Changed xpath to reflect NHANES website upgrade

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: nhanesA
-Version: 0.6.4
-Date: 2016-05-22
+Version: 0.6.4.1
+Date: 2016-07-10
 Title: NHANES Data Retrieval
 Author: Christopher Endres
 Maintainer: Christopher Endres <cjendres1@gmail.com>

R/nhanes.R

@@ -1,7 +1,8 @@
 #nhanesA - retrieve data from the CDC NHANES repository
 nhanesURL <- 'http://wwwn.cdc.gov/Nchs/Nhanes/'
+#varURL <- 'http://wwwn.cdc.gov/Nchs/Nhanes/search/variablelist.aspx'
 varURL <- 'http://wwwn.cdc.gov/nchs/nhanes/search/variablelist.aspx'
-dataURL <- 'http://wwwn.cdc.gov/nchs/nhanes/search/DataPage.aspx'
+dataURL <- 'http://wwwn.cdc.gov/Nchs/Nhanes/search/DataPage.aspx'
 
 # Create a list of nhanes groups
 # Include convenient aliases
@@ -101,7 +102,8 @@ anomalytables2005 <- c('CHLMD_DR', 'SSUECD_R', 'HSV_DR')
 # Internal function to determine if a number is even
 .is.even <- function(x) {x %% 2 == 0}
 
-xpath <- '//*[@id="ContentPlaceHolder1_GridView1"]'
+#xpath <- '//*[@id="ContentPlaceHolder1_GridView1"]'
+xpath <- '//*[@id="GridView1"]'
 
 #------------------------------------------------------------------------------
 #' Returns a list of table names for the specified survey group.
@@ -594,7 +596,8 @@ nhanesSearchVarName <- function(varname=NULL, ystart=NULL, ystop=NULL, includerd
     warning("Multiple variable names entered. Only the first will be matched.")
   }
 
-  xpt <- str_c('//*[@id="ContentPlaceHolder1_GridView1"]/*[td[1]="', varname, '"]', sep='')
+#  xpt <- str_c('//*[@id="ContentPlaceHolder1_GridView1"]/*[td[1]="', varname, '"]', sep='')
+  xpt <- str_c('//*[@id="GridView1"]/tbody/*[td[1]="', varname, '"]', sep='')
   tabletree <- varURL %>% read_html() %>% xml_nodes(xpath=xpt)
   ttlist <- lapply(lapply(tabletree, xml_children), xml_text)
   # Convert the list to a data frame

vignettes/Introducing_nhanesA.Rmd

@@ -44,6 +44,9 @@ nhanesTableVars('EXAM', 'BMX_D')
 ```
 
 We see that there are 27 columns in table BMX_D. The first column (SEQN) is the respondent sequence number and is included in every NHANES table. Effectively, SEQN is a subject identifier that is used to join information across tables.
+
+### Import NHANES Tables
+
 We now import BMX\_D along with the demographics table DEMO\_D.
 ```{r}
 bmx_d  <- nhanes('BMX_D')
@@ -100,7 +103,7 @@ names(q2007tables) <- q2007names
 
