qjhart / ahb-pnw.hart14model-poplar Goto Github PK

• Highlight number 2, please replace "exsiting" with existing
• Page 2. Please provide a brief overview about the 3PG model, to understand how the growth is modeled and what are the main parameters? How the parameters are adjusted? What are the assumptions and simplifications of the 3PG model?
• Page 2, line 27. There is no validation of the 3PG model for coppiced SRWC against empirical data.
• Page 3 Lines 61-62. What field studies were used to validate the 3PG model? Please cite or report the methods you used to compare the model to actual data. I think this part corresponds to the methods not the introduction.
• Page 3, line 65. I think the climate change scenario is out of the scope of this study. It is more important to validate the model first before making assumption and modeling different scenarios.
• Page 4, line 85. What are the implications in relation to the model results of having such a large pixel size? I understand that having such a large pixel size reduce complexity but it is not clear (or discussed) how accuracy and quality of the results could be affected. Discuss or cite literature that had used a similar approach with good quality results.
• Page 5, figure 1, I would suggest eliminating figure 1, since it adds very little to the description section.
• Page 6 line 105. How sensitive is the model to the monthly step run? Does the result from the model growth would be different if the 3PG model is run at daily or yearly timestep?
• Page 6 line 113. There is no reference provide in cite # 8. Is that an internal report of a review from the authors? Is this report available for reader of the article?
• Page 6 lines 117 to 122: Is there any empirical data to compared root contribution modeled against real?
• Page 7, figure 2. Is there any hierarchy in the graph? Some elements are not connected, so it is not clear how the different inputs are related.
• Page 8, line 125. Explain when conditions are favorable and not favorable. Do favorable (and unfavorable) conditions change across the region?
• Page 8, line 131. Revise cite 8.
• Page 9, line 165-166 . What are the assumptions when ground stations are not available no validate the data?
• Page 10 and 11, how does pixel size of mean annual temperature and annual rainfall raster compares to the pixel size used to do the grid partitions of the region? In other words if a grid pixel contains two different rainfall pixels, what rainfall values is assumed for the grid partition?
• Page 9-12. I would prefer to have a table of the 3PG parameters estimates used in the model to show the value used, the units and the source.
• Page 16, line 244. I would suggest the auhors to concentrate in the model validation before analyzing climte change scenarios.
• Page 16, line 246. Explain in which consist A1B scenario or provide a citation. Is there any particular reason Why this scenario was selected?
• Page 19, line 275. I would be good to explain in the introduction how poplar is managed for liquid fuels production.
• Page 22, lines 355 to 363. Conclusion section needs to be strengthened. Explain what the limitations of the model are. Also how the model is affected by the parameter and how modeled grow compares to actual growth of poplar plots.

@qjhart Need to fix table formatting for table 2. Nots sure whats going on with extension of row \hlines..

Compare the coppicing method for secrets to this one.

However, to my disappointment, I could not see if the model has been validated to empirical data in the Pacific Northwest Region. In modeling it is fundamental to have a validation step in which the model performance is compared against actual empirical data.

there cannot be multiple multiplier prefixes on units so Mha = Mhm2 which is impossible to work out - when areas get beyond a typical farm and your pixels are about 64 km2 - just work in square kilometres.

The introduction does not provide the basic justification necessary. There are no authorities that support factual statements made (i.e. no literature is cited in the introduction). In fact, most information in the introduction includes description of the approach (i.e. methods). The Methods do include citations to foundation 3PG literature, but it is also necessary to include such background in the introduction where the selection of 3PG as a modeling platform should be justified with literature supporting any statements of fact. The justification might explain gaps in original 3PG for short-rotation coppice system, solutions from previous reports that have attempted to implement short rotation coppice culture for poplar or willow (e.g. Deckmyn et al. 2004. B&B. 26:221; Amichev et al. 2011. B&B. 35:473). Justification should also include short-comings of those approaches, and the improvements necessary that you have implemented. Furthermore, there should be
reference to others that have used 3PG to scale to a regional level (e.g. Coops et al. 2011. Appl Veg Sci. 14:268; Headlee et al. 2012. BioEnergy Research. 6:196; Tickle et al 2001. For Ecol Man. 152:275, etc.).and the advantages this model has over other models that have also been used for that purpose (e.g. Waring and Running 2007)

Need to see if there are any table weirdness for B&B submissions. As previous version did not have tables.

The parameter sets used are vague and need to be fully disclosed. Present each of the parameters that have been modified from Headlee et al values. Once tabulated, they can be compared to one another and with other 3PG parameter sets. Justify the use of so many parameter sets, and describe why these have been selected out of the full range of possibilities

@qjhart Something is amiss with the acronym definitions and math mode via $

ERROR: Missing $ inserted.

