deletions | additions
diff --git a/introduction.md b/introduction.md
index 16edfc6..6718e42 100644
--- a/introduction.md
+++ b/introduction.md
...
# Workflow for the Biofuel Ecophysiological Traits and Yields Database (BETYdb)
This is the userguide for entering data into the BETYdb database. The goal of this guide is to provide a consistent method of data entry that is transparent, reproducible, and well documented. The steps here generally accomplish one of two goals. The first goal is to provide data that is associated with the experimental methods, species, site, and other factors associated with the original study. The second goal is to provide a record of all the transformations, assumptions, and data extraction steps used to migrate data from the primary literature to the standardized framework of the database.
You will need to create the following accounts:
...
In the appendix table, George 2003 reports the range of root respiration
rates, converted to $15°C$ and standard units:
$$[11.26, $[11.26, 22.52] \frac{\mathrm{nmol CO}_2}{\mathrm{g}\
\mathrm{s}}$$ \mathrm{s}}$
In the original publication Allen (1969), root respiration was measured
at $27°C$. The values can be found in [Table 3] (#Table 3) and [Figure 2] (#Figure 2). The
...
(Group 3 Newbery, South Carolina), which I assume are the ones used by
George 2003:
$$[27.2, $[27.2, 56.2] \frac{\mu\mathrm{L}\ \mathrm{O}_2}{10\mathrm{mg}\
\mathrm{h}}$$ \mathrm{h}}$
Transformed George 2003 measurements back to the measurement temperature
...
Q$_{10} = 2.075$ from George 2003, and the measurement temperature of
$27°C$ reported by Allen 1969:
$$R_T $R_T = R_{15}[\exp(\ln(Q_{10})(T-
15))/10]$$ 15))/10]$
$$[11.26, $[11.26, 22.52] * exp(log(2.075)*(27 -
15)/10)$$ 15)/10)$
Now we have the values that we would have expected to find in the Allen
paper, except that the units need to be converted back to the original:
$$[27.03,54.07] $[27.03,54.07] \mathrm{nmol CO}_2\
\mathrm{g}^{-1}\mathrm{s}^{-1}$$ \mathrm{g}^{-1}\mathrm{s}^{-1}$
#### Required constants
...
unit of measurement for simplicity
Now convert
$$[27.03,54.07] $[27.03,54.07] \mathrm{nmol CO}_2\
\mathrm{g}^{-1}\mathrm{s}^{-1}$$ \mathrm{g}^{-1}\mathrm{s}^{-1}$ to
units of
$\frac{\mu\mathrm{L}\ \textrm{O}_2}{10\mathrm{mg}\ \mathrm{root}\ \mathrm{h}}$.
The expected result is the original values reported by Allen:
$[27.2, 56.2] \frac{\mu\mathrm{L}\ \mathrm{O}_2}{10\mathrm{mg}\ \mathrm{h}}$
$$[27.03, $[27.03, 54.07]\ \frac{\mathrm{nmol}\ \mathrm{CO}_2}{\mathrm{g}\ \mathrm{root}\ \mathrm{s}} \times \frac{1\ \mathrm{g}}{100\times10\mathrm{mg}} \times \frac{3600\ \mathrm{s}}{\mathrm{h}} \times \frac{\mathrm{nmol}\ \mathrm{O}_2}{\mathrm{nmol}\ \mathrm{CO}_2}\frac{3.2 \times 10^{-8}\ \mathrm{g}\ \mathrm{O}_2}{\mathrm{nmol}\ \mathrm{O}_2}\times \frac{7.69\times10^5\ \mu\mathrm{L}\ \mathrm{O}_2}{\mathrm{g}\
\mathrm{O}_2}$$ \mathrm{O}_2}$
The result is:
$$[23.8, $[23.8, 47.8] \frac{\mu\mathrm{L}\ \textrm{O}_2}{10\mathrm{mg}\ \mathrm{root}\
\mathrm{h}}$$ \mathrm{h}}$
These are the units reported in the Allen paper, but they appear to be
off by the temperature conversion factor,
...
:
$$\textrm{k}\times\frac{\mu\mathrm{L}\ $\textrm{k}\times\frac{\mu\mathrm{L}\ \textrm{O}_2}{10\mathrm{mg}\ \mathrm{root}\ \mathrm{h}} = \frac{\mu\mathrm{mol}\ \mathrm{CO}_2}{\mathrm{kg}\
\mathrm{s}}$$ \mathrm{s}}$
$$k $k = \frac{\mathrm{g}\ \mathrm{O}_2}{7.69\times10^5\ \mu\mathrm{L}\ \mathrm{O}_2}\times\frac{\mu\mathrm{mol}\ \mathrm{O}_2}{3.2 \times 10^{-5}\ \mathrm{g}\ \mathrm{O}_2} \times \frac{10^5\ \times 10\mathrm{mg}}{\mathrm{kg}} \times \frac{\mathrm{h}}{3600\
\mathrm{s}}=$$
$$= 1.13$$ \mathrm{s}}=$
$= 1.13$
#### Calculating $MSE$ given $F$, $df_{\text{group}}$, and $SS$
Given:
$$\label{eq:f} $\label{eq:f}
F =
MS_g/MS_e$$ MS_g/MS_e$
Where $g$ indicates the group, or treatment. Rearranging this equation
gives:
$$MS_e=MS_g/F$$ $MS_e=MS_g/F$
Given
$$MS_x $MS_x =
SS_x/df_x$$ SS_x/df_x$
Substitute $MS_e/df_e$ for $SS_e$ in the first equation
$$F=\frac{SS_g/df_g}{MS_e}$$ $F=\frac{SS_g/df_g}{MS_e}$
Then solve for $MS_e$
$$\label{eq:mse} $\label{eq:mse}
MS_e = \frac{SS_g}{df_g\times
F}$$ F}$
$$\label{eq:dft}
df_{\text{total}}=(df_a+1)\times(df_b+1)...\times(n)-1$$ $\label{eq:dft}
df_{\text{total}}=(df_a+1)\times(df_b+1)...\times(n)-1$
Which depends on the experimental design:
...
Calculate $MS_e$:
$$MS_e $MS_e = \frac{109.58}{0.57 \times 2} =
96.12$$ 96.12$
## Reference Tables
...
| vcmax | irradiance and temperature (leaf or air) | |
|any leaf measurement | | canopy height |
| root\_respiration\_rate | temperature (root or soil, | soil moisture |
| | root\_diameter\_max | root size class (usually
$<2mm$) replace_contentlt;2mm$) |
| any respiration | temperature | |
| root biomass | | min. size cutoff, max. size cutoff |
| root, soil | depth (cm) | used for max and min depths of soil, if only one value, assume min depth = 0; negative values indicate above ground |
...
| From ($X$) | to ($Y$) | Conversion | Notes |
|:-----------|:---------|:-----------|:------|
| $X_2=$root production | $X_1=$root biomass & root turnover rate | $Y =
X_2/X_1$& X_2/X_1replace_contentamp; | Gill [2000] |
| DD$^{\circ}$ MM'SS | XX.ZZZZ | $\textrm{XX.ZZZZ} = \textrm{XX} + \textrm{MM}/60+\textrm{SS}/60$ | to convert latitude or longitude from degrees, minutes, seconds to decimal degrees |
| lb | kg | $Y=X\times 2.2$ | |
| mm/s | $\mu$ mol CO$_2$ m$^{2}$ s$^{-1}$ | $Y=X\times 0.04$ | |
