8

我在 ggplot2 中使用 stat_smooth 函数，决定我想要“拟合优度”，并为此使用了 mgvc gam。我突然想到我应该检查以确保它们是相同的模型（stat_smooth vs mgvc gam），所以我使用下面的代码进行检查。看起来，它们有不同的结果，如图所示（Plot: stat_smoother gam (red), mgcv gam (black)）。但是，我不知道为什么他们有不同的结果。两者之间的某些默认参数是否不同？是 gam 在数字 x 上运行，而 stat_smooth 是在 POSIXct x 上运行（如果是这样 - 我不知道该怎么做）？看起来 stat_smooth 更平滑，但是 k 值是一样的......

我认为有几篇关于如何在 ggplot2 中绘制 gam 输出的帖子，但我真的很想知道为什么 stat_smooth 和 mgcv 首先给出不同的结果。我对 GAM（和 R）很陌生，所以我很可能错过了一些简单的东西。但是，我在询问之前做了谷歌并搜索了这个论坛。

我的数据有点大，很容易共享，所以我使用了一个示例数据集——我已经将源代码放在了代码中，以及dput()所有内容的下方，然后是我sessionInfo()的。

我试图提出一个质量问题，但这只是我的第二个问题。曾经。所以，建设性的批评是值得赞赏的。

谢谢！

library(readxl)
library(data.table)
library(ggplot2)
library(scales)
library(mgcv)

stackOF_data <- read_excel("mean-daily-flow-cumecs-vatnsdals.xlsx", sheet = "Data")
stackOF_data <- data.table(stackOF_data)
stackOF_data <- stackOF_data[,.(timeseries=as.POSIXct(Date,format("%Y-%m-%d")),mdf)]

a <- stackOF_data[,.(x=as.numeric(timeseries),y=mdf)]
a1 <- gam(y~s(x, k=100, bs="cs"),data=a) 
a2=data.table(gam_mdf= predict(a1,a))
a2=cbind(timeseries=stackOF_data$timeseries,a2)

# see if predict and actual are the same
p <- ggplot() + 
geom_line(data = a2, aes(x = timeseries, y = gam_mdf), size=1)+
scale_color_manual(values=c("black","magenta"))+
scale_y_continuous()+
scale_x_datetime(labels = date_format("%Y-%m-%d"), breaks = "1 month", minor_breaks = "1 week")+ 
theme(axis.text.x=element_text(angle=50, size=10,hjust=1))+
stat_smooth(data = stackOF_data, aes(x = (timeseries), y = mdf),method="gam", formula=y~s(x,k=100, bs="cs"), col="red", se=FALSE, size=1)
p

# data from: https://datamarket.com/data/set/235m/mean-daily-flow-cumecs-vatnsdalsa-river-1-jan-1972-31-dec-1974#!ds=235m&display=line&s=14l