--- TeX said ---
<inserted text> 
                $
l.411 ... is moderated by the \ac{LAI}. $\ac{NPPt}
                                                  -\ac{NPP}$ serves

See page 7 in .pdf

Finally the references are just bad - I have provided our extended revision instructions so that you can both understand the units issue, and sort out the references.
However, if you feel that you can suitably address the reviewers' comments (included below), I invite you to revise and resubmit your manuscript within 60 days.

• L 20 either 8 million square kilometres or 8 000 000 km2 but never with the double multiplier form that you have on L20.
• L 136 The order of tables and figures listed in the text is important and is supposed to be an ordinal set. L 136 introduces figure 6 before any of the sequence 1 - 5. This will slow down the production of your paper at the copy writing stage. You need to make figure 6 into figure 1, and renumber the remainder,
  Fixed by referring to the appropriate section instead of the figure
• L 141 JBB does not use footnotes, and a url is not a sufficient reference - see the Philson guide (cited below).
• L 220 whatever does "content" mean. It is unscientific to give a fraction expresses as a % without stating what it is e.g. mass fraction of ??? the dry material?
  I changed to 'comprise as 20% of gross weight
• Many spelling mistakes Intergevernmental? Table 4., maximum ran or rain?
  Spell-checked all .tex files
• L 396 differential temperatures in the SI unit system are always in Kelvin e.g. 1 K.
  changed 1 degree c to 274.15 degree K
• L 402 units immediately follow the value so 19.7 Mg ha-1 with no brackets. Also this journal does not use the slash divisor, so please use superscripts.
  changed all slash notation to exponential
• The Journal references need to follow the format as follows:
  All journal citations follow this form - there is no punctuation in the surname initial,
  No punctuation is used in surnames unless it it the last in the list of authors. Vancouver style places a period after the last author
• the journal name is the ISI/ISO abbreviation followed by the year;
  updated all journal references to abbreviated style
• volume(issue):page start - page last with the last page carrying the most significant digits as the minimum needed for precision.
  This seems to be the case for all already
• Note if there are more than 6 authors, retain only the first 6 and theno use et al.
  This seems to be the case for all already
• In the event there is no issue number, the solution is to place the month of issue after the year.
  For journal abbreviations a useful source is: http://journalseek.net , and or http://cassi.cas.org/search.jsp
• Whatever is the unit mo in table 2? Since month is not a fixed quantity - it is not a unit in the SI - write it out in full and do not attach it as though it is an actual unit. E.g. Parameter Monthly root contribution R-delta avoids creating a non unit, just as you did in Table 3.
  Added monthly to root contribution to acronym definition.
• The various internet references needs significant work - please review The Philson library staff excellent guide to the Vancouver system and it addresses how to best describe a web source. The reference below is in the correct format for a monograph on the web.
  Fixed internet references by using the webpage bibtex type from CTAN

Philson Library. Vancouver Style Referencing Guide. [Monograph on the Internet. Auckland (NZ):University of Auckland. [Updated 2014 May 6; cited 2014 May 16] Available from: http://www.library.auckland.ac.nz/subject-guides/med/setref-vancouver.htm

All of the graphics need to have at least 2 lines of latitude and longitude - you can keep the insert, but give the professional readers the datum to read them.

Unfortunately, the authors do not provide sufficient background information to evaluate the 3PG implementation. One reference provided, Hart et al 2014, attempts to describe that implementation. But that is an internal report that has not been refereed by the modeling community (with many errors of presentation). The accuracy of regional predictions reported in the manuscript under
review must be supported with sufficient peer-reviewed validation data to give readers confidence in the outcome.

Reviewer 3 included a PDF file with a number embedded comments. These will be addressed by referencing the line number:

