Question

我正在使用R. 我想使用一个特定的公式来将曲线拟合到我的一个数据集（附件）

> dput(data)
structure(list(Gossypol = c(1036.331811, 4171.427741, 6039.995102, 
5909.068158, 4140.242559, 4854.985845, 6982.035521, 6132.876396, 
948.2418407, 3618.448997, 3130.376482, 5113.942098, 1180.171957, 
1500.863038, 4576.787021, 5629.979049, 3378.151945, 3589.187889, 
2508.417927, 1989.576826, 5972.926124, 2867.610671, 450.7205451, 
1120.955, 3470.09352, 3575.043632, 2952.931863, 349.0864019, 
1013.807628, 910.8879471, 3743.331903, 3350.203452, 592.3403778, 
1517.045807, 1504.491931, 3736.144027, 2818.419785, 723.885643, 
1782.864308, 1414.161257, 3723.629772, 3747.076592, 2005.919344, 
4198.569251, 2228.522959, 3322.115942, 4274.324792, 720.9785449, 
2874.651764, 2287.228752, 5654.858696, 1247.806111, 1247.806111, 
2547.326207, 2608.716056, 1079.846532), Treatment = structure(c(2L, 
3L, 4L, 5L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 5L, 1L, 2L, 3L, 4L, 5L, 
1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 
2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 
3L, 4L, 5L, 1L, 2L, 3L, 1L), .Label = c("C", "1c_2d", "3c_2d", 
"9c_2d", "1c_7d"), class = "factor"), Damage_cm = c(0.4955, 1.516, 
4.409, 3.2665, 0.491, 2.3035, 3.51, 1.8115, 0, 0.4435, 1.573, 
1.8595, 0, 0.142, 2.171, 4.023, 4.9835, 0, 0.6925, 1.989, 5.683, 
3.547, 0, 0.756, 2.129, 9.437, 3.211, 0, 0.578, 2.966, 4.7245, 
1.8185, 0, 1.0475, 1.62, 5.568, 9.7455, 0, 0.8295, 2.411, 7.272, 
4.516, 0, 0.4035, 2.974, 8.043, 4.809, 0, 0.6965, 1.313, 5.681, 
3.474, 0, 0.5895, 2.559, 0)), .Names = c("Gossypol", "Treatment", 
"Damage_cm"), row.names = c(NA, -56L), class = "data.frame")

等式为：y~yo+a*(1-b^x) 哪里： y = Gossypol（来自我的数据集） x = Damage_cm（来自我的数据集）

其他3个参数未知： yo = Intercept，a = asymptote和b = slope

我想我必须使用包nls2。到目前为止，我编写了以下代码：

data<-read.csv("Regression_exp2.csv",header=T, sep = ",")
library(nls2)
attach(data)
m<-nls(Gossypol~Y+A*(1-B^Damage_cm),data=data,start = list(Y=1700,A=4000,B=1))