> dput(a)
structure(list(x = c(126230400, 126316800, 126403200, 126489600, 
126576000, 126662400, 126748800, 126835200, 126921600, 127008000, 
127094400, 127180800, 127267200, 127353600, 127440000, 127526400, 
127612800, 127699200, 127785600, 127872000, 127958400, 128044800, 
128131200, 128217600, 128304000, 128390400, 128476800, 128563200, 
128649600, 128736000, 128822400, 128908800, 128995200, 129081600, 
129168000, 129254400, 129340800, 129427200, 129513600, 129600000, 
129686400, 129772800, 129859200, 129945600, 130032000, 130118400, 
130204800, 130291200, 130377600, 130464000, 130550400, 130636800, 
130723200, 130809600, 130896000, 130982400, 131068800, 131155200, 
131241600, 131328000, 131414400, 131500800, 131587200, 131673600, 
131760000, 131846400, 131932800, 132019200, 132105600, 132192000, 
132278400, 132364800, 132451200, 132537600, 132624000, 132710400, 
132796800, 132883200, 132969600, 133056000, 133142400, 133228800, 
133315200, 133401600, 133488000, 133574400, 133660800, 133747200, 
133833600, 133920000, 134006400, 134092800, 134179200, 134265600, 
134352000, 134438400, 134524800, 134611200, 134697600, 134784000, 
134870400, 134956800, 135043200, 135129600, 135216000, 135302400, 
135388800, 135475200, 135561600, 135648000, 135734400, 135820800, 
135907200, 135993600, 136080000, 136166400, 136252800, 136339200, 
136425600, 136512000, 136598400, 136684800, 136771200, 136857600, 
136944000, 137030400, 137116800, 137203200, 137289600, 137376000, 
137462400, 137548800, 137635200, 137721600, 137808000, 137894400, 
137980800, 138067200, 138153600, 138240000, 138326400, 138412800, 
138499200, 138585600, 138672000, 138758400, 138844800, 138931200, 
139017600, 139104000, 139190400, 139276800, 139363200, 139449600, 
139536000, 139622400, 139708800, 139795200, 139881600, 139968000, 
140054400, 140140800, 140227200, 140313600, 140400000, 140486400, 
140572800, 140659200, 140745600, 140832000, 140918400, 141004800, 
141091200, 141177600, 141264000, 141350400, 141436800, 141523200, 
141609600, 141696000, 141782400, 141868800, 141955200, 142041600, 
142128000, 142214400, 142300800, 142387200, 142473600, 142560000, 
142646400, 142732800, 142819200, 142905600, 142992000, 143078400, 
143164800, 143251200, 143337600, 143424000, 143510400, 143596800, 
143683200, 143769600, 143856000, 143942400, 144028800, 144115200, 
144201600, 144288000, 144374400, 144460800, 144547200, 144633600, 
144720000, 144806400, 144892800, 144979200, 145065600, 145152000, 
145238400, 145324800, 145411200, 145497600, 145584000, 145670400, 
145756800, 145843200, 145929600, 146016000, 146102400, 146188800, 
146275200, 146361600, 146448000, 146534400, 146620800, 146707200, 
146793600, 146880000, 146966400, 147052800, 147139200, 147225600, 
147312000, 147398400, 147484800, 147571200, 147657600, 147744000, 
147830400, 147916800, 148003200, 148089600, 148176000, 148262400, 
148348800, 148435200, 148521600, 148608000, 148694400, 148780800, 
148867200, 148953600, 149040000, 149126400, 149212800, 149299200, 
149385600, 149472000, 149558400, 149644800, 149731200, 149817600, 
149904000, 149990400, 150076800, 150163200, 150249600, 150336000, 