• 51 - Fixed complicated sentence
• 55 - Acknowledge and discuss other approaches to this problem (e.g. Deckmyn et al, Amichev et al.). How do their approaches differ from your's. Which one is preferable and explain why.
• 59 - Upon what is this based? Justify the proportion of root stores using authorities showing this is accurate.
• 61 - Methods These are methods, details of which don't belong in the introduciton. Cite peer-reviewed authorities where validation took place.
• 64 -Again, this does not belong in the introduction. It should be described in the results.
• 66 Results
• 88 Note about citatation
• 90 Binary information
• 97 - Describe these calculations. Even someone with expert knowledge could not understand and duplicate this approach.
• 103 Redundant use of soil parameters in this sentence.
• 109 - Modify this to something like: "... allocates biomass production from photosynthesis..." No production results directly from transpiration. This confusion between transpiration and photosynthesis also appears in the Quinn et al 2014 publication. Of course, transpiration and photosynthesis occur simultaneously when stomata are open, which might suggest transpiration drives production, but it is photosynthesis that directly assimilates the carbon used to produce biomass while water vapor is lost from the leaf through the process of transpiration.
• 113 The reference presented does not meet the reference style. Include institute for which report is written, report number and URL.
• 115 Redundant use in this sentence of this uncommon word. Rephrase to eliminate redundancy. I suggest using common simple synonym such as "excess"
• 115 How much is used, and what is the basis for selecting that specific amount.
• 116 Incomplete thought. Apparently the original model begins to supply new biomass once some level of canopy has developed.
• 117 can't make sense out of this sentence.
• 119 What difference? No previous mention of a difference. I guess the comparison between actual to potential is calculated as a difference?
• 121 It is not apparent when in the coppice regrowth this is describing.
• Figure 2. Parameters (Credit inspiration for this figure, e.g. Landsberg and Sands Fig 9.1, etc.)
• 123 To say that regrowth is timed with climate is not accurate because it implies that time is controlling growth. Actually, climate is controlling growth and both climate and growth are correlated with the time of year. Causation of growth in this case is climate, not time. Very different timing of
• 131 Remove
• 135 This appears to result from the fact that there was a wide range of parameters from Hart et al (2014) trying to fit multiple clonal growth responses. The parameters and their values included in each of the six sets should be presented for the reader to understand how the various parameter sets vary. Furthermore, the presentation should include justification for varying the various parameter sets. This is especially important if some parameter is changed that has typically been set at the default level for other 3PG parameter sets.
• 137 This section is OK
• 151 Sixteen ? I guess
• 154 -Figure 4 shows
• Figure 4 Total Annual Rainfall (precipication vs. rainfall)
• 205 Poplar
• 208 - Bad Reference
• 212 - Figure 10 is yield for irrigated crops not some sort of masked area without high slope and salinity.
• [X ] 257 spatial and Spatial
• 271 Move stuff to methods
• 273 Justify using deferent parameter sets. Implies uncertainty in which parameters to use. Revise sentence to eliminate "was run ... were run" confusion.
• 274 Placing this statement around line 135 would help avoid the ensemble confusion. In fact, all statements in this first paragraph of the Results section belong in Methods section.
• 275 Do you mean an 18 year total lifetime?
• 283 Lines 278-279 describe expressing on "per year basis", i.e. Mg/ha/year, or NPP. But these units suggest that this is cumulative yield over 18 years. The values are too large to be expressed on a per year basis, which suggests lines 278-9 should be modified to something like cumulative annual yield. See table in the AHB overview article showing annual NPP (http://www.extension.org/pages/70456/poplar-populus-spp-trees-for-biofuel-production#.VH9_FWf-mpE)
• 286 Be specific, this is not a term commonly used to describe any region of the PNW.
• 305 Bad Figure reference Fixed

Bibliography Fixes

-[x] 384
-[ ] 387
-[ ] 395

Long note about

• 131 Hart et al (2014) is a non-refereed publication that intends to describe the logic used for implementing and validating the coppice modification to 3PG. Review of that publication leaves numerous questions about the basis for the model implementation and raises concern about the accuracy of predictions due to uncertain model parameterization. Questions include: What physiological process determines target LAI ? A logic gate controlling productive potential flowing from the roots to support shoot growth occurs when target LAI reaches zero. How does target LAI change with coppice development? There is a partitioning factor built into 3PG. Hart et al (2014) say that the factor pR%x "defines the root size with respect to the total plant biomass", which contrasts with Sands 2010 3PG User Manual which describes pRx as the maximum fraction of NPP partitioned to roots. So Hart et al use it to describe a pool and Sands defines it as a flux. How to rectify these contrasting definitions and the use of pR%x in Hart et al's equation (4) where it appears that a flux is subtracted from a pool?

The validation data sets used in Hart et al (2014) use different parameters for the various clones. It is not clear what parameter sets are appropriate for clones used to project production potential regionally. Unfortunately, the parameters used to fit experimentally derived output data, the value ranges of parameters used, and a systematic approach for selecting parameters and their range are not presented.

Given these open questions about the implementation of the model, and uncertain parameterization, the subsequent validation is not solid. To use such a base upon which to project poplar growth regionally is worrisome. In order for regional projections to be on a solid footing, the information in Hart et al 2014 should be published in a refereed journal after passing the review of experts in physiological growth process models.