这项研究由中央大学基础研究基金资助，资助编号为2019GJZL04。我们感谢中国国家林业和草原管理局森林盘点与规划学院的曾伟生教授提供数据。

1. 数据准备
<ol><li>准备建模数据，包括单树信息（1.3米乳房高度的物种和直径）和绘图信息（坡度、侧面和海拔）。在这项研究中，数据取自中国西北新疆省第8次（2009年）和第9次（2014年）中国国家森林清查，其中包括对779个样本地块的21，898次观测。这些样本地块为方形，面积为1亩（面积相当于0.067公顷），系统地排列在4公里×8公里的网格上。 注:建模（基础区域）增量的数据至少需要一个增长期（即两个观测点）。</li>
	<li>随机将数据分成两个数据集，其中 80% 的数据来自用于模型拟合的样本图（模型开发数据集），其中包括来自 623 个样本图的 17，145 个观测结果和 20% 的模型验证（模型验证数据集），其中包括来自 156 个样本图的 4，753 个观测结果。 表 1中提供了关键变量的描述性统计数据。 注:可以省略建模过程的这一步骤，所有数据都用于模型开发。</li>
</ol><table border="1" fo:keep-together.within-page="1"><tbody>
<tr>
<td rowspan="2">变量</td>
			<td colspan="4">拟合数据</td>
			<td></td>
			<td colspan="4">验证数据</td>
		</tr>
<tr>
<td>最小</td>
			<td>麦克斯</td>
			<td>意味 着</td>
			<td>S.D.</td>
			<td></td>
			<td>最小</td>
			<td>麦克斯</td>
			<td>意味 着</td>
			<td>S.D.</td>
		</tr>
<tr>
<td>DBH1 （厘米）</td>
			<td>5</td>
			<td>124.8</td>
			<td>19.9</td>
			<td>13.2</td>
			<td></td>
			<td>5</td>
			<td>101.5</td>
			<td>19.5</td>
			<td>13.4</td>
		</tr>
<tr>
<td>QMD（厘米）</td>
			<td>6.7</td>
			<td>82.3</td>
			<td>22.5</td>
			<td>8.5</td>
			<td></td>
			<td>9.2</td>
			<td>73.3</td>
			<td>21.8</td>
			<td>9.2</td>
		</tr>
<tr>
<td>ID（厘米）</td>
			<td>0.1</td>
			<td>14.4</td>
			<td>1.1</td>
			<td>1</td>
			<td></td>
			<td>0.1</td>
			<td>16.9</td>
			<td>1</td>
			<td>1.1</td>
		</tr>
<tr>
<td>巴尔 （米3）</td>
			<td>0</td>
			<td>5.2</td>
			<td>1.7</td>
			<td>0.9</td>
			<td></td>
			<td>0</td>
			<td>5.4</td>
			<td>1.7</td>
			<td>1</td>
		</tr>
<tr>
<td>NT（树木/公顷）</td>
			<td>14.9</td>
			<td>3642</td>
			<td>1072</td>
			<td>673.7</td>
			<td></td>
			<td>14.9</td>
			<td>3418</td>
			<td>1205</td>
			<td>829.3</td>
		</tr>
<tr>
<td>BA（米2/公顷）</td>
			<td>0.1</td>
			<td>77.5</td>
			<td>34.2</td>
			<td>13.9</td>
			<td></td>
			<td>0.1</td>
			<td>80.6</td>
			<td>34.5</td>
			<td>15.3</td>
		</tr>
<tr>
<td>埃尔 （米）</td>
			<td>2</td>
			<td>3302</td>
			<td>2189</td>
			<td>340.3</td>
			<td></td>
			<td>1441</td>
			<td>3380</td>
			<td>2256</td>
			<td>308.3</td>
		</tr>
</tbody></table>表 1.拟合和验证数据的摘要统计。DBH1: 乳房高度在 1.3 米 （DBH） 的初始直径， DBH2:DBH 在生长 5 年后测量， QMD: 二次平均直径， ID: 直径增量 5 年 （DBH2 - DBH1），BAL: 大于主题树的树木的基底面积 （主题树: 计算竞争指数的树）， NT: 每公顷的树木数量， BA: 每公顷的基底面积， EL: 海拔， S.D.: 标准偏差.
2. 基本模型开发
<ol><li>请查阅引用，以确定影响单树基底区域增量的变量。</li>
	<li>根据数据选择和计算变量。一般来说，单树基底面积增量受三组变量的影响:树的大小、竞争和场地条件27、28、29、30。<ol>
<li>考虑树大小的效果，如 DBH1的方形 <img alt="Equation 11" src="/files/ftp_upload/60827/60827eq11.jpg"> （）、DBH1 （1/DBH 1）的逆向转换，以及 DBH 1 （logDBH1）的常见对数或它们的组合。</li>
		<li>考虑竞争效应，如单边和双面竞争指数，以更全面地量化树木所经历的竞争水平，以及其在展台内的社会地位。片面竞争包括BAL和相对密度指数（RD+DBH 1/QMD）:双面竞争包括NT和英航。 注:如果有数据，应考虑距离依赖竞争指数。</li>
		<li>考虑现场效果，如方面 （ASP）， 斜坡 （SL）， 和 EL. SL 和 ASP 应该包括使用阶段的转换31.</li>
	</ol>
</li>
	<li>选择日志 <img alt="Equation 12" src="/files/ftp_upload/60827/60827eq12.jpg"> <img alt="Equation 11" src="/files/ftp_upload/60827/60827eq11.jpg"> （-+1）（ <img alt="Equation 12" src="/files/ftp_upload/60827/60827eq12.jpg"> 表示DBH2的正方形）作为附属变量。</li>
	<li>使用渐进回归法开发基本模型。确保模型在生物学上合理，并显示独立变量之间的显著差异。利用方差通货膨胀系数 （VIF） 来检查多共性。</li>
	<li>在基本模型中保留 p < 0.05 和 VIF +lt 的独立变量。</li>
	<li>输出基本模型结果和剩余图。这里生产的基本模型是进一步发展混合效应模型的基础。</li>
</ol>3. 与R软件中的包"nlme"一起开发线性混合效应模型
<ol><li>阅读模型开发数据集并加载包"nlme"。 •模型.开发.数据集=读取.csv（"电子数据/JoVE/建模数据.csv" 标题=真实） •库（内姆）</li>