150422400, 150508800, 150595200, 150681600, 150768000, 150854400, 
150940800, 151027200, 151113600, 151200000, 151286400, 151372800, 
151459200, 151545600, 151632000, 151718400, 151804800, 151891200, 
151977600, 152064000, 152150400, 152236800, 152323200, 152409600, 
152496000, 152582400, 152668800, 152755200, 152841600, 152928000, 
153014400, 153100800, 153187200, 153273600, 153360000, 153446400, 
153532800, 153619200, 153705600, 153792000, 153878400, 153964800, 
154051200, 154137600, 154224000, 154310400, 154396800, 154483200, 
154569600, 154656000, 154742400, 154828800, 154915200, 155001600, 
155088000, 155174400, 155260800, 155347200, 155433600, 155520000, 
155606400, 155692800, 155779200, 155865600, 155952000, 156038400, 
156124800, 156211200, 156297600, 156384000, 156470400, 156556800, 
156643200, 156729600, 156816000, 156902400, 156988800, 157075200, 
157161600, 157248000, 157334400, 157420800, 157507200, 157593600, 
157680000), y = c(4.65, 4.65, 4.65, 4.48, 5.16, 5.52, 5.34, 5.34, 
4.82, 4.65, 4.48, 4.31, 4.31, 4.31, 4.14, 3.82, 3.98, 3.98, 4.31, 
5.71, 6.5, 6.3, 5.71, 5.71, 5.16, 4.65, 4.14, 3.98, 4.48, 4.48, 
4.31, 4.65, 4.31, 3.98, 3.98, 3.98, 3.98, 3.98, 3.98, 3.82, 3.67, 
3.67, 3.98, 3.98, 3.82, 3.82, 3.82, 4.14, 5.9, 4.48, 3.98, 3.98, 
3.82, 3.67, 3.67, 3.67, 4.65, 3.98, 4.31, 4.31, 3.67, 4.31, 6.1, 
7.3, 7.5, 7.5, 8.14, 10.8, 16.1, 14.8, 12.5, 9.9, 8.14, 6.9, 
6.1, 5.34, 5.16, 4.99, 4.99, 4.99, 4.99, 5.52, 6.3, 7.3, 6.9, 
5.9, 5.71, 5.71, 8.58, 31.5, 33.7, 18.4, 11.3, 16.1, 32.9, 45.3, 
54, 25.7, 18, 15.9, 15.6, 14.5, 15.9, 35.9, 37.5, 29.4, 27.5, 
30.1, 27.5, 30.8, 29.4, 22, 20.1, 35.9, 36.7, 32.9, 22, 18, 15.9, 
15.2, 14.8, 13, 12.7, 12.5, 11, 9.68, 8.8, 7.92, 7.3, 6.9, 7.3, 
10.3, 11, 11.3, 11.9, 12.5, 13.6, 12.2, 10.8, 9.9, 9.46, 8.8, 
7.5, 7.1, 7.71, 7.1, 6.1, 5.34, 5.34, 5.34, 5.52, 5.52, 6.3, 
6.7, 6.5, 5.9, 5.71, 5.9, 5.71, 5.52, 7.3, 7.5, 7.1, 7.3, 6.7, 
6.9, 7.3, 7.5, 10.8, 11.6, 8.58, 7.92, 7.1, 6.7, 6.5, 6.1, 5.9, 
5.9, 5.71, 5.52, 5.52, 5.52, 5.9, 5.9, 5.71, 5.52, 5.52, 5.34, 
5.34, 5.52, 6.5, 6.5, 5.71, 5.34, 5.16, 4.99, 4.82, 4.82, 4.99, 
4.82, 4.82, 4.82, 4.82, 4.82, 4.65, 4.48, 4.48, 4.31, 4.31, 4.14, 
4.14, 4.31, 4.48, 4.31, 4.31, 4.31, 4.99, 5.71, 6.3, 6.1, 6.1, 
5.9, 5.71, 5.52, 5.52, 5.52, 5.52, 5.52, 5.34, 5.34, 5.52, 5.52, 
5.52, 5.34, 5.34, 5.52, 5.34, 5.52, 5.52, 5.34, 5.34, 5.34, 5.34, 
5.71, 5.9, 6.3, 6.9, 7.5, 6.5, 6.1, 6.1, 5.9, 6.1, 6.1, 5.9, 
6.5, 6.5, 6.1, 5.9, 5.9, 5.71, 5.9, 5.9, 5.71, 4.99, 4.65, 5.16, 
5.34, 5.34, 4.65, 4.99, 5.71, 5.34, 5.34, 5.34, 5.34, 4.99, 5.34, 
5.34, 5.34, 5.34, 5.52, 5.34, 5.52, 5.71, 6.5, 7.71, 6.9, 6.5, 
6.7, 6.1, 5.9, 6.1, 5.9, 5.71, 7.92, 7.71, 7.1, 7.92, 5.34, 5.16, 
8.14, 10.1, 7.92, 7.3, 6.9, 6.9, 6.9, 8.58, 7.3, 6.9, 7.3, 6.3, 
5.16, 6.1, 5.52, 4.99, 5.34, 5.34, 5.34, 5.16, 5.71, 5.52, 5.52, 
5.16, 4.82, 5.52, 6.1, 5.9, 5.71, 5.52, 5.16, 4.99, 4.48, 4.82, 
5.16, 5.16, 5.16, 5.16, 5.16, 4.82, 4.65, 3.82, 4.14, 4.65, 4.65, 
4.31, 4.31, 5.16, 5.16, 5.16, 5.16, 5.16, 4.99, 4.65, 5.16, 5.16, 
5.16, 5.16, 5.16, 5.16, 5.16, 5.16, 5.34, 5.34)), .Names = c("x", 
"y"), row.names = c(NA, -365L), class = c("data.table", "data.frame"
), .internal.selfref = <pointer: 0x0000000005860788>)

