Merge pull request #19 from mathesong/Development

Development

Author: mathesong

DESCRIPTION

@@ -1,15 +1,15 @@
 Package: kinfitr
 Title: Kinetic Modelling of PET Time Activity Curves
-Date: 2020-03-06
-Version: 0.4.6
+Date: 2020-08-18
+Version: 0.6
 Authors@R: person("Granville", "Matheson", email = "[email protected]", role = c("aut", "cre"))
 Description: This package calculates outcome parameters for PET data using time activity curves (TACs). The will allow for more reproducible PET modelling research.
 Depends:
     R (>= 3.4.0)
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.0
 Imports:
     pracma,
     minpack.lm,
@@ -34,7 +34,9 @@ Imports:
     invgamma,
     cowplot,
     car,
-    mgcv
+    mgcv,
+    fs,
+    stringr
 Suggests:
     knitr,
     devtools,

NAMESPACE

@@ -3,6 +3,7 @@
 S3method(plot,blooddata)
 S3method(plot,interpblood)
 S3method(plot,kinfit)
+export("%>%")
 export(Logan_tstar)
 export(Loganplot)
 export(Patlak_tstar)
@@ -14,9 +15,16 @@ export(bd_addfit)
 export(bd_addfitpars)
 export(bd_addfitted)
 export(bd_blood_dispcor)
+export(bd_create_input)
+export(bd_extract)
 export(bd_getdata)
+export(bd_tidy_times)
+export(bids_create_blooddata)
+export(bids_filename_attributes)
+export(bids_parse_blood)
+export(bids_parse_files)
+export(bids_parse_study)
 export(blmod_exp)
-export(blmod_exp_sep)
 export(blmod_exp_startpars)
 export(blmod_splines)
 export(blmod_tidyinput)
@@ -29,8 +37,10 @@ export(create_blooddata_components)
 export(decay_correct)
 export(decay_uncorrect)
 export(fix_multstartpars)
+export(frame_cumsum)
 export(get_se)
 export(kinfit_convolve)
+export(lin2tcm)
 export(ma1)
 export(ma1_tstar)
 export(ma2)
@@ -65,6 +75,7 @@ export(plot_inptac_fit)
 export(plot_inptac_timings)
 export(plot_input)
 export(plot_kinfit)
+export(plot_lin2tcmfit)
 export(plot_ma1fit)
 export(plot_ma2fit)
 export(plot_mlLoganfit)
@@ -100,10 +111,9 @@ export(twotcm1k_model)
 export(twotcm_fitDelay_model)
 export(twotcm_model)
 export(unit_convert)
+export(update_blooddata)
 export(weights_create)
+export(weights_create_bids)
 import(ggplot2)
-import(grDevices)
-import(graphics)
-import(stats)
-import(utils)
 importFrom(dplyr,"%>%")
+importFrom(magrittr,"%>%")

R/kinfitr_1tcm.R

@@ -217,9 +217,9 @@ onetcm <- function(t_tac, tac, input, weights = NULL, inpshift = NULL, vB = NULL
     ) {
     warning(
       paste0(
-        "Fitted parameters are hitting upper or lower limit bounds. Consider \n",
+        "\nFitted parameters are hitting upper or lower limit bounds. Consider \n",
         "either modifying the upper and lower limit boundaries, or else using \n",
-        "multstart when fitting the model (see the function documentation).") )
+        "multstart when fitting the model (see the function documentation).\n") )
   }
 
   # Output

R/kinfitr_2tcm.R

@@ -235,9 +235,9 @@ twotcm <- function(t_tac, tac, input, weights = NULL, inpshift = NULL, vB = NULL
   ) {
     warning(
       paste0(
-        "Fitted parameters are hitting upper or lower limit bounds. Consider \n",
+        "\nFitted parameters are hitting upper or lower limit bounds. Consider \n",
         "either modifying the upper and lower limit boundaries, or else using \n",
-        "multstart when fitting the model (see the function documentation).") )
+        "multstart when fitting the model (see the function documentation).\n") )
   }
 
   # Output

R/kinfitr_2tcm1k.R

@@ -248,9 +248,9 @@ twotcm1k <- function(t_tac, tac, input, weights = NULL, inpshift = NULL, vB = NU
   ) {
     warning(
       paste0(
-        "Fitted parameters are hitting upper or lower limit bounds. Consider \n",
+        "\nFitted parameters are hitting upper or lower limit bounds. Consider \n",
         "either modifying the upper and lower limit boundaries, or else using \n",
-        "multstart when fitting the model (see the function documentation).") )
+        "multstart when fitting the model (see the function documentation).\n") )
   }
 
   # Output