bates, D. M. (2000) Mixed-effects Models in S and S-PLUS, Springer.

Examples

require(stats); require(graphics)
coplot(uptake ~ conc | Plant, data = CO2, show.given = FALSE, type = "b")
## fit the data for the first plant
fm1 <- nls(uptake ~ SSasymp(conc, Asym, lrc, c0),
   data = CO2, subset = Plant == 'Qn1')
summary(fm1)
## fit each plant separately
fmlist <- list()
for (pp in levels(CO2$Plant)) {
  fmlist[[pp]] <- nls(uptake ~ SSasymp(conc, Asym, lrc, c0),
      data = CO2, subset = Plant == pp)
}
## check the coefficients by plant
sapply(fmlist, coef)

Example output

Loading required package: lme4
Loading required package: Matrix

Attaching package: 'MEMSS'

The following objects are masked from 'package:datasets':

    CO2, Orange, Theoph


Formula: uptake ~ SSasymp(conc, Asym, lrc, c0)

Parameters:
     Estimate Std. Error t value Pr(>|t|)    
Asym  38.1398     0.9164  41.620 1.99e-06 ***
lrc  -34.2766    18.9661  -1.807    0.145    
c0    -4.3806     0.2042 -21.457 2.79e-05 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 1.663 on 4 degrees of freedom

Number of iterations to convergence: 0 
Achieved convergence tolerance: 1.663e-06

           Mc1       Mc2         Mc3       Mn1        Mn2        Mn3       Qc1
Asym 21.787232 13.555203   18.535062 34.084807  32.128265  28.482853 36.428732
lrc   2.448758 -1.982271 -136.114734 -8.813218 -29.044263 -17.370807 -9.901194
c0   -5.142256 -4.560851   -3.465158 -5.064579  -4.466157  -4.591566 -4.861741
            Qc2        Qc3        Qn1        Qn2        Qn3
Asym  39.819497  40.683704  38.139782  42.871686  44.227996
lrc  -51.534564 -11.541640 -34.276585 -29.656171 -37.626788
c0    -4.463838  -4.945218  -4.380647  -4.665728  -4.486118

MEMSS documentation built on May 2, 2019, 5:50 p.m.