	<li>选择样本图作为随机效果，以开发混合效应模型。</li>
	<li>将所有可能的随机效果组合与最大可能性 （ML） 方法配合并输出结果。 •模型+lt;-lme（Y~1/DBH1=BAL+NT+EL，数据=模型.开发.数据集， 方法="ML"，随机=~1|图） •摘要（模型） 
	<ol>
<li>随机设置=~1是拦截到随机参数。更改随机语句，直到安装所有组合。例如，将 1/DBH1 和 BAL 设置为随机参数，代码如下:随机 +1/DBH1=BAL-1。此外，在拟合过程中，代码可能会报告由于安装模型不融合而出现的错误。</li>
	</ol></li>
	<li>通过 Akaike 的信息标准 （AIC）、贝叶斯信息标准 （BIC）、对数可能性 （Loglik） 和可能性比率测试 （LRT） 选择最佳模型。 •新星（型号.1，型号。6） •新星（型号.6，型号.23） •新星（型号.23，型号.30）</li>
	<li>确定 R i.的结构。解决Ri32的异质性和自动相关性。Ri的编写如下: <img alt="Equation 1" src="/files/ftp_upload/60827/60827eq1.jpg">(1) 其中σ2 是一个未知的缩放因子，等于模型残差方差 ，Gi 是描述异构性的对角矩阵 ，Γi 是描述自相关性的矩阵。<ol>
<li>观察残余物是否具有残余情节的异构性。如果存在异构性（残余物具有清晰的模式或趋势），则引入三个常用的方差函数-常数加功率函数、功率函数和指数函数-以模拟误差方差结构。 >型号.30.1=lme（Y~1/DBH 1=BAL+NT+EL，数据+模型.开发.数据集，方法="ML"，随机=1/DBH1=BAL+NT|情节 重量=瓦尔康斯特电源（形式=*安装） >摘要（模型.30.1） >型号.30.2+lme（Y~1/DBH1=BAL+NT+EL，数据+模型.开发.数据集，方法="ML"，随机=1/DBH1=BAL+NT|情节 重量=功率（形式=*安装） >摘要（模型.30.2） >型号.30.3+lme（Y~1/DBH1=BAL+NT+EL，数据+模型.开发.数据集，方法="ML"，随机=1/DBH1=BAL+NT|情节 重量=变量（形式=*安装） >摘要（型号.30.3）
</li>
		<li>根据 AIC、BIC、洛格利克和轻轨确定模型的最佳方差函数。 >新星（型号.30，型号.30.1） >新星（型号.30，型号.30.2） •新星（型号.30，型号。30.3）
</li>
		<li>引入三种常用的自动对关系结构（复合对称结构 （CS）、一阶自动反向结构 [AR（1）]，以及一阶自动反向结构和移动平均结构 [ARMA（1，1））的组合 -以解释自动反向结构。 •型号.30.3.1=lme（Y~1/DBH1+BAL+NT+EL，数据=模型.开发.数据集，方法="ML"， 随机=~1/DBH1=巴尔+NT|情节，重量=变量（形式=*安装），科雷科姆（ •摘要（型号.30.3.1） •型号.30.3.2=lme（Y~1/DBH1+BAL+NT+EL，数据=模型.开发.数据集，方法="ML"， 随机=~1/DBH1=巴尔+NT|情节，重量=变量（形式=*安装），科雷科拉尔1（ •摘要（型号.30.3.2） •型号.30.3.3=lme（Y~1/DBH1+BAL+NT+EL，数据=模型.开发.数据集，方法="ML"， 随机=~1/DBH1=巴尔+NT|情节，重量=瓦勒普（形式=*安装（），科拉玛（q=1，p=1）） •摘要（型号.30.3.3）
</li>
		<li>根据 AIC、BIC、洛格利克和轻轨确定最佳的自动相关结构。 •新星（型号.30.3，型号。30.3.2） 注:如果没有异质性和自动关联性，则无法定义Gi和Γi。</li>
		<li>使用受限的最大可能性 （REML） 方法输出混合效应模型的最终结果。 •混合.模型（Y~1/DBH1=BAL+NT+EL，数据+模型.开发.数据集，方法="REML"，随机=1/DBH 1=BAL+NT|情节 重量=变量（形式=*安装），科雷科拉尔1（ •摘要（混合模型）
</li>
	</ol></li>
</ol>4. 偏差校正
<ol><li>使用对数刻度上的最终模型将基底区域增量的预测值转换为原始刻度。但是，从日志转换模型中对预测值的这种线性反向转换会产生相关的日志转换偏差。为了处理日志偏差，生成了一个修正因子并集成到预测方程中，该方程估计了给定树的实际预测基数面积增量 [方程 （2）]: <img alt="Equation 2" src="/files/ftp_upload/60827/60827eq2.jpg">(2) <img alt="Equation 13" src="/files/ftp_upload/60827/60827eq13.jpg">从模型中预测基底区域增量的对数值在哪里，而 <img alt="Equation 14" src="/files/ftp_upload/60827/60827eq14.jpg"> 基底区域增量在修正日志转换偏差后5年的预测回转值 <img alt="Equation 15" src="/files/ftp_upload/60827/60827eq15.jpg"> σ。</li>
	<li>将基底区域增量 <img alt="Equation 14" src="/files/ftp_upload/60827/60827eq14.jpg"> （） 转换为直径增量。</li>
</ol>5. 模型预测和评估
<ol><li>准备第 1.2 节中生成的模型验证数据集以供预测。</li>
	<li>使用线性混合效应模型预测单树基底面积增量。随机组件使用以下最佳线性公正预测器计算: <img alt="Equation 3" src="/files/ftp_upload/60827/60827eq3.jpg">(3) <img alt="Equation 16" src="/files/ftp_upload/60827/60827eq16.jpg">随机组件的载体在哪里: <img alt="Equation 17" src="/files/ftp_upload/60827/60827eq17.jpg"> 是图之间变异的方差-共变矩阵: <img alt="Equation 18" src="/files/ftp_upload/60827/60827eq18.jpg"> 是随机组件在补充观测中作用的设计矩阵: <img alt="Equation 19" src="/files/ftp_upload/60827/60827eq19.jpg"> 是残余载体，其成分是由基底区域增量与使用固定效应模型预测增量之间的差异给出的。</li>
	<li>使用以下三个统计指标23、33来评估和比较基础模型和线性混合效应模型的预测能力。 <img alt="Equation 4" src="/files/ftp_upload/60827/60827eq4.jpg">(4) <img alt="Equation 5" src="/files/ftp_upload/60827/60827eq5.jpg">(5) <img alt="Equation 6" src="/files/ftp_upload/60827/60827eq6.jpg">(6) 其中obji是基底区域增量，esti是预测的基底区域增量， <img alt="Equation 20" src="/files/ftp_upload/60827/60827eq20.jpg"> 是观测的平均值，N是观测次数。</li>
</ol>