这给了我错误信息：

nlsModel中的错误（formula，mf，start，wts）：奇异梯度矩阵在初始参数估计值

最后我想用方程式绘制一条曲线（有SE间隔，我通常使用ggplot2）

此外，我想知道R2和p值。我也会对参数yo，a和b

感兴趣

我之前从未这样做过，如果有人能帮助我或者给我一个提示如何在R中做到这一点，我将非常感激？我想我必须使用非线性方法（glm（...））

非常感谢，麦克

Answer 1

您必须稍微调整一下起始值：

TID: [0] [ESB] [2015-08-07 22:13:21,497] DEBUG {org.apache.synapse.transport.http.wire} -  >> "POST /internal/employees HTTP/1.1[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,497] DEBUG {org.apache.synapse.transport.http.wire} -  >> "Accept-Encoding: gzip,deflate[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,498] DEBUG {org.apache.synapse.transport.http.wire} -  >> "Content-Type: application/json[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,498] DEBUG {org.apache.synapse.transport.http.wire} -  >> "Content-Length: 70[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,498] DEBUG {org.apache.synapse.transport.http.wire} -  >> "Host: 192.168.1.167:8280[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,499] DEBUG {org.apache.synapse.transport.http.wire} -  >> "Connection: Keep-Alive[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,499] DEBUG {org.apache.synapse.transport.http.wire} -  >> "User-Agent: Apache-HttpClient/4.1.1 (java 1.5)[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,499] DEBUG {org.apache.synapse.transport.http.wire} -  >> "[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,500] DEBUG {org.apache.synapse.transport.http.wire} -  >> "{"employee":{"firstName":"Jackie","lastName":"Chan","team":"Finance"}}" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,552]  INFO {org.apache.synapse.core.axis2.TimeoutHandler} -  This engine will expire all callbacks after : 120 seconds, irrespective of the timeout action, after the specified or optional timeout {org.apache.synapse.core.axis2.TimeoutHandler}
TID: [0] [ESB] [2015-08-07 22:13:21,572] DEBUG {org.apache.synapse.transport.http.wire} -  << "POST /services/EmployeesDataService/employees HTTP/1.1[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,573] DEBUG {org.apache.synapse.transport.http.wire} -  << "Accept-Encoding: gzip,deflate[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,573] DEBUG {org.apache.synapse.transport.http.wire} -  << "Content-Type: application/json[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,573] DEBUG {org.apache.synapse.transport.http.wire} -  << "SOAPAction: [\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,573] DEBUG {org.apache.synapse.transport.http.wire} -  << "Transfer-Encoding: chunked[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,574] DEBUG {org.apache.synapse.transport.http.wire} -  << "Host: 192.168.1.167:9773[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,574] DEBUG {org.apache.synapse.transport.http.wire} -  << "Connection: Keep-Alive[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,574] DEBUG {org.apache.synapse.transport.http.wire} -  << "User-Agent: Synapse-PT-HttpComponents-NIO[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,574] DEBUG {org.apache.synapse.transport.http.wire} -  << "[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,575] DEBUG {org.apache.synapse.transport.http.wire} -  << "57[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,575] DEBUG {org.apache.synapse.transport.http.wire} -  << "{"insert_Employee_operation":{"FirstName":"Jackie","LastName":"Chan","Team":"Finance"}}[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,575] DEBUG {org.apache.synapse.transport.http.wire} -  << "0[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,575] DEBUG {org.apache.synapse.transport.http.wire} -  << "[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,658] DEBUG {org.apache.synapse.transport.http.wire} -  >> "HTTP/1.1 500 Internal Server Error[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,659] DEBUG {org.apache.synapse.transport.http.wire} -  >> "Transfer-Encoding: chunked[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,659] DEBUG {org.apache.synapse.transport.http.wire} -  >> "Date: Sat, 08 Aug 2015 02:13:21 GMT[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,659] DEBUG {org.apache.synapse.transport.http.wire} -  >> "Connection: close[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,659] DEBUG {org.apache.synapse.transport.http.wire} -  >> "Server: WSO2 Carbon Server[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,660] DEBUG {org.apache.synapse.transport.http.wire} -  >> "[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,660] DEBUG {org.apache.synapse.transport.http.wire} -  >> "114[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,660] DEBUG {org.apache.synapse.transport.http.wire} -  >> "{"Fault":{"faultcode":"axis2ns1:Client","faultstring":"The endpoint reference (EPR) for the Operation not found is /services/EmployeesDataService/employees and the WSA Action = null. If this EPR was previously reachable, please contact the server administrator.","detail":""}}[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,666] DEBUG {org.apache.synapse.transport.http.wire} -  >> "0[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,666] DEBUG {org.apache.synapse.transport.http.wire} -  >> "[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,672] ERROR {org.apache.synapse.util.xpath.SynapseJsonPath} -  #stringValueOf. Error evaluating JSON Path <$.GeneratedKeys.Entry.ID>. Returning empty result. Error>>> invalid path {org.apache.synapse.util.xpath.SynapseJsonPath}
TID: [0] [ESB] [2015-08-07 22:13:21,674] DEBUG {org.apache.synapse.transport.http.wire} -  << "HTTP/1.1 500 Internal Server Error[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,674] DEBUG {org.apache.synapse.transport.http.wire} -  << "Content-Type: application/json[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,675] DEBUG {org.apache.synapse.transport.http.wire} -  << "Date: Sat, 08 Aug 2015 02:13:21 GMT[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,675] DEBUG {org.apache.synapse.transport.http.wire} -  << "Server: WSO2-PassThrough-HTTP[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,675] DEBUG {org.apache.synapse.transport.http.wire} -  << "Transfer-Encoding: chunked[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,675] DEBUG {org.apache.synapse.transport.http.wire} -  << "Connection: Keep-Alive[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,675] DEBUG {org.apache.synapse.transport.http.wire} -  << "[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,676] DEBUG {org.apache.synapse.transport.http.wire} -  << "43[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,677] DEBUG {org.apache.synapse.transport.http.wire} -  << "{"EmployeeRecord":{"EmployeeID":, "Status":"Successfully created"}}[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,677] DEBUG {org.apache.synapse.transport.http.wire} -  << "0[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:13:21,677] DEBUG {org.apache.synapse.transport.http.wire} -  << "[\r][\n]" {org.apache.synapse.transport.http.wire}
TID: [0] [ESB] [2015-08-07 22:14:56,503]  INFO {org.wso2.carbon.core.init.CarbonServerManager} -  Shutdown hook triggered.... {org.wso2.carbon.core.init.CarbonServerManager}
TID: [0] [ESB] [2015-08-07 22:14:56,504]  INFO {org.wso2.carbon.core.init.CarbonServerManager} -  Gracefully shutting down WSO2 Enterprise Service Bus... {org.wso2.carbon.core.init.CarbonServerManager}
TID: [0] [ESB] [2015-08-07 22:14:56,506]  INFO {org.wso2.carbon.core.ServerManagement} -  Starting to switch to maintenance mode... {org.wso2.carbon.core.ServerManagement}
TID: [0] [ESB] [2015-08-07 22:14:56,506]  INFO {org.apache.synapse.transport.passthru.PassThroughHttpSSLListener} -  Stopping Pass-through HTTPS Listener.. {org.apache.synapse.transport.passthru.PassThroughHttpSSLListener}
