deletions | additions       diff --git a/introduction.md b/introduction.md  index 89a6188..85bb008 100644  --- a/introduction.md  +++ b/introduction.md 
...
relevant for domesticated species. Fields with an asterisk (*) are  required.     **Table 1: List of current projects, PI's, Managers, and Technicians**  | Current Projects | List of Current Projects | PI's | Managers | Technicians | Status |  |:-----------------|:-------------------------|:----------|:------------|:--------------|:---------|  | Folders | Project | | | | |  | Arctic | Arctic | M. Dietze | C. Davidson | M. Azimi | active |  | Prairie | Prairie | M. Dietze | X. Feng | * | active |  | Poplar, Willow, Woody | Hardwood | M. Dietze | D. Wang | *N. Brady | active |  | Sugarcane | Sugarcane | F. Miguez | D. Jaiswal | F. Hussain | active |  | Syntheses | Synthesis Papers | M. Dietze | D. LeBauer | *D. Bettinardi | complete |  | Face | FACE/NCEAS | M. Dietze | D. LeBauer | * Andy Tu | complete |  | Switchgrass | Switchgrass | M. Dietze | D. LeBauer | | inactive |  ### Adding a Citation  Citation provides information regarding the source of the data. This  section should allow us to locate and access the paper of interest. 
...
when only Trait data is collected.  **When not to use treatment**: predictor variables that are not based on distinct managements, or that are distinguished by information already contained in the trait (e.g. site, cultivar, date fields) should not be given distinct treatments. For example, a study that compares two different species, cultivars or genotypes can be assigned the same control treatment; these categories will be distinguished by the species or cultivar field. Another example is when the observation is made at two sites: the site field will include this information.   - *  A treatment name is used as a categorical (rather than continuous) variable: it should be easy to find the treatment in the paper based on  the name in the database. The treatment name does not have to indicate  the level of treatment used in a particular treatment - this information  will be included in the management table.  - *  It is essential that a control group is identified with each study. If there is no experimental manipulation, then there is only one treatment. In  this case, the treatment should be named 'observational' and listed as  control. To determine the control when it is not explicitly stated, first 
...
  ### Adding a Management   Managements refers to something that occurs at a specific time and has a  quantity. Managements include actions that are done to a plant or  ecosystem, such as the planting density or rate of fertilization, for example. 
...
order to standardize across studies.  When root data is recorded, the root size class needs to be entered as a  covariate. The term ’fine root’ often refers to the \<2mm \(<\)2mm  size class, and in this case, the covariate `root_maximum_diameter` would be set to 2. If the size class is a range, then the `root_minimum_diameter` can also be used. To add a new covariate, go to the [new covariate](http:www.betydb.org/covariates/new) page ### Adding a PFT, Species, and Cultivar 
...
google spreadsheet following instructions)  - For any trait data that requires a covariate  ## Converting Units and Adjustment to Temperature  Convert from root respiration data reported in George et al (where O\(_2\)  was measured in µL to units of mass  In the appendix table, George 2003 reports the range of root respiration  rates, converted to \(15°C\) and standard units:  \([11.26, 22.52] \frac{\mathrm{nmol CO}_2}{\mathrm{g}\ \mathrm{s}}\)  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  data include a minimum (Group 2 Brunswick, NJ plants) and a maximum  (Group 3 Newbery, South Carolina), which I assume are the ones used by  George 2003:  \([27.2, 56.2] \frac{\mu\mathrm{L}\ \mathrm{O}_2}{10\mathrm{mg}\ \mathrm{h}}\)  Transformed George 2003 measurements back to the measurement temperature  using a rearrangement of equation 1 from George, the standardized  temperature of \(15°C\) stated in the Georgeh table legend, and  Q\(_{10} = 2.075\) from George 2003, and the measurement temperature of  \(27°C\) reported by Allen 1969:  \(R_T = R_{15}[\exp(\ln(Q_{10})(T- 