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E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+Forest+Inventory+and+Analysis+surveys,+basal+area+models,+and+fitting+methods+for+the+aspen+forest+type+in+Minnesota.">Comparison of Forest Inventory and Analysis surveys, basal area models, and fitting methods for the aspen forest type in Minnesota.</a> Forest Ecology &amp; Management. 262 (2), 188-194 (2011).</li><li>Sharma, M., Parton, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Height-diameter+equations+for+boreal+tree+species+in+Ontario+using+a+mixed-effects+modeling+approach.">Height-diameter equations for boreal tree species in Ontario using a mixed-effects modeling approach.</a> Forest Ecology &amp; Management. 249 (3), 187-198 (2007).</li><li>Crecente-Campo, F., Tom&#233;, M., Soares, P., Di&#233;guez-Aranda, U. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+generalized+nonlinear+mixed-effects+height&#8211;diameter+model+for+Eucalyptus+globulus+L.+in+northwestern+Spain.">A generalized nonlinear mixed-effects height&#8211;diameter model for Eucalyptus globulus L. in northwestern Spain.</a> Forest Ecology &amp; Management. 259 (5), 943-952 (2010).</li><li>Fu, L., Sharma, R. P., Hao, K., Tang, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+generalized+interregional+nonlinear+mixed-effects+crown+width+model+for+Prince+Rupprecht+larch+in+northern+China.">A generalized interregional nonlinear mixed-effects crown width model for Prince Rupprecht larch in northern China.</a> Forest Ecology &amp; Management. 389 (2017), 364-373 (2017).</li><li>Hao, X., Yujun, S., Xinjie, W., Jin, W., Yao, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Linear+mixed-effects+models+to+describe+individual+tree+crown+width+for+China-fir+in+Fujian+Province,+southeast+China.">Linear mixed-effects models to describe individual tree crown width for China-fir in Fujian Province, southeast China.</a> Plos One. 10 (4), 0122257 (2015).</li><li>Vanderschaaf, C. L., Burkhart, H. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparing+methods+to+estimate+Reineke's+Maximum+Size-Density+Relationship+species+boundary+line+slope.">Comparing methods to estimate Reineke's Maximum Size-Density Relationship species boundary line slope.</a> Forest Science. 53 (3), 435-442 (2007).</li><li>Zhang, L., Bi, H., Gove, J. H., Heath, L. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+comparison+of+alternative+methods+for+estimating+the+self-thinning+boundary+line.">A comparison of alternative methods for estimating the self-thinning boundary line.</a> Canadian Journal of Forest Research. 35 (6), 1507-1514 (2005).</li><li>Hart, D. R., Chute, A. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Estimating+von+Bertalanffy+growth+parameters+from+growth+increment+data+using+a+linear+mixed-effects+model,+with+an+application+to+the+sea+scallop+Placopecten+magellanicus.">Estimating von Bertalanffy growth parameters from growth increment data using a linear mixed-effects model, with an application to the sea scallop Placopecten magellanicus.</a> Ices Journal of Marine Science. 66 (9), 2165-2175 (2009).</li><li>Uzoh, F. C. C., Oliver, W. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Individual+tree+diameter+increment+model+for+managed+even-aged+stands+of+ponderosa+pine+throughout+the+western+United+States+using+a+multilevel+linear+mixed+effects+model.">Individual tree diameter increment model for managed even-aged stands of ponderosa pine throughout the western United States using a multilevel linear mixed effects model.</a> Forest Ecology &amp; Management. 256 (3), 438-445 (2008).</li><li>Cond&#233;s, S., Sterba, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparing+an+individual+tree+growth+model+for+Pinus+halepensis+Mill.+in+the+Spanish+region+of+Murcia+with+yield+tables+gained+from+the+same+area.">Comparing an individual tree growth model for Pinus halepensis Mill. in the Spanish region of Murcia with yield tables gained from the same area.</a> European Journal of Forest Research. 127 (3), 253-261 (2008).</li><li>Pokharel, B., Dech, J. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mixed-effects+basal+area+increment+models+for+tree+species+in+the+boreal+forest+of+Ontario,+Canada+using+an+ecological+land+classification+approach+to+incorporate+site+effects.">Mixed-effects basal area increment models for tree species in the boreal forest of Ontario, Canada using an ecological land classification approach to incorporate site effects.</a> Forestry. 85 (2), 255-270 (2012).</li><li>Wykoff, W. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+basal+area+increment+model+for+individual+conifers+in+the+northern+Rocky+Mountains.">A basal area increment model for individual conifers in the northern Rocky Mountains.</a> Forest Science. 36 (4), 1077-1104 (1990).</li><li>Stage, A. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Notes:+An+Expression+for+the+Effect+of+Aspect,+Slope,+and+Habitat+Type+on+Tree+Growth.">Notes: An Expression for the Effect of Aspect, Slope, and Habitat Type on Tree Growth.</a> Forest Science. 22 (4), 457-460 (1976).</li><li>Gregorie, T. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Generalized+Error+Structure+for+Forestry+Yield+Models.">Generalized Error Structure for Forestry Yield Models.</a> Forest Science. 33 (2), 423-444 (1987).</li><li>Zhao, L., Li, C., Tang, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Individual-tree+diameter+growth+model+for+fir+plantations+based+on+multi-level+linear+mixed+effects+models+across+southeast+China.">Individual-tree diameter growth model for fir plantations based on multi-level linear mixed effects models across southeast China.</a> Journal of Forest Research. 18 (4), 305-315 (2013).</li><li>Hall, D. B., Bailey, R. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modeling+and+Prediction+of+Forest+Growth+Variables+Based+on+Multilevel+Nonlinear+Mixed+Models.">Modeling and Prediction of Forest Growth Variables Based on Multilevel Nonlinear Mixed Models.</a> Forest Science. 47 (3), 311-321 (2001).</li><li>Yang, Y., Huang, S., Meng, S. X., Trincado, G., Vanderschaaf, C. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+multilevel+individual+tree+basal+area+increment+model+for+aspen+in+boreal+mixedwood+stands+:+Journal+canadien+de+la+recherche+forestie&#768;re.">A multilevel individual tree basal area increment model for aspen in boreal mixedwood stands : Journal canadien de la recherche forestie&#768;re.</a> Revue Canadienne De Recherche Foresti&#232;re. 39 (39), 2203-2214 (2009).</li><li>Pinheiro, J. C., Bates, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mixed-effects+models+in+S+and+S-Plus.">Mixed-effects models in S and S-Plus.</a> Publications of the American Statistical Association. 96 (455), 1135-1136 (2000).</li></ol>

