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Merge pull request #2 from gjmmarquesDEB/next-version-pet-templates
new version of pet templates
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| %% mydata_my_pet | ||
| % Sets referenced data | ||
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| %% | ||
| function [data, txt_data, metadata] = mydata_my_pet | ||
| % created by Starrlight Augustine, Bas Kooijman, Dina Lika, Goncalo Marques and Laure Pecquerie 2015/03/31 | ||
| % last modified: 07/07/2015 by starrlight | ||
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| %% Syntax | ||
| % [data, txt_data, metadata] = <../mydata_my_pet.m *mydata_my_pet*> | ||
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| %% Description | ||
| % Sets data, pseudodata, metadata, explanatory text, weight coefficients. | ||
| % Meant to be a template in add-my-pet | ||
| % | ||
| % Output | ||
| % | ||
| % * data: structure with data | ||
| % * txt_data: text vector for the presentation of results | ||
| % * metadata: structure with info about this entry | ||
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| %% To do (remove these remarks after editing this file) | ||
| % * copy this template; replace 'my_pet' by the name of your species | ||
| % * fill in metadata fields with the proper information | ||
| % * insert references for the data (an example is given), for multiple references, please use commas to separate references | ||
| % * edit fact-list for your species, where you can add species and/or data properties | ||
| % * edit real data; remove all data that to not belong to your pet | ||
| % * complete reference list | ||
| % * OPTIONAL : add discussion points / comments before the reference list | ||
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| %% set metadata | ||
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| T_C = 273.15; % K, temperature at 0 degrees C (used in T_typical) | ||
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| metadata.phylum = 'phylum'; | ||
| metadata.class = 'class'; | ||
| metadata.order = 'order'; | ||
| metadata.family = 'family'; | ||
| metadata.species = 'my_pet'; | ||
| metadata.species_en = 'my_pet_english_name'; | ||
| metadata.T_typical = T_C + 20; % K | ||
| metadata.data_0 = {'ab'; 'ap'; 'am'; 'Lb'; 'Lp'; 'Li'; 'Wdb'; 'Wdp'; 'Wdi'; 'Ri'}; % tags for different types of zero-variate data | ||
| metadata.data_1 = {'t-L'; 'L-W'}; % tags for different types of uni-variate data | ||
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| metadata.COMPLETE = 2.5; % using criteria of LikaKear2011 | ||
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| metadata.author = {'FirstName1 LastName1'}; % put names as authors as separate strings: {'FirstName1 LastName2','FirstName2 LastName2'} , with corresponding author in first place | ||
| metadata.date_subm = [2015 04 20]; % [year month day], date at which the entry is submitted | ||
| metadata.email = {'myname@myuniv.univ'}; % e-mail of corresponding author | ||
| metadata.address = {'affiliation, zipcode, country'}; % affiliation, postcode, country of the corresponding author | ||
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| % uncomment and fill in the following fields when the entry is updated: | ||
| % metadata.author_mod_1 = {'FirstName3 LastName3'}; % put names as authors as separate strings: {'author1','author2'} , with corresponding author in first place | ||
| % metadata.date_mod_1 = [2017 09 18]; % [year month day], date modified entry is accepted into the collection | ||
| % metadata.email_mod_1 = {'myname@myuniv.univ'}; % e-mail of corresponding author | ||
| % metadata.address_mod_1 = {'affiliation, zipcode, country'}; % affiliation, postcode, country of the corresponding author | ||
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| % for curators only ------------------------------ | ||
| % metadata.curator = {'FirstName LastName'}; | ||
| % metadata.email_cur = {'myname@myuniv.univ'}; | ||
| % metadata.date_acc = [2015 04 22]; | ||
| %------------------------------------------------- | ||
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| %% set data | ||
| % zero-variate data; | ||
| % typically depend on scaled functional response f. | ||
| % here assumed to be equal for all real data; the value of f is specified in pars_init_my_pet. | ||
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| % age 0 is at onset of embryo development | ||
| data.ab = 15; units.ab = 'd'; label.ab = 'age at birth'; bibkey.ab = 'MollCano2010'; comment.ab = 'mean value taken from several measurements'; | ||