TID: [0] [ESB] [2015-08-07 22:14:56,508]  INFO {org.apache.synapse.transport.passthru.PassThroughHttpListener} -  Stopping Pass-through HTTP Listener.. {org.apache.synapse.transport.passthru.PassThroughHttpListener}
TID: [0] [ESB] [2015-08-07 22:14:56,508]  INFO {org.apache.synapse.transport.passthru.PassThroughHttpSSLListener} -  HTTPS Listener shutdown. {org.apache.synapse.transport.passthru.PassThroughHttpSSLListener}
TID: [0] [ESB] [2015-08-07 22:14:56,509]  INFO {org.apache.synapse.transport.passthru.PassThroughHttpListener} -  HTTP Listener shutdown. {org.apache.synapse.transport.passthru.PassThroughHttpListener}
TID: [0] [ESB] [2015-08-07 22:14:56,509]  INFO {org.wso2.carbon.core.ServerManagement} -  Stopped all transport listeners {org.wso2.carbon.core.ServerManagement}
TID: [0] [ESB] [2015-08-07 22:14:56,510]  INFO {org.wso2.carbon.core.ServerManagement} -  Waiting for request service completion... {org.wso2.carbon.core.ServerManagement}
TID: [0] [ESB] [2015-08-07 22:14:56,511]  INFO {org.wso2.carbon.core.ServerManagement} -  All requests have been served. {org.wso2.carbon.core.ServerManagement}
TID: [0] [ESB] [2015-08-07 22:14:56,512]  INFO {org.wso2.carbon.core.ServerManagement} -  Waiting for deployment completion... {org.wso2.carbon.core.ServerManagement}
TID: [0] [ESB] [2015-08-07 22:14:56,512]  INFO {org.wso2.carbon.core.ServerManagement} -  All deployment tasks have been completed. {org.wso2.carbon.core.ServerManagement}
TID: [0] [ESB] [2015-08-07 22:14:56,513]  INFO {org.wso2.carbon.core.ServerManagement} -  Waiting for server task completion... {org.wso2.carbon.core.ServerManagement}
TID: [0] [ESB] [2015-08-07 22:14:56,514]  INFO {org.wso2.carbon.core.ServerManagement} -  All server tasks have been completed. {org.wso2.carbon.core.ServerManagement}
TID: [0] [ESB] [2015-08-07 22:14:56,514]  INFO {org.wso2.carbon.core.init.CarbonServerManager} -  Shutting down WSO2 Enterprise Service Bus... {org.wso2.carbon.core.init.CarbonServerManager}
TID: [0] [ESB] [2015-08-07 22:14:56,514]  INFO {org.wso2.carbon.core.init.CarbonServerManager} -  Shutting down OSGi framework... {org.wso2.carbon.core.init.CarbonServerManager}
TID: [0] [ESB] [2015-08-07 22:14:56,563]  INFO {org.apache.synapse.task.SynapseTaskManager} -  Shutting down the task manager {org.apache.synapse.task.SynapseTaskManager}
TID: [0] [ESB] [2015-08-07 22:14:58,709]  INFO {org.wso2.carbon.core.init.CarbonServerManager} -  Stopping CarbonServerManager... {org.wso2.carbon.core.init.CarbonServerManager}
TID: [0] [ESB] [2015-08-07 22:14:58,711]  INFO {org.apache.synapse.transport.passthru.PassThroughHttpSSLSender} -  HTTPS Sender shutdown {org.apache.synapse.transport.passthru.PassThroughHttpSSLSender}
TID: [0] [ESB] [2015-08-07 22:14:58,712]  INFO {org.apache.synapse.transport.passthru.PassThroughHttpSender} -  HTTP Sender shutdown {org.apache.synapse.transport.passthru.PassThroughHttpSender}
TID: [0] [ESB] [2015-08-07 22:14:58,712]  INFO {org.apache.synapse.transport.passthru.PassThroughHttpSSLListener} -  Destroying PassThroughHttpListener {org.apache.synapse.transport.passthru.PassThroughHttpSSLListener}
TID: [0] [ESB] [2015-08-07 22:14:58,713]  INFO {org.apache.synapse.transport.passthru.PassThroughHttpListener} -  Destroying PassThroughHttpListener {org.apache.synapse.transport.passthru.PassThroughHttpListener}
TID: [0] [ESB] [2015-08-07 22:14:58,960]  INFO {org.wso2.carbon.tomcat.ext.internal.CarbonTomcatServiceComponent} -  Stopping the carbon web-app registered under : / {org.wso2.carbon.tomcat.ext.internal.CarbonTomcatServiceComponent}
TID: [0] [ESB] [2015-08-07 22:15:00,251]  INFO {org.wso2.carbon.core.init.CarbonServerManager} -  Shutdown complete {org.wso2.carbon.core.init.CarbonServerManager}
TID: [0] [ESB] [2015-08-07 22:15:00,252]  INFO {org.wso2.carbon.core.init.CarbonServerManager} -  Halting JVM {org.wso2.carbon.core.init.CarbonServerManager}