作者没有什么可透露的。

发展混合效应模型的一个关键问题是确定哪些参数可以被视为随机效应，哪些参数应被视为固定效应34，35。提出了两种方法。最常见的方法是将所有参数视为随机效应，然后由 AIC、BIC、Loglik 和 LRT 选择最佳模型。这是我们研究35所采用的方法。另一种选择是为 OLS 回归的每个示例图安装基底区域增量模型。在这些模型的样本图中具有?...

与均匀的单一栽培、不均匀年龄的混合种林管理相比，具有多重目标的混合物种森林管理最近受到越来越多的关注。预测不同的管理备选方案是制定强有力的森林管理战略的必要条件，特别是对于复杂的不均匀年龄的混合物种森林4。森林生长和产量模型已被广泛使用，以预测树木或站在发展和收获下的各种管理计划5，6，7。森林生长和产量模型分为个体树模型、大小级模型和全站生长模型6、7、8。不幸的是，大小类模型和全站模型不适合年龄不均匀的混合物种森林，这需要更详细的描述来支持森林管理决策过程。因此，单树生长和产量模型在过去几十年中受到越来越多的关注，因为它们能够预测森林站与各种物种组成，结构和管理策略9，10，11。
普通最小正方形 （OLS） 回归是开发单树生长模型 12、13、14、15 的最常用方法。在同一采样单元（即样本图或树）上，在同一采样单元（即样本图或树）上反复收集的单树生长模型数据集具有层次结构，在观测点 10、16之间缺乏独立性和高空间和时间相关性。分层随机结构违反了 OLS 回归的基本假设:即独立残余和通常分布的数据具有相等的方差。因此，OLS回归的使用不可避免地会产生对这些数据13、14参数估计标准误差的偏颇估计。
混合效应模型为分析结构复杂的数据提供了强大的工具，例如重复测量数据、纵向数据和多级数据。混合效应模型由固定组件和随机组件组成，这些组件是每个采样水平所特有的。此外，混合效应模型通过定义非对角方差-共变结构矩阵17、18、19来考虑空间和时间的异构性和自动校际性。为此，混合效应模型已广泛应用于林业，如直径高度模型20，21，冠模型22，23，自瘦模型24，25，生长模型26，27。
在这里，主要目标是使用线性混合效应方法开发单树基底区域增量模型。我们希望混合效应方法能够得到广泛应用。

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development of an individual-tree basal area increment model using a linear mixed-effects approach

在这里，我们根据一个数据集开发了一个5年基底面积增量的单树模型，其中包括来自中国西北部新疆省779个样本地块的21898 棵皮卡阿斯佩拉塔 树。为了防止来自同一采样单元的观测结果之间的高相关性，我们使用具有随机绘图效果的线性混合效应方法开发了该模型，以考虑随机变异性。各种树和立级变量，如树的大小、竞争和场地条件的指数，都作为固定效应包括在内，以解释残余变异性。此外，通过引入方差函数和自动相关结构来描述异构性和自动相关性。最佳线性混合效应模型由几个合适的统计数据决定:Akaike 的信息标准、贝叶斯信息标准、对数可能性和可能性比率测试。结果表明，单树基底面积增量的重要变量为胸高直径的反向转化、大于主体树的树木基底面积、每公顷树木数量和海拔高度。此外，方差结构中的错误最成功地通过指数函数建模，并且通过一阶自动反向结构 （AR（1）显著纠正了自动反差。与使用普通最小正方形回归的模型相比，线性混合效应模型的性能显著提高。

P. asperata的基本基底区域增量模型表示为方程 （7）。参数估计值、相应的标准误差和不合适的统计数据显示在表 2中。残余情节显示在图 1中。观察到残留物的明显异构性。 <img alt="Equation 7" src="/files/ftp_upload/60827/60827eq7.jpg">(7)
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			<td>估计</td>
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			<td>t 测试</st...

Watch this Scientific Journal Video about Development of an Individual-Tree Basal Area Increment Model using a Linear Mixed-Effects Approach at JoVE.com

Development of an Individual-Tree Basal Area Increment Model using a Linear Mixed-Effects Approach

混合效应模型是分析林业中分层随机结构数据的灵活而有用的工具，也可用于显著提高森林生长模型的性能。在这里，提出了一个协议，合成与线性混合效应模型相关的信息。

使用线性混合效应方法开发单树基数增量模型

Here, we developed an individual-tree model of 5-year basal area increments based on a dataset including 21898 Picea asperata trees from 779 sample plots ...

development-an-individual-tree-basal-area-increment-model-using

Research

JoVE Journal

Biology

3.2K 次观看.  Beijing Forestry University. 混合效应模型是分析林业中分层随机结构数据的灵活而有用的工具，也可用于显著提高森林生长模型的性能。在这里，提出了一个协议，合成与线性混合效应模型相关的信息。

视频: Development of an Individual-Tree Basal Area Increment Model using a Linear Mixed-Effects Approach

Microfabricated Post-Array-Detectors (mPADs): an Approach to Isolate Mechanical Forces

In this video, we will present our approach to measure cellular traction forces using a microfabricated array of posts.  Traction forces are generated through myosin-actin interactions and play an important role in our physiology.  During development, they enable cells to move from one location to the next in order to form the early structures of tissue.  Traction forces help in the healing processes.  They are necessary for the proper closure of wounds or the migration and crawling of leukocytes through our body.  These same forces can be detrimental to our health in the case of cancer metastasis or vascular growth towards a tumor.  The most common method by which to study cells in vitro has been to use a glass or polystyrene dish.  However, the rigidity of the substrates makes it impossible to physically measure cell traction forces, and there are relatively few methods to study traction forces.  Our lab has developed a technique to overcome these limitations.  The method is based on a vertical array of flexible cantilevers, the stiffness and size scale of which are such that individual cells spread across many cantilevers and deflect them in the process.  The pillars we use are 3 &mu;m in diameter, 10 &mu;m tall, and are configured in a regular array with 9 &mu;m center-to-center spacing.  But these physical dimensions can be readily varied to accommodate a variety of studies.  We start with a silicon master, but the final posts are made out of silicone rubber called poly (dimethyl siloxane), or PDMS.  We can measure the deflections under a microscope and calculate the magnitude and direction of traction forces required to produce the observed deflections.  We call these substrates microfabricated post-array-detectors, or mPADs.  Here, we will show you how we fabricate and use the mPADs to assess modulations of cellular contractility.

Microfabricated Post-Array-Detectors mPADs: an Approach to Isolate Mechanical Forces

In this video, we demonstrate how to fabricate and utilize microfabricated post array detectors (mPADs) to assess modulations of cellular contractility.

微阵列后探测器（mPADs）:机械力的方法来隔离

In this video, we will present our approach to measure cellular traction forces using a microfabricated array of posts.  Traction forces are generated ...

科研

生物学

Spatial Multiobjective Optimization of Agricultural Conservation Practices using a SWAT Model and an Evolutionary Algorithm

Finding the cost-efficient (i.e., lowest-cost) ways of targeting conservation practice investments for the achievement of specific water quality goals across the landscape is of primary importance in watershed management. Traditional economics methods of finding the lowest-cost solution in the watershed context (e.g.,5,12,20) assume that off-site impacts can be accurately described as a proportion of on-site pollution generated. Such approaches are unlikely to be representative of the actual pollution process in a watershed, where the impacts of polluting sources are often determined by complex biophysical processes. The use of modern physically-based, spatially distributed hydrologic simulation models allows for a greater degree of realism in terms of process representation but requires a development of a simulation-optimization framework where the model becomes an integral part of optimization.
Evolutionary algorithms appear to be a particularly useful optimization tool, able to deal with the combinatorial nature of a watershed simulation-optimization problem and allowing the use of the full water quality model. Evolutionary algorithms treat a particular spatial allocation of conservation practices in a watershed as a candidate solution and utilize sets (populations) of candidate solutions iteratively applying stochastic operators of selection, recombination, and mutation to find improvements with respect to the optimization objectives. The optimization objectives in this case are to minimize nonpoint-source pollution in the watershed, simultaneously minimizing the cost of conservation practices. A recent and expanding set of research is attempting to use similar methods and integrates water quality models with broadly defined evolutionary optimization methods3,4,9,10,13-15,17-19,22,23,25. In this application, we demonstrate a program which follows Rabotyagov et al.'s approach and integrates a modern and commonly used SWAT water quality model7 with a multiobjective evolutionary algorithm SPEA226, and user-specified set of conservation practices and their costs to search for the complete tradeoff frontiers between costs of conservation practices and user-specified water quality objectives. The frontiers quantify the tradeoffs faced by the watershed managers by presenting the full range of costs associated with various water quality improvement goals. The program allows for a selection of watershed configurations achieving specified water quality improvement goals and a production of maps of optimized placement of conservation practices.

This work demonstrates an integration of a water quality model with an optimization component utilizing evolutionary algorithms to solve for optimal (lowest-cost) placement of agricultural conservation practices for a specified set of water quality improvement objectives. The solutions are generated using a multi-objective approach, allowing for explicit quantification of tradeoffs.

空间使用SWAT模型的农业保护的做法和多目标优化的进化算法

Finding the cost-efficient (i.e., lowest-cost) ways of targeting conservation practice investments for the achievement of specific water quality goals ...

A Semi-quantitative Approach to Assess Biofilm Formation Using Wrinkled Colony Development

Biofilms, or surface-attached communities of cells encapsulated in an extracellular matrix, represent a common lifestyle for many bacteria. Within a biofilm, bacterial cells often exhibit altered physiology, including enhanced resistance to antibiotics and other environmental stresses 1. Additionally, biofilms can play important roles in host-microbe interactions. Biofilms develop when bacteria transition from individual, planktonic cells to form complex, multi-cellular communities 2. In the laboratory, biofilms are studied by assessing the development of specific biofilm phenotypes. A common biofilm phenotype involves the formation of wrinkled or rugose bacterial colonies on solid agar media 3. Wrinkled colony formation provides a particularly simple and useful means to identify and characterize bacterial strains exhibiting altered biofilm phenotypes, and to investigate environmental conditions that impact biofilm formation. Wrinkled colony formation serves as an indicator of biofilm formation in a variety of bacteria, including both Gram-positive bacteria, such as Bacillus subtilis 4, and Gram-negative bacteria, such as Vibrio cholerae 5, Vibrio parahaemolyticus 6, Pseudomonas aeruginosa 7, and Vibrio fischeri 8.
The marine bacterium V. fischeri has become a model for biofilm formation due to the critical role of biofilms during host colonization: biofilms produced by V. fischeri promote its colonization of the Hawaiian bobtail squid Euprymna scolopes 8-10. Importantly, biofilm phenotypes observed in vitro correlate with the ability of V. fischeri cells to effectively colonize host animals: strains impaired for biofilm formation in vitro possess a colonization defect 9,11, while strains exhibiting increased biofilm phenotypes are enhanced for colonization 8,12. V. fischeri therefore provides a simple model system to assess the mechanisms by which bacteria regulate biofilm formation and how biofilms impact host colonization.
In this report, we describe a semi-quantitative method to assess biofilm formation using V. fischeri as a model system. This method involves the careful spotting of bacterial cultures at defined concentrations and volumes onto solid agar media; a spotted culture is synonymous to a single bacterial colony. This 'spotted culture' technique can be utilized to compare gross biofilm phenotypes at single, specified time-points (end-point assays), or to identify and characterize subtle biofilm phenotypes through time-course assays of biofilm development and measurements of the colony diameter, which is influenced by biofilm formation. Thus, this technique provides a semi-quantitative analysis of biofilm formation, permitting evaluation of the timing and patterning of wrinkled colony development and the relative size of the developing structure, characteristics that extend beyond the simple overall morphology.

We provide a simple, semi-quantitative method to investigate biofilm formation in vitro. This method takes advantage of the Zeiss stemi 2000-C Dissecting Microscope (with camera attachment) to monitor both the timing and pattern of biofilm formation, as assessed by the development of wrinkled colonies.

一个半定量的方法来评估生物膜形成皱殖民地的发展

Biofilms, or surface-attached communities of cells encapsulated in an extracellular matrix, represent a common lifestyle for many bacteria. Within a ...

Conversion of a Capture ELISA to a Luminex xMAP Assay using a Multiplex Antibody Screening Method

The enzyme-linked immunosorbent assay (ELISA) has long been the primary tool for detection of analytes of interest in biological samples for both life science research and clinical diagnostics. However, ELISA has limitations. It is typically performed in a 96-well microplate, and the wells are coated with capture antibody, requiring a relatively large amount of sample to capture an antigen of interest . The large surface area of the wells and the hydrophobic binding of capture antibody can also lead to non-specific binding and increased background. Additionally, most ELISAs rely upon enzyme-mediated amplification of signal in order to achieve reasonable sensitivity. Such amplification is not always linear and can thus skew results.
In the past 15 years, a new technology has emerged that offers the benefits of the ELISA, but also enables higher throughput, increased flexibility, reduced sample volume, and lower cost, with a similar workflow 1, 2. Luminex xMAP Technology is a microsphere (bead) array platform enabling both monoplex and multiplex assays that can be applied to both protein and nucleic acid applications 3-5. The beads have the capture antibody covalently immobilized on a smaller surface area, requiring less capture antibody and smaller sample volumes, compared to ELISA, and non-specific binding is significantly reduced. Smaller sample volumes are important when working with limiting samples such as cerebrospinal fluid, synovial fluid, etc. 6. Multiplexing the assay further reduces sample volume requirements, enabling multiple results from a single sample.
Recent improvements by Luminex include: the new MAGPIX system, a smaller, less expensive, easier-to-use analyzer; Low-Concentration Magnetic MagPlex Microspheres which eliminate the need for expensive filter plates and come in a working concentration better suited for assay development and low-throughput applications; and the xMAP Antibody Coupling (AbC) Kit, which includes a protocol, reagents, and consumables necessary for coupling beads to the capture antibody of interest. (See Materials section for a detailed list of kit contents.)
In this experiment, we convert a pre-optimized ELISA assay for TNF-alpha cytokine to the xMAP platform and compare the performance of the two methods 7-11. TNF-alpha is a biomarker used in the measurement of inflammatory responses in patients with autoimmune disorders.
We begin by coupling four candidate capture antibodies to four different microsphere sets or regions. When mixed together, these four sets allow for the simultaneous testing of all four candidates with four separate detection antibodies to determine the best antibody pair, saving reagents, sample and time. Two xMAP assays are then constructed with the two most optimal antibody pairs and their performance is compared to that of the original ELISA assay in regards to signal strength, dynamic range, and sensitivity.

An ELISA can be easily converted to a Luminex xMAP assay and, through the benefits of multiplexing, several antibodies can be screened simultaneously to identify an optimum antibody pair, resulting in increased sensitivity and dynamic range, while reducing assay cost.

转换到一个点阵仪XMAP含量，使用多重抗体筛查方法的捕获ELISA

The enzyme-linked immunosorbent assay (ELISA) has long been the primary tool for detection of analytes of interest in biological samples for both life ...

Cell Tracking Using Photoconvertible Proteins During Zebrafish Development

Embryogenesis is a dynamic process that is best studied by using techniques that allow the documentation of developmental changes in vivo. The use of genetically-encoded fluorescent proteins has proven a valuable strategy for elucidating dynamic morphogenetic processes as they occur in the intact organism. During the past decade, the development of photoactivatable and photoconvertible fluorescent proteins has opened the possibility to investigate the fate of discrete subpopulations of tagged proteins1. Unlike photoactivatable proteins, photoconvertible fluorescent proteins (PCFPs) are readily tracked and imaged in their native emission state prior to photoconversion, making it easier to identify and select regions by optical inspection. PCFPs, such as Kaede2, KikGR3, Dendra4 and EosFP5, can be shifted from green to red upon exposure to UV or blue light due to a His-Tyr-Gly tripeptide sequence which forms a green chromophore that can be photoconverted to a red one by a light-catalyzed &beta;-elimination and subsequent extension of a &pi;-conjugated system3. PCFPs and their monomeric variants are useful tools for tracking cells6-10 and studying protein dynamics11-14, respectively. During recent years, PCFPs have been expressed in different animal model, such as zebrafish6, chicken7,8 and mouse9,10 for cell fate tracking. Here we report a protocol for cell-specific photoconversion of PCFPs in the living zebrafish embryo and further tracking of photoconverted proteins at later developmental stages. This methodology allows studying, in a tissue-specific manner, cell biological events underlying morphogenesis in the zebrafish animal model.

Here, we present a method for the photoactivated switch of photoconvertible fluorescent proteins (PCFPs) in the living zebrafish embryo and further tracking of photoconverted protein at specific time points during development. This methodology allows monitoring of cell biological events underlying different developmental processes in a live vertebrate organism.

在斑马鱼发育的细胞追踪使用Photoconvertible蛋白

Embryogenesis is a dynamic process that is best studied by using techniques that allow the documentation of developmental changes in vivo. The use of ...

Assessing Species-specific Contributions To Craniofacial Development Using Quail-duck Chimeras

The generation of chimeric embryos is a widespread and powerful approach to study cell fates, tissue interactions, and species-specific contributions to the histological and morphological development of vertebrate embryos. In particular, the use of chimeric embryos has established the importance of neural crest in directing the species-specific morphology of the craniofacial complex. The method described herein utilizes two avian species, duck and quail, with remarkably different craniofacial morphology. This method greatly facilitates the investigation of molecular and cellular regulation of species-specific pattern in the craniofacial complex.&#160;Experiments in quail and duck chimeric embryos have already revealed neural crest-mediated tissue interactions and cell-autonomous behaviors that regulate species-specific pattern in the craniofacial skeleton, musculature, and integument. The great diversity of neural crest derivatives suggests significant potential for future applications of the quail-duck chimeric system to understanding vertebrate development, disease, and evolution.

This article describes a method to generate chimeric embryos that are&#160;designed to test the species-specific contributions of neural crest and/or other tissues to craniofacial development.

评估具体物种的贡献颅面开发利用鹌鹑，鸭嵌合体

The generation of chimeric embryos is a widespread and powerful approach to study cell fates, tissue interactions, and species-specific contributions to ...

Development of a Quantitative Recombinase Polymerase Amplification Assay with an Internal Positive Control

It was recently demonstrated that recombinase polymerase amplification (RPA), an isothermal amplification platform for pathogen detection, may be used to quantify DNA sample concentration using a standard curve. In this manuscript, a detailed protocol for developing and implementing a real-time quantitative recombinase polymerase amplification assay (qRPA assay) is provided. Using HIV-1 DNA quantification as an example, the assembly of real-time RPA reactions, the design of an internal positive control (IPC) sequence, and co-amplification of the IPC and target of interest are all described. Instructions and data processing scripts for the construction of a standard curve using data from multiple experiments are provided, which may be used to predict the concentration of unknown samples or assess the performance of the assay. Finally, an alternative method for collecting real-time fluorescence data with a microscope and a stage heater as a step towards developing a point-of-care qRPA assay is described. The protocol and scripts provided may be used for the development of a qRPA assay for any DNA target of interest.