15))/10]\)  \([11.26, 22.52] * exp(log(2.075)*(27 - 15)/10)\)  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:  \([27.03,54.07] \mathrm{nmol CO}_2\ \mathrm{g}^{-1}\mathrm{s}^{-1}\)  #### Required constants  - \(1\ \mathrm{mol}\ \mathrm{O}_2 = 1\ \mathrm{mol}\ \mathrm{CO}_2\)  since respiration is  \(\mathrm{CH}_2\mathrm{O} + \mathrm{O}_2 \to \mathrm{CO}_2 + \mathrm{H}_2\mathrm{O}\)  - Density of \(\mathrm{O}_2\) at \(27^\circ C\):  \(\frac{7.69 \times 10^5\ \mathrm{ml}\ \mathrm{O}_2}{\mathrm{g}\ \mathrm{O}_2}\)  first assume that Allen converted to sea level pressure (101 kPa),  although maybe they were measured at elevation (Allen may have  worked at \~ 900 kPa near Brevard, NC)  - Molar mass of \(\mathrm{O}_2\):  \(\frac{32\mathrm{g}\ \mathrm{O}_2}{\mathrm{mol}}\)  - Treat 10mg, which is in the unit of root mass used by Allen, as a  unit of measurement for simplicity  Now convert  \([27.03,54.07] \mathrm{nmol CO}_2\ \mathrm{g}^{-1}\mathrm{s}^{-1}\) 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:  \([27.2, 56.2] \frac{\mu\mathrm{L}\ \mathrm{O}_2}{10\mathrm{mg}\ \mathrm{h}}\)  \([27.03, 54.07]\ \frac{\mathrm{nmol}\ \mathrm{CO}_2}{\mathrm{g}\ \mathrm{root}\ \mathrm{s}} \times \frac{1\ \mathrm{g}}{100\times10\mathrm{mg}} \times \frac{3600\ \mathrm{s}}{\mathrm{h}} \times \frac{\mathrm{nmol}\ \mathrm{O}_2}{\mathrm{nmol}\ \mathrm{CO}_2}\frac{3.2 \times 10^{-8}\ \mathrm{g}\ \mathrm{O}_2}{\mathrm{nmol}\ \mathrm{O}_2}\times \frac{7.69\times10^5\ \mu\mathrm{L}\ \mathrm{O}_2}{\mathrm{g}\ \mathrm{O}_2}\)  The result is:  \([23.8, 47.8] \frac{\mu\mathrm{L}\ \textrm{O}_2}{10\mathrm{mg}\ \mathrm{root}\ \mathrm{h}}\)  These are the units reported in the Allen paper, but they appear to be  off by the temperature conversion factor,  \(exp(log(2.075)*(27 - 15)/10)=2.4\), e.g.  \([11.9, 23.9]\times 2.4= [28.6,57.4]\), values which are only 5 and 2  percent larger than the original values of \([27.2, 56.2]\), respectively  to be acceptable, but not exact. Since the ratio of observed:expected  values are different, it is not likely that Q\(_{10}\) or the atmospheric  pressure at time of measurement would explain this error.  #### Convert to units in BETYdb, find \(\textrm{k}\)  :  \(\textrm{k}\times\frac{\mu\mathrm{L}\ \textrm{O}_2}{10\mathrm{mg}\ \mathrm{root}\ \mathrm{h}} = \frac{\mu\mathrm{mol}\ \mathrm{CO}_2}{\mathrm{kg}\ \mathrm{s}}\)  \(k = \frac{\mathrm{g}\ \mathrm{O}_2}{7.69\times10^5\ \mu\mathrm{L}\ \mathrm{O}_2}\times\frac{\mu\mathrm{mol}\ \mathrm{O}_2}{3.2 \times 10^{-5}\ \mathrm{g}\ \mathrm{O}_2} \times \frac{10^5\ \times 10\mathrm{mg}}{\mathrm{kg}} \times \frac{\mathrm{h}}{3600\ \mathrm{s}}=\)  \(= 1.13\)  #### Calculating \(MSE\) given \(F\), \(df_{\text{group}}\), and \(SS\)  Given:  \(\label{eq:f}  F = MS_g/MS_e\)  Where \(g\) indicates the group, or treatment. Rearranging this equation  gives: \(MS_e=MS_g/F\)  Given  \(MS_x = SS_x/df_x\)  Substitute \(MS_e/df_e\) for \(SS_e\) in the first equation  \(F=\frac{SS_g/df_g}{MS_e}\)  Then solve for \(MS_e\)  \(\label{eq:mse}  MS_e = \frac{SS_g}{df_g\times F}\)  \(\label{eq:dft}  df_{\text{total}}=(df_a+1)\times(df_b+1)...\times(n)-1\)  Which depends on the experimental design:  For factors a, b... (usually 1 or 2, sometimes 3) where \(n\) is the  number of replicates within each treatment combination.  - One-way anova \(df_{\text{total}}=an-1\); where \(a\) is the number of  treatments  - Two-way anova without replication \(df_{\text{total}}=(a+1)(b+1)-1\)  also known as ’’randomized complete block design’’ (RCBD)  - Two-way anova with \(n\) replicates  \(df_{\text{total}}=(a+1)(b+1)(n)-1\) aka ’’RCBD with replication’’  #### Example  An example application of this is in Starr et al. [2008] table 3 [Figure 11] (Figure 11).  The results are from one (two?) factor ANOVA with repeated measures,  with treatment and week as the factors and no replication.  We will calculate MSE from the \(SS_{\text{treatment}}\)  \(df_{\text{treatment}}\), and \(F\)-value given in the table; these are  \(109.58\), \(2\), and \(0.570\), respectively; \(df_{\text{weeks}}\) is given  as \(10\).  For the 1997 *Eriphorium vaginatum*, the mean \(A_{max}\) in table 4 is  \(13.49\).  Calculate \(MS_e\):  \(MS_e = \frac{109.58}{0.57 \times 2} = 96.12\)