然后你可以打电话：

> data
    Gossypol Treatment Damage_cm
1  1036.3318     1c_2d    0.4955
2  4171.4277     3c_2d    1.5160
3  6039.9951     9c_2d    4.4090
4  5909.0682     1c_7d    3.2665
5  4140.2426     1c_2d    0.4910
...
54 2547.3262     1c_2d    0.5895
55 2608.7161     3c_2d    2.5590
56 1079.8465         C    0.0000

打印m<-nls(data$Gossypol~Y+A*(1-B^data$Damage_cm),data=data,start = list(Y=1000,A=3000,B=0.5))为您提供：

现在您可以根据合适情况获取数据：

> m
Nonlinear regression model
  model: data$Gossypol ~ Y + A * (1 - B^data$Damage_cm)
   data: data
        Y         A         B 
1303.4450 2796.0385    0.4939 
 residual sum-of-squares: 1.03e+08

绘制数据以比较拟合和原始数据：

fitData <- 1303.4450 + 2796.0385*(1-0.4939^data$Damage_cm)

给你：

如果您想使用plot(data$Damage_cm, data$Gossypol, col='black') par(new=T) plot(data$Damage_cm,fitData, col='red', ylim=c(0,8000), axes=F, ylab='')确保已安装，如果不是，则可以使用

nls2

这样做。

install.packages('nls2')

为您提供与library(nls2) m2<-nls2(data$Gossypol~Y+A*(1-B^data$Damage_cm),data=data,start = list(Y=1000,A=3000,B=0.5))相同的值：

nls

如果您更喜欢> m2 Nonlinear regression model model: data$Gossypol ~ Y + A * (1 - B^data$Damage_cm) data: structure(list(Gossypol = c(1036.331811, 4171.427741, 6039.995102, 5909.068158, 4140.242559, 4854.985845, 6982.035521, 6132.876396, 948.2418407, 3618.448997, 3130.376482, 5113.942098, 1180.171957, 1500.863038, 4576.787021, 5629.979049, 3378.151945, 3589.187889, 2508.417927, 1989.576826, 5972.926124, 2867.610671, 450.7205451, 1120.955, 3470.09352, 3575.043632, 2952.931863, 349.0864019, 1013.807628, 910.8879471, 3743.331903, 3350.203452, 592.3403778, 1517.045807, 1504.491931, 3736.144027, 2818.419785, 723.885643, 1782.864308, 1414.161257, 3723.629772, 3747.076592, 2005.919344, 4198.569251, 2228.522959, 3322.115942, 4274.324792, 720.9785449, 2874.651764, 2287.228752, 5654.858696, 1247.806111, 1247.806111, 2547.326207, 2608.716056, 1079.846532), Treatment = structure(c(2L, 3L, 4L, 5L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 1L), .Label = c("C", "1c_2d", "3c_2d", "9c_2d", "1c_7d"), class = "factor"), Damage_cm = c(0.4955, 1.516, 4.409, 3.2665, 0.491, 2.3035, 3.51, 1.8115, 0, 0.4435, 1.573, 1.8595, 0, 0.142, 2.171, 4.023, 4.9835, 0, 0.6925, 1.989, 5.683, 3.547, 0, 0.756, 2.129, 9.437, 3.211, 0, 0.578, 2.966, 4.7245, 1.8185, 0, 1.0475, 1.62, 5.568, 9.7455, 0, 0.8295, 2.411, 7.272, 4.516, 0, 0.4035, 2.974, 8.043, 4.809, 0, 0.6965, 1.313, 5.681, 3.474, 0, 0.5895, 2.559, 0)), .Names = c("Gossypol", "Treatment", "Damage_cm"), row.names = c(NA, -56L), class = "data.frame") Y A B 1303.4450 2796.0385 0.4939 residual sum-of-squares: 1.03e+08 Number of iterations to convergence: 2 Achieved convergence tolerance: 4.936e-06：

ggplot2

虽然我担心标准错误必须在ggplot(data, aes(x = Damage_cm, y = Gossypol)) + geom_point() + geom_smooth(method = "nls", formula = y ~ Y + A * (1 - B^x), start = c(Y=1000, A=3000, B=0.5), se = F)之外进行模拟。

使用R使用特定方程将曲线拟合到数据集

1 个答案: