这些天来,我正在尝试对 vegan 包进行 db-RDA 分析。我有 24 个解释变量和 46 个样本。问题是,在开发 db-RDA 时,我只能得到前 7 个环境变量的结果,而不管它们的排列顺序如何。可能是什么原因?我用代码解释问题
#1 我收取包裹素食主义者的费用
library(vegan)
#2 我上传了 OTU 数据帧,并以正确的格式进行了调整
featuretable16 <-read.table(file = '16Sfeaturetable.txt', sep = '\t', header = TRUE)
featuretable162 <- featuretable16[,2:57]
row.names(featuretable162) <- featuretable16$Rep
ft16stransponed <- t (featuretable162)
#3 我上传了环境条件并以正确的格式进行了调整(解释变量)
ambiental16 <-read.table(file = 'environmental16.txt', sep = '\t', header = TRUE)
rownames (ambiental16) = ambiental16$SampleID
ambiental162 <- ambiental16[,2:24]
#4 执行dbrda分析和绘图,只出现前7个解释变量
dbrda <- dbrda(ft16stransponed ~ ., ambiental162, dist="bray")
plot(dbrda)
#5 我用方差分析进行了显着性。尽管分析评估了所有环境因素,但仅显示了前七个解释变量的结果。
anova(dbrda, by="terms", permu=999)
Permutation test for dbrda under reduced model
Terms added sequentially (first to last)
Permutation: free
Number of permutations: 999
Model: dbrda(formula = ft16stransponed ~ time + Location + pH + DO + Conductivity + Temperature + Water.Flow + Water.depth + Nitrogen + Nitrate + Ammonium + Phosphorus + TOC + Amoxicillin + Azithromycin + Ciprofloxacin + Clarithromycin + Erythromycin + Lincomicina + Metronidazol + Sulfametoxazol + Ofloxacino + Trimetoprima, data = ambiental162, distance = "bray")
Df SumOfSqs F Pr(>F)
time 1 0.6731 3.5504 0.004 **
Location 1 4.7222 24.9074 0.001 ***
pH 1 0.9193 4.8488 0.002 **
DO 1 0.6811 3.5926 0.004 **
Conductivity 1 0.5441 2.8700 0.004 **
Temperature 1 0.6336 3.3418 0.004 **
Water.Flow 1 0.9761 5.1486 0.001 ***
Residual 48 9.1003
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
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我也做了一个 R 笔记本,但我不知道如何在这里提交,但可以更清楚。