套索回归中newx的格式在R中出现错误
套索回归中newx的格式在R中出现错误
提问于 2019-04-02 20:57:43
我正在尝试实现套索线性回归。我训练我的模型，但当我试图对未知数据进行预测时，它会给我以下错误：
Error in cbind2(1, newx) %*% nbeta :
invalid class 'NA' to dup_mMatrix_as_dgeMatrix我的数据总结如下：
我想预测未知的percent_gc。我最初使用percent_gc已知的数据训练我的模型
set.seed(1)
###training data
data.all <- tibble(description = c('Xylanimonas cellulosilytica XIL07, DSM 15894','Teredinibacter turnerae T7901',
'Desulfotignum phosphitoxidans FiPS-3, DSM 13687','Brucella melitensis bv. 1 16M'),
phylum = c('Actinobacteria','Proteobacteria','Proteobacteria','Bacteroidetes'),
genus = c('Acaryochloris','Acetohalobium','Acidimicrobium','Acidithiobacillus'),
Latitude = c('63.93','69.372','3.493.11','44.393.704'),
Longitude = c('-22.1','88.235','134.082.527','-0.130781'),
genome_size = c(8361599,2469596,2158157,3207552),
percent_gc = c(34,24,55,44),
percent_psuedo = c(0.0032987747,0.0291222313,0.0353728489,0.0590663703),
percent_signalpeptide = c(0.02987198,0.040607055,0.048757170,0.061606859))
###data for prediction
data.prediction <- tibble(description = c('Liberibacter crescens BT-1','Saprospira grandis Lewin',
'Sinorhizobium meliloti AK83','Bifidobacterium asteroides ATCC 25910'),
phylum = c('Actinobacteria','Proteobacteria','Proteobacteria','Bacteroidetes'),
genus = c('Acaryochloris','Acetohalobium','Acidimicrobium','Acidithiobacillus'),
Latitude = c('39.53','69.372','5.493.12','44.393.704'),
Longitude = c('20.1','-88.235','134.082.527','-0.130781'),
genome_size = c(474832,2469837,2158157,3207552),
percent_gc = c(NA,NA,NA,NA),
percent_psuedo = c(0.0074639239,0.0291222313,0.0353728489,0.0590663703),
percent_signalpeptide = c(0.02987198,0.040607055,0.048757170,0.061606859))
x=model.matrix(percent_gc~.,data.all)
y=data.all$percent_gc
cv.out <- cv.glmnet (x, y, alpha = 1,family = "gaussian")
best.lambda= cv.out$lambda.min
fit <- glmnet(x,y,alpha=1)然后，我想对未知的percent_gc做出预测。
newX = matrix(data = data.prediction %>% select(-percent_gc))
data.prediction$percent_gc <-
predict(object = fit ,type="response", s=best.lambda, newx=newX)这会产生我上面提到的错误。
我不明白为了摆脱这个帮助，newX应该是哪种格式。如果您有真知灼见，我们将不胜感激。
回答 1
Stack Overflow用户
回答已采纳
发布于 2019-04-02 22:18:23
我真的不知道如何构造合适的矩阵，但是package glmnetUtils提供了将公式直接拟合到数据帧并进行预测的功能。有了这个，我得到了预测值：
library(glmnetUtils)
fit <- glmnet(percent_gc~.,data.all,alpha=1)
cv.out <- cv.glmnet (percent_gc~.,data.all, alpha = 1,family = "gaussian")
best.lambda= cv.out$lambda.min
predict(object = fit,data.prediction,s=best.lambda)页面原文内容由Stack Overflow提供。腾讯云小微IT领域专用引擎提供翻译支持
原文链接：
https://stackoverflow.com/questions/55475399
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