Provided is a protocol for developing a real-time recombinase polymerase amplification assay to quantify initial concentration of DNA samples using either a thermal cycler or a microscope and stage heater. Also described is the development of an internal positive control. Scripts are provided for processing raw real-time fluorescence data.

一个定量聚合酶重组酶扩增法的发展与内部阳性对照

It was recently demonstrated that recombinase polymerase amplification (RPA), an isothermal amplification platform for pathogen detection, may be used to ...

Using a Whole-mount Immunohistochemical Method to Study the Innervation of the Biliary Tract in Suncus murinus

This work describes the whole-mount immunohistochemistry staining method in detail, using neurofilament protein antibody to label the innervation of the biliary tract in Suncus murinus (S. murinus&#160;). First, the specimen was dissected from S. murinus and fixed in 4% paraformaldehyde (PFA). Second, an enzymatic treatment and potential endogenous peroxidase inactivation were performed. The specimen was then exposed to the primary antibody, anti-neurofilament protein antibody, for 3-6 days. It was then incubated with the secondary antibody conjugated with horseradish peroxidase. The color reaction was revealed by reacting the specimen with a 3,3&#39;-diaminobenzidine (DAB) substrate. This method can be applied to analyze the innervation of all visceral organs. Furthermore, this protocol can also be adapted to test other neuronal antibodies, but optimization of the antibodies should be done first. This method was originally introduced by Kuratani and Tanaka1,2,3.

Using a Whole-mount Immunohistochemical Method to Study the Innervation of the Biliary Tract in Suncus murinus

A whole-mount immunohistochemical approach, to visualize neurofilament protein expression in the extrahepatic biliary tract in Suncus murinus. is presented here. This protocol can be used to analyze the innervation of all visceral organs in S. murinus or other species.

使用全身免疫组织化学方法研究胆道的神经支配<em&gt; Suncus murinus</em

This work describes the whole-mount immunohistochemistry staining method in detail, using neurofilament protein antibody to label the innervation of the ...

Mass Spectrometry Analysis to Identify Ubiquitylation of EYFP-tagged CENP-A (EYFP-CENP-A)

Studying the structure and the dynamics of kinetochores and centromeres is important in understanding chromosomal instability (CIN) and cancer progression. How the chromosomal location and function of a centromere (i.e., centromere identity) are determined and participate in accurate chromosome segregation is a fundamental question. CENP-A is proposed to be the non-DNA indicator (epigenetic mark) of centromere identity, and CENP-A ubiquitylation is required for CENP-A deposition at the centromere, inherited through dimerization between cell division, and indispensable to cell viability.
Here we describe mass spectrometry analysis to identify ubiquitylation of EYFP-CENP-A K124R mutant suggesting that ubiquitylation at a different lysine is induced because of the EYFP tagging in the CENP-A K124R mutant protein. Lysine 306 (K306) ubiquitylation in EYFP-CENP-A K124R was successfully identified, which corresponds to lysine 56 (K56) in CENP-A through mass spectrometry analysis. A caveat is discussed in the use of GFP/EYFP or the tagging of high molecular weight protein as a tool to analyze the function of a protein. Current technical limit is also discussed for the detection of ubiquitylated bands, identification of site-specific ubiquitylation(s), and visualization of ubiquitylation in living cells or a specific single cell during the whole cell cycle.
The method of mass spectrometry analysis presented here can be applied to human CENP-A protein with different tags and other centromere-kinetochore proteins. These combinatory methods consisting of several assays/analyses could be recommended for researchers who are interested in identifying functional roles of ubiquitylation.

Mass Spectrometry Analysis to Identify Ubiquitylation of EYFP-tagged CENP-A EYFP-CENP-A

CENP-A ubiquitylation is an important requirement for CENP-A deposition at the centromere, inherited through dimerization between cell division, and indispensable to cell viability. Here we describe mass spectrometry analysis to identify ubiquitylation of EYFP-tagged CENP-A (EYFP-CENP-A) protein.

质谱分析，用于识别 EYFP 标记 CENP-A （EYFP-CENP-A） 的泛化

Studying the structure and the dynamics of kinetochores and centromeres is important in understanding chromosomal instability (CIN) and cancer ...

Quantification of Cell-Substrate Adhesion Area and Cell Shape Distributions in MCF7 Cell Monolayers

The methods presented here quantify some parameters of confluent adherent cell monolayers from multiple appropriately stained confocal images: adhesion to the substrate as a function of the number and size of focal adhesions, and cell shape, characterized by the cell shape index and other shape descriptors. Focal adhesions were visualized by paxillin staining and cell-cell borders were marked by junction plakoglobin and actin. The methods for cell culture and staining were standard; images represent single focal planes; image analysis was performed using publicly available image processing software. The presented protocols are used to quantify the number and size of focal adhesions and the differences in cell shape distribution in the monolayers, but they can be repurposed for the quantification of the size and shape of any other distinct cellular structure that can be stained (e.g., mitochondria or nuclei). Assessing these parameters is important in the characterization of the dynamic forces in adherent cell layer, including cell adhesion and actomyosin contractility that affects cell shape.

The article describes quantification of 1) the size and number of focal adhesions and 2) cell shape index and its distribution from confocal images of the confluent monolayers of MCF7 cells.

MCF7细胞单层中细胞基质粘附面积和细胞形状分布的定量

The methods presented here quantify some parameters of confluent adherent cell monolayers from multiple appropriately stained confocal images: adhesion to ...