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United         States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] data.table_1.9.6 readxl_0.1.0     mgcv_1.8-7       nlme_3.1-121         scales_0.3.0     sos_1.3-8        brew_1.0-6       ggplot2_1.0.1   
[9] MASS_7.3-43     

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.1      lattice_0.20-33  digest_0.6.8     chron_2.3-47     grid_3.2.2       plyr_1.8.3       gtable_0.1.2     magrittr_1.5    
 [9] stringi_0.5-5    reshape2_1.4.1   Matrix_1.2-2     labeling_0.3     proto_0.3-10     tools_3.2.2      stringr_1.0.0    munsell_0.4.2   
[17] colorspace_1.2-6

部分解决方案

我仍然不知道为什么这两种方法会给出不同的答案，这让我很困扰。但是，经过大量互联网搜索，我确实找到了以下解决方法：

library(readxl)
library(data.table)
library(ggplot2)
library(scales)
library(mgcv)

stackOF_data <- read_excel("C:/Users/jel4049/Desktop/mean-daily-flow-cumecs-    vatnsdals.xlsx", sheet = "Data")
stackOF_data <- data.table(stackOF_data)

stackOF_data <- stackOF_data[,.(timeseries=as.POSIXct(Date,format("%Y-%m-%d")),mdf)]
a <- stackOF_data[,.(x=as.numeric(timeseries),y=mdf)]
a1 <- gam(y~s(x, k=100, bs="cs"),data=a) 
a2=data.table(gam_mdf = predict(a1,a))

preds <- predict(a1,se.fit=TRUE)
my_data <- data.frame(mu=preds$fit, low =(preds$fit - 1.96 * preds$se.fit), high = (preds$fit + 1.96 * preds$se.fit))


m <- ggplot()+
  geom_line(data = a2, aes(x=stackOF_data$timeseries, y=gam_mdf), size=1, col="blue")+
  geom_smooth(data=my_data,aes(ymin = low, ymax = high, x=stackOF_data$timeseries, y = mu), stat = "identity", col="green")
m

现在至少我知道我可以从一些 mgcv 函数中获得的摘要和数据符合质量信息与我的图相匹配。

4

1 回答 1

9

事实证明，您看到的差异是因为您n在stat_smooth.

从帮助页面：

n个点来评估更平滑

当然，我并没有马上想到这意味着n控制newdata参数的数据集的大小，predict因此stat_smooth在进行预测时不使用原始数据集。但是我在另一个问题上阅读了这个不错的答案stat_smooth，并意识到要弄清楚发生了什么，我应该仔细研究一下拟合模型 的stat_smooth预测与手动预测。gam

因此，使用我命名的 OP 中的数据集dat，我们可以检查发生了什么。

k = 100在通过拟合模型gam并将预测添加到数据集之后的情节。如您所述，蓝色 ( stat_smooth) 和黑色（手动预测）不匹配。

dat$predgam = predict(gam(y ~ s(x, k = 100), data = dat))

(p1 = ggplot(dat, aes(x, y)) +
    geom_point() +
    geom_smooth(method = "gam", formula = y ~ s(x, k = 100)) +
    geom_line(aes(y = predgam)))

在此处输入图像描述

您总是可以ggplot_build用来查看您的绘图对象并查看组成它的所有部分（我没有在这里显示结果，因为它占用了太多空间，但输出将打印到您的控制台）。

ggplot_build(p1)

的预测数据集stat_smooth是数据集列表中的第二个。

ggplot_build(p1)$data[[2]]

但是看看该数据集有多少行：

nrow(ggplot_build(p1)$data[[2]])
[1] 80

该n参数的默认设置为 80，但您的数据集中有 365 行。那么如果换成n365会怎么样呢？我会让平滑线更粗，这样你就可以真正看到它（蓝色）。

(p2 = ggplot(dat, aes(x, y)) +
    geom_point() +
    geom_smooth(method = "gam", formula = y ~ s(x, k = 100), n = 365, size = 2) +
    geom_line(aes(y = predgam)))

在此处输入图像描述

nrow(ggplot_build(p2)$data[[2]])
[1] 365

如果您查看帮助页面predictdf的详细信息部分中提到的函数的代码，stat_smooth您会发现在进行预测时未使用原始数据集。相反，序列是由原始解释变量组成的。这在处理小型数据集时非常重要，您需要更多的预测点才能使线条看起来平滑。但是，在您的情况下，原始数据集已经是一个很好的平滑序列，x因此使用与原始数据集n = 365获得相同的预测stat_smooth。

您可以在predictdf 此处查看代码。

于 2015-10-16T18:10:59.167 回答