 ### Import Dual X-Ray Absorptiometry Data
 Dual X-Ray Absorptiometry (DXA) Data were acquired from 1999-2006. The tables are considerably larger than most
-NHANES data tables and are available via ftp server only. More information may be found at http://www.cdc.gov/nchs/nhanes/dxx/dxa.htm. By default the DXA data are imported into the R environment, however, because the tables are quite large it may be desirable to save the data to a local file then import to R as needed. When nhanesTranslate is applied to DXA data, only the 2005-2006 translation tables are used as those are the only DXA codes that are currently available in html format. Note that in a recent upgrade to the NHANES website it appears that the DXA tables may have been moved or deleted.
+NHANES data tables and are available via ftp server only. More information may be found at http://www.cdc.gov/nchs/nhanes/dxx/dxa.htm. By default the DXA data are imported into the R environment, however, because the tables are quite large it may be desirable to save the data to a local file then import to R as needed. When nhanesTranslate is applied to DXA data, only the 2005-2006 translation tables are used as those are the only DXA codes that are currently available in html format. **Note that in a recent upgrade to the NHANES website it appears that the DXA tables may have been moved or deleted.**
 ```{r, eval=FALSE}
 #Import into R
 dxx_b <- nhanesDXA(2001)

vignettes/Introducing_nhanesA.html

@@ -12,7 +12,7 @@
 
 <meta name="author" content="Christopher Endres" />
 
-<meta name="date" content="2016-05-22" />
+<meta name="date" content="2016-07-10" />
 
 <title>Introducing nhanesA</title>
 
@@ -70,7 +70,7 @@
 
 <h1 class="title toc-ignore">Introducing nhanesA</h1>
 <h4 class="author"><em>Christopher Endres</em></h4>
-<h4 class="date"><em>2016-05-22</em></h4>
+<h4 class="date"><em>2016-07-10</em></h4>
 
 
 
@@ -136,7 +136,11 @@ <h3>List Variables in an NHANES Table</h3>
 ## 25        BMITRI            Triceps Skinfold Comment
 ## 26        BMXSUB           Subscapular Skinfold (mm)
 ## 27        BMISUB        Subscapular Skinfold Comment</code></pre>
-<p>We see that there are 27 columns in table BMX_D. The first column (SEQN) is the respondent sequence number and is included in every NHANES table. Effectively, SEQN is a subject identifier that is used to join information across tables. We now import BMX_D along with the demographics table DEMO_D.</p>
+<p>We see that there are 27 columns in table BMX_D. The first column (SEQN) is the respondent sequence number and is included in every NHANES table. Effectively, SEQN is a subject identifier that is used to join information across tables.</p>
+</div>
+<div id="import-nhanes-tables" class="section level3">
+<h3>Import NHANES Tables</h3>
+<p>We now import BMX_D along with the demographics table DEMO_D.</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">bmx_d  &lt;-<span class="st"> </span><span class="kw">nhanes</span>(<span class="st">'BMX_D'</span>)</code></pre></div>
 <pre><code>## Processing SAS dataset BMX_D      ..</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">demo_d &lt;-<span class="st"> </span><span class="kw">nhanes</span>(<span class="st">'DEMO_D'</span>)</code></pre></div>
@@ -265,18 +269,30 @@ <h3>Searching for tables by name pattern</h3>
 <span class="kw">nhanesSearchTableNames</span>(<span class="st">'BMX'</span>)</code></pre></div>
 <pre><code>## [1] &quot;BMX&quot;   &quot;BMX_B&quot; &quot;BMX_C&quot; &quot;BMX_D&quot; &quot;BMX_E&quot; &quot;BMX_F&quot; &quot;BMX_G&quot; &quot;BMX_H&quot;</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">nhanesSearchTableNames</span>(<span class="st">'HPVS'</span>, <span class="dt">includerdc=</span><span class="ot">TRUE</span>, <span class="dt">nchar=</span><span class="dv">42</span>, <span class="dt">details=</span><span class="ot">TRUE</span>)</code></pre></div>
-<pre><code>##        Years                             Data.File.Name     Doc.File
-## 1  2005-2006 Human Papillomavirus (HPV) - 6, 11, 16 &amp; 1 HPVSER_D Doc
-## 2  2007-2008 Human Papillomavirus (HPV) - 6, 11, 16 &amp; 1 HPVSER_E Doc
-## 3  2009-2010 Human Papillomavirus (HPV) - 6, 11, 16 &amp; 1 HPVSER_F Doc
-## 4  2005-2006 Human Papillomavirus (HPV) - 6, 11, 16 &amp; 1 HPVS_D_R Doc
-## 5  2005-2006 Human Papillomavirus (HPV) - Multiplexed 6 HPVSRM_D Doc
-## 6  2005-2006 Human Papillomavirus (HPV) DNA - Vaginal S HPVSWR_D Doc
-## 7  2007-2008 Human Papillomavirus (HPV) DNA - Vaginal S HPVSWR_E Doc
-## 8  2009-2010 Human Papillomavirus (HPV) DNA - Vaginal S HPVSWR_F Doc
-## 9  2009-2010 Human Papillomavirus (HPV) DNA - Vaginal S HPVS_F_R Doc
-## 10 2011-2012 Human Papillomavirus (HPV) DNA - Vaginal S HPVS_G_R Doc
-## 11 2011-2012 Human Papillomavirus (HPV) DNA - Vaginal S HPVSWR_G Doc
+<pre><code>##                X1     X2     Years
+## 1  Search The CDC submit 2005-2006
+## 2  Search The CDC submit 2007-2008
+## 3  Search The CDC submit 2009-2010
+## 4  Search The CDC submit 2005-2006
+## 5  Search The CDC submit 2005-2006
+## 6  Search The CDC submit 2005-2006
+## 7  Search The CDC submit 2007-2008
+## 8  Search The CDC submit 2009-2010
+## 9  Search The CDC submit 2009-2010
+## 10 Search The CDC submit 2011-2012
+## 11 Search The CDC submit 2011-2012
+##                                Data.File.Name     Doc.File
+## 1  Human Papillomavirus (HPV) - 6, 11, 16 &amp; 1 HPVSER_D Doc
+## 2  Human Papillomavirus (HPV) - 6, 11, 16 &amp; 1 HPVSER_E Doc
+## 3  Human Papillomavirus (HPV) - 6, 11, 16 &amp; 1 HPVSER_F Doc
+## 4  Human Papillomavirus (HPV) - 6, 11, 16 &amp; 1 HPVS_D_R Doc
+## 5  Human Papillomavirus (HPV) - Multiplexed 6 HPVSRM_D Doc
+## 6  Human Papillomavirus (HPV) DNA - Vaginal S HPVSWR_D Doc
+## 7  Human Papillomavirus (HPV) DNA - Vaginal S HPVSWR_E Doc
+## 8  Human Papillomavirus (HPV) DNA - Vaginal S HPVSWR_F Doc
+## 9  Human Papillomavirus (HPV) DNA - Vaginal S HPVS_F_R Doc
+## 10 Human Papillomavirus (HPV) DNA - Vaginal S HPVS_G_R Doc
+## 11 Human Papillomavirus (HPV) DNA - Vaginal S HPVSWR_G Doc
 ##                        Data.File Date.Published
 ## 1  HPVSER_D Data [XPT, 151.6 KB]     July, 2013
 ## 2  HPVSER_E Data [XPT, 155.7 KB] November, 2013