| temp.ab = T_C + 20; % K, temperature | ||
| % observed age at birth is frequently larger than ab, because of diapauzes during incubation | ||
| data.ap = 261; units.ap = 'd'; label.ap = 'age at puberty'; bibkey.ap = 'Anon2015'; | ||
| temp.ap = T_C + 20; % K, temperature | ||
| % observed age at puberty is frequently larger than ap, | ||
| % because allocation to reproduction starts before first eggs appear | ||
| data.am = 591; units.am = 'd'; label.am = 'life span'; bibkey.am = 'Wiki'; | ||
| temp.am = T_C + 20; % K, temperature | ||
| % (accounting for aging only) | ||
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| % Please specify what type of length measurement is used for your species. | ||
| % We put here snout-to-vent length, but you should change this depending on your species: | ||
| % add an optional comment structure to give any additional explanations on | ||
| % how the value was chosen, see the last column of the Lb data set for an | ||
| % example | ||
| data.Lb = 0.45; units.Lb = 'cm'; label.Lb = 'snout to vent length at birth'; bibkey.Lb = 'Anon2015'; | ||
| data.Lp = 2.36; units.Lp = 'cm'; label.Lp = 'snout to vent length at puberty'; bibkey.Lp = {'Anon2015','Wiki'}; % for multiple references, please use commas to separate references | ||
| data.Li = 6.25; units.Li = 'cm'; label.Li = 'ultimate snout to vent length'; bibkey.Li = 'Wiki'; | ||
| data.Wdb = 5.8e-5; units.Wdb = 'g'; label.Wdb = 'dry weight at birth'; bibkey.Wdb = 'Anon2015'; | ||
| data.Wdp = 8e-3; units.Wdp = 'g'; label.Wdp = 'dry weight at puberty'; bibkey.Wdp = 'Anon2015'; | ||
| data.Wdi = 0.15; units.Wdi = 'g'; label.Wdi = 'ultimate dry weight'; bibkey.Wdi = 'Wiki'; | ||
| data.Ri = 2.3; units.Ri = '#/d'; label.Ri = 'maximum reprod rate'; bibkey.Ri = 'Wiki'; | ||
| % for an individual of ultimate length Li | ||
| temp.Ri = T_C + 20; % K, temperature | ||
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| % uni-variate data | ||
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| % uni-variate data at f = 0.8 (this value should be added in pars_init_my_pet as a parameter f_tL) | ||
| % snout-to-vent length and wet weight were measured at the same time | ||
| data.tL = [0 50 100 200 300 400 500 600; % d, time since birth | ||
| 0.45 1.1 1.7 2.7 3.4 4.0 4.5 4.9]'; % cm, snout-to-vent length at f and T | ||
| units.tL = {'d', 'cm'}; label.tL = {'time since birth', 'snout to vent length'}; bibkey.tL = 'Anon2015'; | ||
| temp.tL = T_C + 25; % K, temperature | ||
| comment.tL = 'Put here any remarks about the experimental protocol'; % optional field | ||
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| data.LW = [0.9 1.8 3.2 4.3 5.0; % cm, snout-to-vent length at f | ||
| 0.004 0.03 0.20 0.55 1.1]'; % g, wet weight at f and T | ||
| units.LW = {'cm', 'g'}; label.LW = {'snout to vent length', 'wet weight'}; bibkey.LW = 'Anon2015'; | ||
| comment.LW = 'Put here any remarks about the experimental protocol'; % optional field | ||
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| %% set weights for all real data | ||
| weight = setweights(data, []); | ||
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| %% overwriting weights (remove these remarks after editing the file) | ||
| % the weights were set automatically with the function setweigths, | ||
| % if one wants to ovewrite one of the weights it should always present an explanation example: | ||
| % | ||
| % zero-variate data: | ||
| % weight.Wdi = 100 * weight.Wdi; % Much more confidence in the ultimate dry | ||
| % % weight than the other data points | ||
| % uni-variate data: | ||
| % weight.tL = 2 * weight.tL; | ||
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| %% set pseudodata and respective weights | ||
| % (pseudo data are in data.psd and weights are in weight.psd) | ||
| [data, units, label, weight] = addpseudodata(data, units, label, weight); | ||
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| %% overwriting pseudodata and respective weights (remove these remarks after editing the file) | ||
| % the pseudodata and respective weights were set automatically with the function setpseudodata | ||
| % if one wants to overwrite one of the values it should always present an explanation | ||
| % example: | ||
| % data.psd.p_M = 1000; % my_pet belongs to a group with high somatic maint | ||
| % weight.psd.kap = 10 * weight.psd.kap; % I need to give this pseudo data a higher weight | ||
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| %% Facts | ||
| % list facts: F1, F2, etc. | ||
| % make sure each fact has a corresponding bib key | ||
| % do not put any DEB modelling assumptions here, only relevant information on | ||
| % biology and life-cycles etc. | ||
| F1 = 'The larval stage last 202 days and no feeding occurs'; | ||
| metadata.bibkey.F1 = 'Wiki'; % optional bibkey | ||
| metadata.facts = struct('F1',F1); | ||
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| %% Discussion points | ||
| D1 = 'Author_mod_1: I found information on the number of eggs per female as a function of length in Anon2013 that was much higher than in Anon2015 but chose to not include it as the temperature was not provided'; | ||
| % optional bibkey: bibkey.D1 = 'Anon2013'; | ||
| D2 = 'Author_mod_1: I was surprised to observe that the weight coefficient for ab changed so much the parameter values'; | ||
| % optional bibkey: bibkey.D2 = 'Kooy2010'; | ||
| metadata.discussion = struct('D1', D1, 'D2', D2); | ||
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| %% pack data and txt_data for output | ||
| data.weight = weight; | ||
| data.temp = temp; | ||
| txt_data.units = units; | ||
| txt_data.label = label; | ||
| txt_data.bibkey = bibkey; | ||
| if exist('comment','var') | ||
| txt_data.comment = comment; | ||
| end | ||
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| %% References | ||
| % the following two references should be kept----------------------------------------------------------- | ||
| bibkey = 'Kooy2010'; type = 'Book'; bib = [ ... % used in setting of chemical parameters and pseudodata | ||
| 'author = {Kooijman, S.A.L.M.}, ' ... | ||
| 'year = {2010}, ' ... | ||
| 'title = {Dynamic Energy Budget theory for metabolic organisation}, ' ... | ||
| 'publisher = {Cambridge Univ. Press, Cambridge}, ' ... | ||
| 'pages = {Table 4.2 (page 150), 8.1 (page 300)}, ' ... | ||
| 'howpublished = {\url{http://www.bio.vu.nl/thb/research/bib/Kooy2010.html}}']; | ||
| eval(['metadata.biblist.' bibkey, '= ''@', type, '{', bibkey, ', ' bib, '}'';']); | ||
| % | ||
| bibkey = 'LikaKear2011'; type = 'Article'; bib = [ ... % used for the estimation method | ||
| 'author = {Lika, K. and Kearney, M.R. and Freitas, V. and van der Veer, H.W. and van der Meer, J. and Wijsman, J.W.M. and Pecquerie, L. and Kooijman, S.A.L.M.},'... | ||
| 'year = {2011},'... | ||
| 'title = {The ''''covariation method'''' for estimating the parameters of the standard Dynamic Energy Budget model \textrm{I}: Philosophy and approach},'... | ||
| 'journal = {Journal of Sea Research},'... | ||
| 'volume = {66},'... | ||
| 'number = {4},'... | ||
| 'pages = {270-277},'... | ||
| 'DOI = {10.1016/j.seares.2011.07.010},'... | ||
| 'howpublished = {\url{http://www.sciencedirect.com/science/article/pii/S1385110111001055}}']; | ||
| eval(['metadata.biblist.' bibkey, '= ''@', type, '{', bibkey, ', ' bib, '}'';']); | ||
| %------------------------------------------------------------------------------------------------------ | ||
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| % References for the data, following BibTex rules | ||
| % author names : author = {Last Name, F. and Last Name2, F2. and Last Name 3, F3. and Last Name 4, F4.} | ||
| % latin names in title e.g. \emph{Pleurobrachia pileus} | ||
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| bibkey = 'Wiki'; type = 'Misc'; bib = [... | ||
| 'howpublished = {\url{http://en.wikipedia.org/wiki/my_pet}},'...% replace my_pet by latin species name | ||
| 'note = {Accessed : 2015-04-30}']; | ||
| eval(['metadata.biblist.' bibkey, '= ''@', type, '{', bibkey, ', ' bib, '}'';']); | ||
| % | ||
| bibkey = 'MollCano2010'; type = 'Article'; bib = [ ... % meant as example; replace this and further bib entries | ||
| 'author = {M{\o}ller, L. F. and Canon, J. M. and Tiselius, P.}, ' ... | ||
| 'year = {2010}, ' ... | ||
| 'title = {Bioenergetics and growth in the ctenophore \emph{Pleurobrachia pileus}}, ' ... | ||
| 'journal = {Hydrobiologia}, ' ... | ||
| 'volume = {645}, ' ... | ||
| 'number = {4}, '... | ||
| 'pages = {167-178}']; | ||
| eval(['metadata.biblist.' bibkey, '= ''@', type, '{', bibkey, ', ' bib, '}'';']); | ||
| % | ||
| bibkey = 'Anon2015'; type = 'Misc'; bib = [ ... | ||
| 'author = {Anonymous}, ' ... | ||
| 'year = {2015}, ' ... | ||
| 'howpublished = {\url{http://www.fishbase.org/summary/Rhincodon-typus.html}}']; | ||
| eval(['metadata.biblist.' bibkey, '= ''@', type, '{', bibkey, ', ' bib, '}'';']); | ||
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